Cytoscape PluginsThese plugins have been submitted to Cytoscape by their authors, they may have their own licensing requirements. Please contact the plugin authors with any questions.http://cytoscape.org167addParentNeighborsAdd neighboring nodes from a parent network to this networkOther1.02.62008-08-30John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=150jar165AdvancedNetworkMergeProvides utilities for mapping attributes of source ID types to new attributes of destination ID types.Network generation1.102.62009-09-02Jianjiong GaoU. of MissouriKeiichiro Ono UCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=231jar165AdvancedNetworkMergeProvides utilities for mapping attributes of source ID types to new attributes of destination ID types.Network generation1.122.62010-01-20Jianjiong GaoU. of MissouriKeiichiro Ono UCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=261jar103AgilentLiteratureSearchCreates a CyNetwork based on searching the scientific literature.Network generation2.552.5Agilent Literature Search License Agreement AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW. TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENT'S SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE READ, UNDERSTAND AND AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "AGREE" BOX AT THE BOTTOM OF THIS PAGE. THE SOFTWARE WILL THEN BE DOWNLOADED TO OR INSTALLED ON YOUR COMPUTER. IF YOU DO NOT AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "DO NOT AGREE" BOX AT THE BOTTOM OF THIS PAGE AND CANCEL THE DOWNLOAD OR INSTALLATION OF THE SOFTWARE. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. Software. "Software" means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format. License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilent's third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the applicable license, you may store or run one copy of the Software on one machine or instrument. If the Software is otherwise licensed for concurrent or network use, you may not allow more than the maximum number of authorized users to access and use the Software concurrently. License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network. Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement. No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification. High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer. Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software. Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations. U.S. Government Restricted Rights. Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data - Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Computer Software Documentation). NO WARRANTY. TO THE EXTENT ALLOWED BY LOCAL LAW, AND EXCEPT TO THE EXTENT AGILENT HAS PROVIDED A SPECIFIC WRITTEN WARRANTY APPLICABLE TO THIS PRODUCT, THIS SOFTWARE IS PROVIDED TO YOU "AS IS" WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN, EXPRESS OR IMPLIED. AGILENT SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE RISK AND COST RESULTING FROM OR RELATING TO THE DEFECT. SOME JURISDICTIONS DO NOT ALLOW EXCLUSIONS OF IMPLIED WARRANTIES OR CONDITIONS, SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. YOU MAY HAVE OTHER RIGHTS THAT VARY ACCORDING TO LOCAL LAW. LIMITATION OF LIABILITY. TO THE EXTENT ALLOWED BY LOCAL LAW, IN NO EVENT WILL AGILENT OR ITS SUBSIDIARIES, AFFILIATES OR SUPPLIERS BE LIABLE FOR DIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR OTHER DAMAGES (INCLUDING LOST PROFIT, LOST DATA, OR DOWNTIME COSTS), ARISING OUT OF THE USE, INABILITY TO USE, OR THE RESULTS OF USE OF THE SOFTWARE, WHETHER BASED IN WARRANTY, CONTRACT, TORT OR OTHER LEGAL THEORY, AND WHETHER OR NOT ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. YOUR USE OF THE SOFTWARE IS ENTIRELY AT YOUR OWN RISK. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. Applicable Law. Disputes arising in connection with this Agreement will be governed by the laws of the United States and of the State of New York, without regard to choice of law provisions. The United Nations Convention for Contracts for the International Sale of Goods will not apply to this Agreement. Unenforceability. To the extent that any provision of this Agreement is determined to be illegal or unenforceable, the remainder of this Agreement will remain in full force and effect. Entire Agreement. This Agreement constitutes the entire agreement between you and Agilent, and supersedes any previous communications, representations or agreements between the parties, whether oral or written, regarding transactions hereunder except for a specific warranty issued by Agilent with regard to this product. Your additional or different terms and conditions will not apply. This Agreement may not be changed except by an amendment signed by an authorized representative of each party. Rev 05-21-2004 2007-07-17Allan Kuchinsky and Aditya Vailaya,Agilent LabsMichael Creech,Blue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=18jar103AgilentLiteratureSearchCreates a CyNetwork based on searching the scientific literature.Network generation2.712.6.3Agilent Literature Search License Agreement AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW. TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENT'S SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE READ, UNDERSTAND AND AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "AGREE" BOX AT THE BOTTOM OF THIS PAGE. THE SOFTWARE WILL THEN BE DOWNLOADED TO OR INSTALLED ON YOUR COMPUTER. IF YOU DO NOT AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "DO NOT AGREE" BOX AT THE BOTTOM OF THIS PAGE AND CANCEL THE DOWNLOAD OR INSTALLATION OF THE SOFTWARE. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. Software. "Software" means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format. License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilent's third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the applicable license, you may store or run one copy of the Software on one machine or instrument. If the Software is otherwise licensed for concurrent or network use, you may not allow more than the maximum number of authorized users to access and use the Software concurrently. License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network. Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement. No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification. High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer. Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software. Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations. U.S. Government Restricted Rights. Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data - Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Computer Software Documentation). NO WARRANTY. TO THE EXTENT ALLOWED BY LOCAL LAW, AND EXCEPT TO THE EXTENT AGILENT HAS PROVIDED A SPECIFIC WRITTEN WARRANTY APPLICABLE TO THIS PRODUCT, THIS SOFTWARE IS PROVIDED TO YOU "AS IS" WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN, EXPRESS OR IMPLIED. AGILENT SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE RISK AND COST RESULTING FROM OR RELATING TO THE DEFECT. SOME JURISDICTIONS DO NOT ALLOW EXCLUSIONS OF IMPLIED WARRANTIES OR CONDITIONS, SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. YOU MAY HAVE OTHER RIGHTS THAT VARY ACCORDING TO LOCAL LAW. LIMITATION OF LIABILITY. TO THE EXTENT ALLOWED BY LOCAL LAW, IN NO EVENT WILL AGILENT OR ITS SUBSIDIARIES, AFFILIATES OR SUPPLIERS BE LIABLE FOR DIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR OTHER DAMAGES (INCLUDING LOST PROFIT, LOST DATA, OR DOWNTIME COSTS), ARISING OUT OF THE USE, INABILITY TO USE, OR THE RESULTS OF USE OF THE SOFTWARE, WHETHER BASED IN WARRANTY, CONTRACT, TORT OR OTHER LEGAL THEORY, AND WHETHER OR NOT ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. YOUR USE OF THE SOFTWARE IS ENTIRELY AT YOUR OWN RISK. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. Applicable Law. Disputes arising in connection with this Agreement will be governed by the laws of the United States and of the State of New York, without regard to choice of law provisions. The United Nations Convention for Contracts for the International Sale of Goods will not apply to this Agreement. Unenforceability. To the extent that any provision of this Agreement is determined to be illegal or unenforceable, the remainder of this Agreement will remain in full force and effect. Entire Agreement. This Agreement constitutes the entire agreement between you and Agilent, and supersedes any previous communications, representations or agreements between the parties, whether oral or written, regarding transactions hereunder except for a specific warranty issued by Agilent with regard to this product. Your additional or different terms and conditions will not apply. This Agreement may not be changed except by an amendment signed by an authorized representative of each party. Rev 05-21-2004 2009-07-01Allan Kuchinsky and Aditya VailayaAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=237jar103AgilentLiteratureSearchCreates a CyNetwork based on searching the scientific literature.Network generation2.762.8Agilent Literature Search License Agreement AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW. TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENT'S SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE READ, UNDERSTAND AND AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "AGREE" BOX AT THE BOTTOM OF THIS PAGE. THE SOFTWARE WILL THEN BE DOWNLOADED TO OR INSTALLED ON YOUR COMPUTER. IF YOU DO NOT AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "DO NOT AGREE" BOX AT THE BOTTOM OF THIS PAGE AND CANCEL THE DOWNLOAD OR INSTALLATION OF THE SOFTWARE. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. Software. "Software" means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format. License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilent's third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the applicable license, you may store or run one copy of the Software on one machine or instrument. If the Software is otherwise licensed for concurrent or network use, you may not allow more than the maximum number of authorized users to access and use the Software concurrently. License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network. Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement. No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification. High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer. Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software. Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations. U.S. Government Restricted Rights. Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data - Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Computer Software Documentation). NO WARRANTY. TO THE EXTENT ALLOWED BY LOCAL LAW, AND EXCEPT TO THE EXTENT AGILENT HAS PROVIDED A SPECIFIC WRITTEN WARRANTY APPLICABLE TO THIS PRODUCT, THIS SOFTWARE IS PROVIDED TO YOU "AS IS" WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN, EXPRESS OR IMPLIED. AGILENT SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE RISK AND COST RESULTING FROM OR RELATING TO THE DEFECT. SOME JURISDICTIONS DO NOT ALLOW EXCLUSIONS OF IMPLIED WARRANTIES OR CONDITIONS, SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. YOU MAY HAVE OTHER RIGHTS THAT VARY ACCORDING TO LOCAL LAW. LIMITATION OF LIABILITY. TO THE EXTENT ALLOWED BY LOCAL LAW, IN NO EVENT WILL AGILENT OR ITS SUBSIDIARIES, AFFILIATES OR SUPPLIERS BE LIABLE FOR DIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR OTHER DAMAGES (INCLUDING LOST PROFIT, LOST DATA, OR DOWNTIME COSTS), ARISING OUT OF THE USE, INABILITY TO USE, OR THE RESULTS OF USE OF THE SOFTWARE, WHETHER BASED IN WARRANTY, CONTRACT, TORT OR OTHER LEGAL THEORY, AND WHETHER OR NOT ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. YOUR USE OF THE SOFTWARE IS ENTIRELY AT YOUR OWN RISK. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. Applicable Law. Disputes arising in connection with this Agreement will be governed by the laws of the United States and of the State of New York, without regard to choice of law provisions. The United Nations Convention for Contracts for the International Sale of Goods will not apply to this Agreement. Unenforceability. To the extent that any provision of this Agreement is determined to be illegal or unenforceable, the remainder of this Agreement will remain in full force and effect. Entire Agreement. This Agreement constitutes the entire agreement between you and Agilent, and supersedes any previous communications, representations or agreements between the parties, whether oral or written, regarding transactions hereunder except for a specific warranty issued by Agilent with regard to this product. Your additional or different terms and conditions will not apply. This Agreement may not be changed except by an amendment signed by an authorized representative of each party. Rev 05-21-2004 2011-03-15Allan Kuchinsky and Aditya VailayaAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=393jar103AgilentLiteratureSearchCreates a CyNetwork based on searching the scientific literature.Network generation2.772.8Agilent Literature Search License Agreement AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW. TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENT'S SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE READ, UNDERSTAND AND AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "AGREE" BOX AT THE BOTTOM OF THIS PAGE. THE SOFTWARE WILL THEN BE DOWNLOADED TO OR INSTALLED ON YOUR COMPUTER. IF YOU DO NOT AGREE TO BE BOUND BY THE SOFTWARE LICENSE AGREEMENT BELOW, YOU SHOULD CLICK ON THE "DO NOT AGREE" BOX AT THE BOTTOM OF THIS PAGE AND CANCEL THE DOWNLOAD OR INSTALLATION OF THE SOFTWARE. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. Software. "Software" means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format. License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilent's third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the applicable license, you may store or run one copy of the Software on one machine or instrument. If the Software is otherwise licensed for concurrent or network use, you may not allow more than the maximum number of authorized users to access and use the Software concurrently. License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network. Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement. No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification. High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer. Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software. Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations. U.S. Government Restricted Rights. Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data - Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Computer Software Documentation). NO WARRANTY. TO THE EXTENT ALLOWED BY LOCAL LAW, AND EXCEPT TO THE EXTENT AGILENT HAS PROVIDED A SPECIFIC WRITTEN WARRANTY APPLICABLE TO THIS PRODUCT, THIS SOFTWARE IS PROVIDED TO YOU "AS IS" WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN, EXPRESS OR IMPLIED. AGILENT SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE RISK AND COST RESULTING FROM OR RELATING TO THE DEFECT. SOME JURISDICTIONS DO NOT ALLOW EXCLUSIONS OF IMPLIED WARRANTIES OR CONDITIONS, SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. YOU MAY HAVE OTHER RIGHTS THAT VARY ACCORDING TO LOCAL LAW. LIMITATION OF LIABILITY. TO THE EXTENT ALLOWED BY LOCAL LAW, IN NO EVENT WILL AGILENT OR ITS SUBSIDIARIES, AFFILIATES OR SUPPLIERS BE LIABLE FOR DIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR OTHER DAMAGES (INCLUDING LOST PROFIT, LOST DATA, OR DOWNTIME COSTS), ARISING OUT OF THE USE, INABILITY TO USE, OR THE RESULTS OF USE OF THE SOFTWARE, WHETHER BASED IN WARRANTY, CONTRACT, TORT OR OTHER LEGAL THEORY, AND WHETHER OR NOT ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. YOUR USE OF THE SOFTWARE IS ENTIRELY AT YOUR OWN RISK. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. Applicable Law. Disputes arising in connection with this Agreement will be governed by the laws of the United States and of the State of New York, without regard to choice of law provisions. The United Nations Convention for Contracts for the International Sale of Goods will not apply to this Agreement. Unenforceability. To the extent that any provision of this Agreement is determined to be illegal or unenforceable, the remainder of this Agreement will remain in full force and effect. Entire Agreement. This Agreement constitutes the entire agreement between you and Agilent, and supersedes any previous communications, representations or agreements between the parties, whether oral or written, regarding transactions hereunder except for a specific warranty issued by Agilent with regard to this product. Your additional or different terms and conditions will not apply. This Agreement may not be changed except by an amendment signed by an authorized representative of each party. Rev 05-21-2004 2011-09-12Allan Kuchinsky and Aditya VailayaAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=424jar249AllegroMCODE<P><a href='http://www.allegroviva.com/allegromcode'>AllegroMCODE</a> is a high-performance Cytoscape plugin to find clusters, or highly interconnected groups of nodes in a huge complex network such as a protein interaction network and a social network.</P><P>It includes our proprietary highly parallel algorithm based on the original sequential MCODE algorithm and exploits our high performance GPU computing architecture to make your analysis task faster than ever. It can achieve a speedup of two orders of magnitude over the MCODE plug-in by a local GPU or our remote GPU server.</P><P>You can get more information from <a href='http://www.allegroviva.com/allegromcode'>www.allegroviva.com/allegromcode</a></P>Clustering1.02.62.72.8Copyright 2011 (c) AllegroViva Corporation. All rights reserved. This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, version 3. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU LGPL(Lesser General Public License) for more details.2011-02-08Jun S. YoonAllegroViva CorporationWon-Hyung JungKorea Research Institute of Bioscience and Biotechnologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=371jar210APClusterThe plugin provides a user-friendly implementation of affinity propagation - a general purpose graph clustering algorithm (Brendan J. Frey and Delbert Dueck, Science 2007). It can be used to identify coherent modules in biological networks.Clustering2.12.6.32010-03-05Michal WozniakUniversity of WarsawJanusz DutkowskiUniversity of Warsawhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=276jar120APID2NETPlugin designed to visualize, explore and analyze the proteins and interactions retrieved from the <b>unified interactome</b> platform APID (which integrates BIND, BioGrid, DIP, HPRD, IncAct and MINT). The retrieved data include the <b>annotations and attributes associated</b> to the network: GO terms, InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs. The tool provides interactive graphical representation of the <b>protein-protein interaction</b> (PPI) networks within Cytoscape, plus new automatic tools to find <b>hubs</b> and <b>concurrent attributes</b> (functional and structural) along the protein pairs of a given network.Integrated analysis1.52.5All rights reserved. Reproduction, distribution, public communication and transformation without prior permission of the authors and institution is forbidden.2007-11-16Hernandez-Toro J, Prieto C, De Las Rivas J.Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL) Salamahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=45jar120APID2NETPlugin designed to visualize, explore and analyze the proteins and interactions retrieved from the <b>unified interactome</b> platform APID (which integrates BIND, BioGrid, DIP, HPRD, IncAct and MINT). The retrieved data include the <b>annotations and attributes associated</b> to the network: GO terms, InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs. The tool provides interactive graphical representation of the <b>protein-protein interaction</b> (PPI) networks within Cytoscape, plus new automatic tools to find <b>hubs</b> and <b>concurrent attributes</b> (functional and structural) along the protein pairs of a given network.Integrated analysis1.512.5All rights reserved. Reproduction, distribution, public communication and transformation without prior permission of the authors and institution is forbidden.2007-12-20Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=58jar120APID2NETPlugin designed to visualize, explore and analyze the proteins and interactions retrieved from the <b>unified interactome</b> platform APID (which integrates BIND, BioGrid, DIP, HPRD, IncAct and MINT). The retrieved data include the <b>annotations and attributes associated</b> to the network: GO terms, InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs. The tool provides interactive graphical representation of the <b>protein-protein interaction</b> (PPI) networks within Cytoscape, plus new automatic tools to find <b>hubs</b> and <b>concurrent attributes</b> (functional and structural) along the protein pairs of a given network.Integrated analysis1.522.6All rights reserved. Reproduction, distribution, public communication and transformation without prior permission of the authors and institution is forbidden.2008-05-14Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=121jar149batchToolThis plugin provides a simple proof-of-concept scripting capability for CytoscapeUtility0.52.62008-03-18John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=102jar149batchToolThis plugin provides a simple proof-of-concept scripting capability for CytoscapeUtility1.02.62008-09-18John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=151jar104BiNGOBiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.Ontology analysis2.12.32.42.52007-08-29Steven MaereVIBMartin KuiperVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=46jar104BiNGOBiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.Ontology analysis2.32.62008-08-05Steven MaereVIBMartin KuiperVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=131jar104BiNGOBiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.Ontology analysis2.312.62009-04-09Steven MaereVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=199jar104BiNGOBiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.Ontology analysis2.422.62.72010-08-01Steven MaereVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=318jar104BiNGOBiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.Ontology analysis2.442.62.72.82010-08-01Steven MaereVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=348jar118BiNoMBiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure. <ul><li>Import of BioPAX, SBML and CellDesigner formats<li>Export to BioPAX, SBML and CellDesigner formats after user manipulations<li>Conversion between standards (CellDesigner-&gt;BioPAX, BioPAX-&gt;SBML)<li>Full support of BioPAX information (reaction network, interaction network, pathway structure, references), concept of BioPAX index and network interfaces<li>Browsing, editing, extracting parts, merging BioPAX files with network graph interface<li>Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)<li>Support of generating network modular view<li>BioPAX network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)<li>Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.) </ul>Other1.02.5LGPL2007-09-01Andrei ZinovyevInstitut CurieEric ViaraInstitut CurieLaurence CalzoneInstitut CurieEmmanuel BarillotInstitut Curiehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=43jar274BiNoMBiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure. <ul><li>Import of BioPAX 3, SBML and CellDesigner formats<li>Export to BioPAX 3, SBML and CellDesigner formats after user manipulations<li>Conversion between standards (CellDesigner-&gt;BioPAX 3, BioPAX 3 -&gt;SBML)<li>Full support of BioPAX 3 information (reaction network, interaction network, pathway structure, references), concept of BioPAX 3 index and network interfaces<li>Browsing, editing, extracting parts, merging BioPAX 3 files with network graph interface<li>Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)<li>Support of generating network modular view<li>BioPAX 3 network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)<li>Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.) </ul>Other2.02.72.82012-04-26Eric BonnetInstitut CurieLaurence CalzoneInstitut CurieDaniel RoveraInstitut CurieEmmanuel BarillotInstitut CurieEric ViaraInstitut CurieAndrei ZinovyevInstitut Curiehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=469jar246bioCycPluginThis plugin provides a web services interface to Pathway Tools repositoriesOnline data import0.92.82010-12-17John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=355jar198BiogridPlugin<p>The BiogridPlugin allows direct import of data from BioGRID .tab files (which are available from www.thebiogrid.org/downloads.php) into a Cytoscape network, with a custom visual style.</p>Interaction database0.12.62009-10-30Andrew Winter, BioGRID, Tyers Group, Wellcome Trust Centre for Cell Biology, University of Edinburgh and The Samuel Lunenfeld Research Institute, Mounhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=243jar131BiomartClient<p>Web Service client module for Biomart (<a href="http://www.biomart.org/">http://www.biomart.org/</a>).</p><p><strong><font color="red">Now GUI is integrated and you do not have to install UI plugin for this version.</font></strong>Online data import0.802.62008-10-16Keiichiro OnoUCSD Bioengineeringhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=172jar131BiomartClient<p>Web Service client module for Biomart (<a href="http://www.biomart.org/">http://www.biomart.org/</a>).</p><p><strong><font color="red">Now GUI is integrated and you do not have to install UI plugin for this version.</font></strong>Online data import0.902.62.72009-12-15Keiichiro OnoUCSD Bioengineeringhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=257jar159BioNetBuilderAccesses BIND,BioGrid,DIP,HPRD,KEGG,IntAct,MINT,MPPI, and Prolinks as well as interolog networks derived from these sources for all species represented in NCBI HomoloGene.Interaction database2.02.62008-06-18Jay Konieczka University of Arizona Kevin Drew Courant Institute, NYU.http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=134jar164BioQualiPluginBioQuali analyses regulatory networks and expression datasets by checking a global consistency between the regulatory model and the expression data. It diagnoses a regulatory network searching for the regulations that are not consistent with the expression data, and it outputs a set of genes which predicted expression is decided in order to explain the expression data provided.<br>The BioQuali Cytoscape Plugin proposes the user to visualize this analysis automatically and in few minutes no matter the size of the network.Integrated analysis1.02.62008-09-17Annabel BourdéCentre INRIA Rennes Bretagne Atlantique, IRISACarito GuziolowskiCentre INRIA Rennes Bretagne Atlantique, IRISAhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=141zip164BioQualiPluginBioQuali analyses regulatory networks and expression datasets by checking a global consistency between the regulatory model and the expression data. It diagnoses a regulatory network searching for the regulations that are not consistent with the expression data, and it outputs a set of genes which predicted expression is decided in order to explain the expression data provided.<br>The BioQuali Cytoscape Plugin proposes the user to visualize this analysis automatically and in few minutes no matter the size of the network.Integrated analysis1.12.62009-02-01Annabel Bourde and Carito Guziolowski IRISAhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=189jar164BioQualiPluginBioQuali analyses regulatory networks and expression datasets by checking a global consistency between the regulatory model and the expression data. It diagnoses a regulatory network searching for the regulations that are not consistent with the expression data, and it outputs a set of genes which predicted expression is decided in order to explain the expression data provided.<br>The BioQuali Cytoscape Plugin proposes the user to visualize this analysis automatically and in few minutes no matter the size of the network.Integrated analysis2.02.82011-04-15Carito GuziolowskiUniversity of HeidelbergAnne Siegel INRIA Renneshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=385jar207BisoGenet\This plugin allows searching molecular interactions from <b>SysBiomics</b>, our in-house \database, and displaying the result as an interaction network within Cytoscape. \<b>SysBiomics</b> integrates data from well-known interaction databases including \<b>DIP</b>, <b>BIOGRID</b>, <b>HPRD</b>, <b>BIND</b>, <b>MINT</b> and <b>INTACT</b>.<br/>\<b>BisoGenet</b> provides an easy to use interface allowing users to customize the searches by \specifying a target set of genes/proteins to retrieve interactions data for, \specifying a subcontext around the targets to narrow the interactions data searching space, \defining a selection filter to discard/include interactions (within the specified \subcontext) given its nature, primary databases and supporting experimental methods. <br/>\Interaction network's gene/protein associated info includes annotations from <b>NCBI</b>, \<b>UniProt</b>, <b>KEGG</b>, and <b>GO</b> databases while interaction info includes \the supporting experimental methods and hyperlinks to their primary databases entries and \related publications.<br/>\<b>BisoGenet</b> also includes network topology analysis tools such as <b>Shortest Paths\</b> between a set of nodes, determination of <b>Equivalent Nodes</b>, and <b>Network \Statistics</b> reports in combination to interactive <b>Transparency filter</b> to help \discernig such analytical results in the context of dense networks.Interaction database1.402.62009-12-07Maria E. Ochagavia, Ricardo Bringas, Alexander Martin, Jamilet Miranda, Jorge Fdez. de Cossio, Laya del Carmen Rabasa<b>Centre for Genetic Engineering and Biotechnology (CIGB)</b>http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=269jar207BisoGenet\This plugin allows searching molecular interactions from <b>SysBiomics</b>, our in-house \database, and displaying the result as an interaction network within Cytoscape. \<b>SysBiomics</b> integrates data from well-known interaction databases including \<b>DIP</b>, <b>BIOGRID</b>, <b>HPRD</b>, <b>BIND</b>, <b>MINT</b> and <b>INTACT</b>.<br/>\<b>BisoGenet</b> provides an easy to use interface allowing users to customize the searches by \specifying a target set of genes/proteins to retrieve interactions data for, \specifying a subcontext around the targets to narrow the interactions data searching space, \defining a selection filter to discard/include interactions (within the specified \subcontext) given its nature, primary databases and supporting experimental methods. <br/>\Interaction network's gene/protein associated info includes annotations from <b>NCBI</b>, \<b>UniProt</b>, <b>KEGG</b>, and <b>GO</b> databases while interaction info includes \the supporting experimental methods and hyperlinks to their primary databases entries and \related publications.<br/>\<b>BisoGenet</b> also includes network topology analysis tools such as <b>Shortest Paths\</b> between a set of nodes, determination of <b>Equivalent Nodes</b>, and <b>Network \Statistics</b> reports in combination to interactive <b>Transparency filter</b> to help \discernig such analytical results in the context of dense networks.Interaction database1.412.62.72010-06-10Maria E. Ochagavia, Ricardo Bringas, Alexander Martin, Jamilet Miranda, Jorge Fdez. de Cossio, Laya del Carmen Rabasa<b>Centre for Genetic Engineering and Biotechnology (CIGB)</b>http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=303jar184BLAST2SimilarityGraphThis plugin uses an all-vs-all BLAST result file and a sequences file in FASTA format as input to generate a (protein) similarity graph.<br><br> Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.Network generation1.012.72009-04-28Jan BaumbachInternational Computer Science Institute, BerkeleyTobias WittkopBielefeld UniversityDorothea EmigMax Planck Institute for Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=314jar184BLAST2SimilarityGraphThis plugin uses an all-vs-all BLAST result file and a sequences file in FASTA format as input to generate a (protein) similarity graph.<br><br> Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.Network generation1.02.62009-04-28Jan BaumbachInternational Computer Science Institute, BerkeleyTobias WittkopBielefeld UniversityDorothea EmigMax Planck Institute for Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=203jar271BNMatchThe BNMatch plugin is designed to search a target network in an original network according to the given homologous tables and then vividly displays the two network graphs in canvas.<br>Project website: <a href="http://code.google.com/p/bnmatch/">http://code.google.com/p/bnmatch/</a>Other1.02.72.82010-01-01Lei YuShanghai UniversityJiang XieShanghai Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=460jar271BNMatchThe BNMatch plugin is designed to search a target network in an original network according to the given homologous tables and then vividly displays the two network graphs in canvas.<br>Project website: <a href="http://code.google.com/p/bnmatch/">http://code.google.com/p/bnmatch/</a>Other1.12.72.82012-01-01Lei YuShanghai UniversityJiang XieShanghai Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=461jar115BubbleRouterThe Bubble Router Plugin allows users to layout a network incrementally and in a semi-automated way. Bubble Router arranges specific nodes in user-drawn regions based on a selected attribute value. Bubble Router works with any node attribute file.Other1.02.52007-08-28Alexander Pico, Kristina Hanspers, Nathan SalomonisThe Gladstone Institutes Allan KuchinskyAgilent Technologieshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=33jar115BubbleRouterThe Bubble Router Plugin allows users to layout a network incrementally and in a semi-automated way. Bubble Router arranges specific nodes in user-drawn regions based on a selected attribute value. Bubble Router works with any node attribute file.Other1.12.62008-03-12Alexander Pico, Kristina Hanspers, Nathan SalomonisThe Gladstone Institutes Allan KuchinskyAgilent Technologieshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=87jar116CABINCABIN allows exploratory analysis and integration of multiple interaction networks obtained from experimental techniques, inference algorithms and/or bioinformatics datasources.Network generation2.12.5---- CABIN TERMS OF USE ---- Notice: This computer software was prepared by Battelle Memorial Institute, hereinafter the Contractor, under Contract No. DE-AC05-76RL0 1830 with the Department of Energy (DOE). All rights in the computer software are reserved by DOE on behalf of the United States Government and the Contractor as provided in the Contract. NEITHER THE GOVERNMENT NOR THE CONTRACTOR MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. This notice including this sentence must appear on any copies of this computer software. ---- CABIN Sample Data Release Policy ---- By using the sample protein-protein interaction datasets provided within CABIN, the user agrees to the following. PNNL/ORNL is not responsible for errors contained in the protein-protein interaction datasets, or for consequences arising from using the protein-protein interaction datasets. Forthcoming publications from us will detail methods and controls used in the acquisition of data underlying the sample protein-protein interaction datasets. The following acknowledgement must be included in any publications, presentations, reports, databases, websites, or data analyses that have used the CABIN protein-protein interaction datasets: \"Protein-protein interaction data were obtained from the Center for Molecular and Cellular Systems (mippi.ornl.gov) which is sponsored at Oak Ridge National Laboratory by the U.S. Department of Energy Office of Biological and Environmental Research.\" The following paper needs to be cited in any research facilitated by CABIN: Singhal, M., Domico, K., \"CABIN: Collective Analysis of Biological Interaction Networks\", Computat. Biol. Chem. (2007), doi:10.1016/j.compbiolchem.2007.03.006. We reserve the right to publish a description of the overall protein-protein interaction datasets, and the methods used to obtain the contents of the dataset. 2007-08-03Mudita Singhal,Pacific Northwest National Laboratoryhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=36jar268CARLSBADCARLSBAD (Confederated Annotated Research Libraries of Small molecule BioActivity Data) Cytoscape plugin for visualization and exploration of chemical pattern bioactivity networks. http://carlsbad.health.unm.eduOnline data import1.02.82012-03-09Oleg UrsuUNMhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=457jar268CARLSBADCARLSBAD (Confederated Annotated Research Libraries of Small molecule BioActivity Data) Cytoscape plugin for visualization and exploration of chemical pattern bioactivity networks. http://carlsbad.health.unm.eduOnline data import1.12.82012-03-21Oleg UrsuUNMhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=464jar157CentiScaPeCentiScaPe computes specific centrality parameters describing the network topology. The centrality parameters aid the users to find the most significant nodes in a complex network. The plugin computation generates both numerical and graphical output making easy to find the key nodes also in large networks. Network topological quantification can be combined with other numerical node attributes to provide biologically meaningful node identification and functional classification.Information about the plugin that will be displayed to users.<br>Please use html tags for all formatting and do not add newlines.<p>Graph analysis1.02.62008-05-19Giovanni Scardoni, Michele PetterliniCenter for Biomedical Computing (CBMC), University of VeronaCarlo LaudannaCBMC, Department of Pathology, University of Veronahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=128zip157CentiScaPeCentiScaPe computes specific centrality parameters describing the network topology. The centrality parameters aid the users to find the most significant nodes in a complex network. The plugin computation generates both numerical and graphical output making easy to find the key nodes also in large networks. Network topological quantification can be combined with other numerical node attributes to provide biologically meaningful node identification and functional classification.Information about the plugin that will be displayed to users.<br>Please use html tags for all formatting and do not add newlines.<p>Graph analysis1.12.62009-11-26Giovanni Scardoni Center for Biomedical Computing (CBMC), University of Veronahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=249jar157CentiScaPeCentiScaPe computes specific centrality parameters describing the network topology. The centrality parameters aid the users to find the most significant nodes in a complex network. The plugin computation generates both numerical and graphical output making easy to find the key nodes also in large networks. Network topological quantification can be combined with other numerical node attributes to provide biologically meaningful node identification and functional classification.Information about the plugin that will be displayed to users.<br>Please use html tags for all formatting and do not add newlines.<p>Graph analysis1.22.72010-07-14Giovanni Scardoni Center for Biomedical Computing (CBMC), University of Veronahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=310jar157CentiScaPeCentiScaPe computes specific centrality parameters describing the network topology. The centrality parameters aid the users to find the most significant nodes in a complex network. The plugin computation generates both numerical and graphical output making easy to find the key nodes also in large networks. Network topological quantification can be combined with other numerical node attributes to provide biologically meaningful node identification and functional classification.Information about the plugin that will be displayed to users.<br>Please use html tags for all formatting and do not add newlines.<p>Graph analysis1.212.82011-12-28Giovanni Scardoni Center for Biomedical Computing (CBMC), University of Veronahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=447jar206ChemVizThis plugin provides cheminformatics tools to cytoscapeOther1.12.6.32.72010-02-04John \"Scooter\" MorrisUCSFDazhi JiaoIndiana University School of Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=265jar256ClojureEngine<p>Clojure engine v1.2.</p>Scripting1.02.82011-08-01Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=416jar177ClueGOClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG.Data visualization1.12.6Free license available here: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml2009-02-16Gabriela Luana BindeaInstitut for Genomics and Bioinformatics (IGB)Bernhard Mlecnik,Jerome GalonINSERM U872 Integrative Cancer Immunology (ICI) Team 15http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=185jar177ClueGOClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG.Data visualization1.22.6Free license available here: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml2009-07-23Gabriela Luana Bindea,Bernhard Mlecnik,Jerome GalonINSERM U872 Integrative Cancer Immunology (ICI) Team 15http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=218jar177ClueGOClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG.Data visualization1.32.7Free license available here: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml2010-05-18Gabriela Luana Bindea,Bernhard Mlecnik,Jerome GalonINSERM U872 Integrative Cancer Immunology (ICI) Team 15http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=290jar177ClueGOClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG.Data visualization1.312.7Free license available here: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml2010-05-18Gabriela Luana Bindea,Bernhard Mlecnik,Jerome GalonINSERM U872 Integrative Cancer Immunology (ICI) Team 15http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=357jar177ClueGOClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG.Data visualization1.42.8Free license available here: http://www.ici.upmc.fr/cluego/cluegoLicense.shtml2011-03-01Gabriela Luana Bindea,Bernhard Mlecnik,Jerome GalonINSERM U872 Integrative Cancer Immunology (ICI) Team 15http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=419jar168clusterExplorerPluginThis plugin can be used to analyse a given similarity graph (edge weight distribution etc.).<br><br> Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.Clustering0.92.62008-09-18Jan BaumbachUniversity of BielefeldTobian WittkpUniversity of Bielefeldhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=152jar168clusterExplorerPluginThis plugin can be used to analyse a given similarity graph (edge weight distribution etc.).<br><br> Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.Clustering1.012.72009-12-01Jan BaumbachInternational Computer Science Institute, BerkeleyTobias WittkopBielefeld UniversityDorothea EmigMax Planck Institute for Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=315jar168clusterExplorerPluginThis plugin can be used to analyse a given similarity graph (edge weight distribution etc.).<br><br> Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.Clustering1.02.62009-04-28Jan BaumbachInternational Computer Science Institute, BerkeleyTobias WittkopBielefeld UniversityDorothea EmigMax Planck Institute for Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=204jar169clusterMakerCluster Nodes and/or EdgesClustering1.12.6.12008-11-04Jan BaumbachTechnical University of BielefeldTobian WittkopTechnical University of BielefeldLeonard ApeltsinUCSFJohn "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=175jar169clusterMakerCluster Nodes and/or EdgesClustering1.02.62008-09-14Jan BaumbachTechnical University of BielefeldTobian WittkopTechnical University of Bielefeldhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=153jar169clusterMakerCluster Nodes and/or EdgesClustering1.62.6.12009-02-25John "Scooter" MorrisUCSFJan BaumbachTechnical University of BielefeldTobian WittkopTechnical University of Bielefeldhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=187jar169clusterMakerCluster Nodes and/or EdgesClustering1.82.82011-04-04John "Scooter" Morris, Leonard ApeltsinUCSFAaron NewmanUCSBJan BaumbachMax Planck Institut fur InformatikTobias WittkopBuck InstituteGang SuUniversity of MichiganGary BaderUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=384jar169clusterMakerCluster Nodes and/or EdgesClustering1.92.82011-04-10John "Scooter" Morris, Leonard ApeltsinUCSFAaron NewmanUCSBJan BaumbachMax Planck Institut fur InformatikTobias WittkopBuck InstituteGang SuUniversity of MichiganGary BaderUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=387jar169clusterMakerCluster Nodes and/or EdgesClustering1.102.82011-10-23John "Scooter" Morris, Leonard ApeltsinUCSFAaron NewmanUCSBJan BaumbachMax Planck Institut fur InformatikTobias WittkopBuck InstituteGang SuUniversity of MichiganGary BaderUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=432jar219ClusterONEThe ClusterONE plugin finds overlapping protein complexes in a protein interaction network loaded into Cytoscape.Clustering0.12.62010-07-12Tamas Nepusz and Alberto PaccanaroRHULhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=309jar219ClusterONEThe ClusterONE plugin finds overlapping protein complexes in a protein interaction network loaded into Cytoscape.Clustering0.92.62.72010-09-20Tamas Nepusz and Alberto PaccanaroRHULhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=330jar219ClusterONEThe ClusterONE plugin finds overlapping protein complexes in a protein interaction network loaded into Cytoscape.Clustering0.912.62.72.82010-12-17Tamas Nepusz and Alberto PaccanaroRHULhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=353jar219ClusterONEThe ClusterONE plugin finds overlapping protein complexes in a protein interaction network loaded into Cytoscape.Clustering0.922.62.72.82011-07-14Tamas Nepusz and Alberto PaccanaroRHULhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=409jar219ClusterONEThe ClusterONE plugin finds overlapping protein complexes in a protein interaction network loaded into Cytoscape.Clustering0.932.62.72.82011-10-20Tamas Nepusz and Alberto PaccanaroRHULhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=434jar194ClusterVizClusterViz finds clusters (highly interconnected regions, protein complexes or functional module) in a network using various clustering algorithms.This project is supported by graduate student creative funding of HuNan, China, NO. CX2009B040.Clustering1.02.6GPLv30000-00-00Juan Cai, Min Li, Jianxin Wang and Gang ChenCentral South University, Chinahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=241jar194ClusterVizClusterViz finds clusters (highly interconnected regions, protein complexes or functional module) in a network using various clustering algorithms.This project is supported by graduate student creative funding of HuNan, China, NO. CX2009B040.Clustering1.12.6GPLv32010-02-22Juan Cai, Gang Chen and Jianxin WangCentral South University, Chinahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=270jar194ClusterVizClusterViz finds clusters (highly interconnected regions, protein complexes or functional module) in a network using various clustering algorithms.This project is supported by graduate student creative funding of HuNan, China, NO. CX2009B040.Clustering1.22.7GPLv32010-04-12Juan Cai, Gang Chen and Jianxin WangCentral South University, Chinahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=281jar143COMAThis plugin performs consistency checks for gene expression data given gene regulatory networks (refer to citation for details).<br><br>Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.<br><br>If you use it for your research please cite:<br><br>Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.Other1.02.52008-02-13Jan BaumbachBielefeld Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=72jar143COMAThis plugin performs consistency checks for gene expression data given gene regulatory networks (refer to citation for details).<br><br>Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.<br><br>If you use it for your research please cite:<br><br>Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.Other1.12.62008-04-21Jan BaumbachBielefeld Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=115jar143COMAThis plugin performs consistency checks for gene expression data given gene regulatory networks (refer to citation for details).<br><br>Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.<br><br>If you use it for your research please cite:<br><br>Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.Other1.1012.62008-04-21Jan BaumbachBielefeld Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=116jar216commandToolThis plugin provides an interface to the new Cytoscape 2.7 command featureScripting0.92.72010-06-01John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=293jar216commandToolThis plugin provides an interface to the new Cytoscape 2.7 command featureScripting0.912.82010-12-20John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=359jar231CommFinderInformation about the plugin that will be displayed to users.<br>Community Finding Tool.<p>Clustering1.12.6.32010-09-29Tamim and RuanUTSAhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=332jar162CommonAttributesFind attributes shared between selected nodes.<br><p>Requires background knowledge network files available at the CommonAttributes download site http://sourceforge.net/projects/hanalyzer/.Utility1.32.52.6GNU Lesser General Public License version 32008-08-12Ronald SchuylerUniversity of Colorado Health Sciences Centerhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=138jar162CommonAttributesFind attributes shared between selected nodes.<br><p>Requires background knowledge network files available at the CommonAttributes download site http://sourceforge.net/projects/hanalyzer/.Utility2.02.6GNU Lesser General Public License version 32009-02-05Ronald SchuylerUniversity of Colorado Health Sciences CenterBill BaumgartnerUniversity of Colorado Health Sciences Centerhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=184jar218ConsensusPathDBpluginThis plugin mines evidences for user-specified protein-protein interactions in the form of publications, containing databases, interaction detection methods and pathways. The annotation basis is ConsensusPathDB - a meta-database that integrates tens of resources for functional interactions in human, yeast and mouse.Interaction database1.02.72010-07-01Konstantin Pentchev, Atanas Kamburov and Ralf HerwigMPIMGKeiichiro Ono and Trey IdekerUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=306jar215coreCommandsThis plugins provides a set of Commands for use by pluginsUtility0.92.72010-06-01John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=292jar142CoryneRegNetLoaderThis plugin downloads gene regulatory networks from the corynebacterial reference database CoryneRegNet (compatible with at least release 4.0). Downloaded are the gene/protein IDs, the gene/protein names, the evidence, and the regulation type (-1 for repression and +1 for activation).<br><br>Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.<br><br>If you use it for your research please cite:<br><br>Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.Other1.02.52008-02-13Jan BaumbachBielefeld Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=71jar142CoryneRegNetLoaderThis plugin downloads gene regulatory networks from the corynebacterial reference database CoryneRegNet (compatible with at least release 4.0). Downloaded are the gene/protein IDs, the gene/protein names, the evidence, and the regulation type (-1 for repression and +1 for activation).<br><br>Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.<br><br>If you use it for your research please cite:<br><br>Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.Other1.12.62008-04-21Jan BaumbachBielefeld Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=117jar142CoryneRegNetLoaderThis plugin downloads gene regulatory networks from the corynebacterial reference database CoryneRegNet (compatible with at least release 4.0). Downloaded are the gene/protein IDs, the gene/protein names, the evidence, and the regulation type (-1 for repression and +1 for activation).<br><br>Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.<br><br>If you use it for your research please cite:<br><br>Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.Other1.1012.62008-04-21Jan BaumbachBielefeld Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=118jar237CyAnimatorAnimate NetworksData visualization0.92.72.82010-10-27Steve FederowiczUCSDJohn "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=339jar242CyClus3DCyClus3D is a plugin for identifying functional modules in integrated networks composed of multiple interaction types. CyClus3D operates by clustering user-defined 3-node network motifs.Clustering3.12.6.12.6.3GNU General Public License2010-12-08Thomas Van ParysVIB/UGentPieter AudenaertUGent/IBBTTom MichoelFreiburg Institute for Advanced Studieshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=349jar242CyClus3DCyClus3D is a plugin for identifying functional modules in integrated networks composed of multiple interaction types. CyClus3D operates by clustering user-defined 3-node network motifs.Clustering3.32.6.12.6.3GNU General Public License2011-03-15Thomas Van ParysVIB/UGentPieter AudenaertUGent/IBBTTom MichoelFreiburg Institute for Advanced Studieshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=378jar122CyGooseThe CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle. The Gaggle is a tool to create a data exploration and analysis environment. Other geese (independent threads/tools which Cytoscape can now interact with through the Gaggle Boss) can be found at <a href="http://gaggle.systemsbiology.org/docs/geese/">http://gaggle.systemsbiology.org/docs/geese/</a>.<p><b>New Features:</b><ul><li>Select a default layout (excluding yFiles layouts) to apply to subsequent incoming <i>network</i> broadcasts</li><li>A Gaggle species can now be set in the text box on the left, and will update based on the species of an incoming broadcasts. <i><font color='red'>Note</font></i> the species of each Goose (network) is not remembered in this box as every incoming broadcast can change it. A user may type in their own species name as well.</li></ul>Scripting2.52.42.52007-07-25Sarah KillcoyneInstitute for Systems BiologyJohn Lin, Kevin Drew and Richard BonneauNYU Bonneau Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=25jar122CyGooseThe CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle. The Gaggle is a tool to create a data exploration and analysis environment. Other geese (independent threads/tools which Cytoscape can now interact with through the Gaggle Boss) can be found at <a href="http://gaggle.systemsbiology.org/docs/geese/">http://gaggle.systemsbiology.org/docs/geese/</a>.<p><b>New Features:</b><ul><li>Select a default layout (excluding yFiles layouts) to apply to subsequent incoming <i>network</i> broadcasts</li><li>A Gaggle species can now be set in the text box on the left, and will update based on the species of an incoming broadcasts. <i><font color='red'>Note</font></i> the species of each Goose (network) is not remembered in this box as every incoming broadcast can change it. A user may type in their own species name as well.</li></ul>Scripting2.62.52007-10-29Sarah Killcoyne and Dan TenenbaumInstitute for Systems BiologyJohn Lin, Kevin Drew and Richard BonneauNYU Bonneau Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=42jar122CyGooseThe CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle. The Gaggle is a tool to create a data exploration and analysis environment. Other geese (independent threads/tools which Cytoscape can now interact with through the Gaggle Boss) can be found at <a href="http://gaggle.systemsbiology.org/docs/geese/">http://gaggle.systemsbiology.org/docs/geese/</a>.<p><b>New Features:</b><ul><li>Select a default layout (excluding yFiles layouts) to apply to subsequent incoming <i>network</i> broadcasts</li><li>A Gaggle species can now be set in the text box on the left, and will update based on the species of an incoming broadcasts. <i><font color='red'>Note</font></i> the species of each Goose (network) is not remembered in this box as every incoming broadcast can change it. A user may type in their own species name as well.</li></ul>Scripting2.72.6.12009-03-19Sarah Killcoyne and Dan TenenbaumInstitute for Systems BiologyJohn Lin, Kevin Drew and Richard BonneauNYU Bonneau Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=196jar122CyGooseThe CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle. The Gaggle is a tool to create a data exploration and analysis environment. Other geese (independent threads/tools which Cytoscape can now interact with through the Gaggle Boss) can be found at <a href="http://gaggle.systemsbiology.org/docs/geese/">http://gaggle.systemsbiology.org/docs/geese/</a>.<p><b>New Features:</b><ul><li>Select a default layout (excluding yFiles layouts) to apply to subsequent incoming <i>network</i> broadcasts</li><li>A Gaggle species can now be set in the text box on the left, and will update based on the species of an incoming broadcasts. <i><font color='red'>Note</font></i> the species of each Goose (network) is not remembered in this box as every incoming broadcast can change it. A user may type in their own species name as well.</li></ul>Scripting2.82.6.12.6.32010-03-23Sarah Killcoyne and Dan TenenbaumInstitute for Systems BiologyJohn Lin, Kevin Drew and Richard BonneauNYU Bonneau Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=277jar122CyGooseThe CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle. The Gaggle is a tool to create a data exploration and analysis environment. Other geese (independent threads/tools which Cytoscape can now interact with through the Gaggle Boss) can be found at <a href="http://gaggle.systemsbiology.org/docs/geese/">http://gaggle.systemsbiology.org/docs/geese/</a>.<p><b>New Features:</b><ul><li>Select a default layout (excluding yFiles layouts) to apply to subsequent incoming <i>network</i> broadcasts</li><li>A Gaggle species can now be set in the text box on the left, and will update based on the species of an incoming broadcasts. <i><font color='red'>Note</font></i> the species of each Goose (network) is not remembered in this box as every incoming broadcast can change it. A user may type in their own species name as well.</li></ul>Scripting2.92.82011-01-19Sarah Killcoyne, Dan Tenenbaum and Wei-ju WuInstitute for Systems BiologyJohn Lin, Kevin Drew and Richard BonneauNYU Bonneau Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=364jar122CyGooseThe CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle. The Gaggle is a tool to create a data exploration and analysis environment. Other geese (independent threads/tools which Cytoscape can now interact with through the Gaggle Boss) can be found at <a href="http://gaggle.systemsbiology.org/docs/geese/">http://gaggle.systemsbiology.org/docs/geese/</a>.<p><b>New Features:</b><ul><li>Select a default layout (excluding yFiles layouts) to apply to subsequent incoming <i>network</i> broadcasts</li><li>A Gaggle species can now be set in the text box on the left, and will update based on the species of an incoming broadcasts. <i><font color='red'>Note</font></i> the species of each Goose (network) is not remembered in this box as every incoming broadcast can change it. A user may type in their own species name as well.</li></ul>Scripting2.102.82011-01-26Sarah Killcoyne, Dan Tenenbaum and Wei-ju WuInstitute for Systems BiologyJohn Lin, Kevin Drew and Richard BonneauNYU Bonneau Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=366jar276CySBGNSBGN aims to be the standard graphical notation for systems biology. This plugin adds the support to Cytoscape to load SBGN-ML networks.Utility1.02.82012-05-21Emanuel GoncalvesEMBL-European Bioinformatics InstituteMartijn van IerselEMBL-European Bioinformatics InstituteJulio Saez-RodriguezEMBL-European Bioinformatics Institutehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=471jar264CyTargetLinkerThe plugin extends biological networks (nodes need to have an attribute containing a biological identifier, eg. Entrez Gene) with regulatory interactions (e.g. miRNA-target gene). Therefore it is necessary to download the provided regulatory interaction networks (RINs) from the website or create your own.<br>Online data import1.02.82012-01-24Martina KutmonMaastricht UniversityThomas KelderTNOPooja MandaviyaMaastricht UniversityNaime DouallinMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=451jar193CyThesaurus-ID-MappingProvides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin">Click for more information</a>.Other1.032.62009-09-21Jianjiong GaoU. of Missourihttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=234jar193CyThesaurus-ID-MappingProvides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin">Click for more information</a>.Other1.042.62009-10-26Jianjiong GaoU. of Missourihttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=244jar193CyThesaurus-ID-MappingProvides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin">Click for more information</a>.Other1.102.62010-03-11Jianjiong GaoU. of Missourihttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=274jar193CyThesaurus-ID-MappingProvides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin">Click for more information</a>.Other1.112.72010-04-18Jianjiong GaoU. of Missourihttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=287jar193CyThesaurus-ID-MappingProvides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin">Click for more information</a>.Other1.202.82010-12-09Jianjiong GaoU. of Missourihttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=351jar193CyThesaurus-ID-MappingProvides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin">Click for more information</a>.Other1.302.82011-11-02Jianjiong GaoMSKCChttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=437jar193CyThesaurus-ID-MappingProvides utilities for mapping attributes of source ID types to new attributes of destination ID types. <a href="http://www.cytoscape.org/cgi-bin/moin.cgi/CyThesaurus_Plugin">Click for more information</a>.Other1.312.82011-11-08Jianjiong GaoMSKCChttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=439jar275CytoCopteRBased on prior knowledge networks CellNOptR can derive functional information about the network using logic modeling. CytoCopteR is a friendly way to use CellNOptR taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge on R.Integrated analysis1.02.82012-05-03Emanuel GoncalvesEMBL-European Bioinformatics InstituteMartijn van IerselEMBL-European Bioinformatics InstituteJulio Saez-RodriguezEMBL-European Bioinformatics Institutehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=470jar185cytoHubba<p>Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.</p>Graph analysis1.02.62009-06-30Chung-Yen Lin, Chia-Hao, Chin and Min-Tat, KoInstitute of Information Science, Academia Sinica, TAIWANhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=212zip185cytoHubba<p>Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.</p>Graph analysis1.12.62009-10-08http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=240jar185cytoHubba<p>Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.</p>Graph analysis1.22.62.72.82011-05-25Chia-Hao Chin, Hsin-Hung Wu, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin Institute of Information Science, Academia Sinica, Taiwan Chin-Wen Ho National Central University, Taiwan Chung-Yen Lin National Taiwan University, Taiwanhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=398jar185cytoHubba<p>Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.</p>Graph analysis1.32.62.72.82011-06-25Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin Institute of Information Science, Academia Sinica, Taiwan Chin-Wen Ho National Central University, Taiwan Chung-Yen Lin National Taiwan University, Taiwanhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=402jar185cytoHubba<p>Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.</p>Graph analysis1.42.62.72.82011-06-25Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin Institute of Information Science, Academia Sinica, Taiwan Chin-Wen Ho National Central University, Taiwan Hsin-Hung Wu Research Center of Information Technology Innovation, Academia Sinica, Taiwanhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=405jar185cytoHubba<p>Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.</p>Graph analysis1.52.62.72.82011-11-15Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin Institute of Information Science, Academia Sinica, Taiwan Chin-Wen Ho National Central University, Taiwan Hsin-Hung Wu Research Center of Information Technology Innovation, Academia Sinica, Taiwanhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=444jar185cytoHubba<p>Explore important nodes/hubs and fragile motifs in an interactome network by several topological algorithms including Degree, Edge Percolated Component (EPC), Maximum Neighborhood Component (MNC), Density of Maximum Neighborhood Component (DMNC), Maximal Clique Centrality (MCC) and centralities based on shortest paths, such as Bottleneck (BN), EcCentricity, Closeness, Radiality, Betweenness, and Stress.</p>Graph analysis1.62.62.72.82012-04-25Chia-Hao Chin, Shu-Hwa Chen, Ming-Tat Ko and Chung-Yen Lin Institute of Information Science, Academia Sinica, Taiwan Chin-Wen Ho National Central University, Taiwan Hsin-Hung Wu Research Center of Information Technology Innovation, Academia Sinica, Taiwanhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=468jar262CytoITMprobe<p>Earlier, we developed a network information flow framework and implemented it as a web application, called <i>ITM Probe</i>. Given a context consisting of one or more user-selected nodes, <i>ITM Probe</i> retrieves other network nodes most related to that context. Although <i>ITM Probe</i> has several desirable features such a requiring neither restriction to subnetwork of interest nor additional and possibly noisy information, it still has a few limitations. For example, users can only query pre-compiled protein interaction networks. Also, manipulating the layout of significant subnetworks is non-trivial. Most importantly, it is difficult to integrate the results of <i>ITM Probe</i> within workflows involving other analysis methods. To resolve these difficulties. we thus developed <i>CytoITMprobe</i>, a <i>Cytoscape</i> plugin.</p><br><p><i>CytoITMprobe</i> provides access to <i>ITM Probe</i> either through a web server or locally. The input, consisting of desired origins and/or destinations of information and a dissipation coefficient, is specified through a query form. The results are shown as a subnetwork of significant nodes and several summary tables. Users can control the composition and appearance of the subnetwork.</p><br><p>Saving results as node and network attributes, <i>CytoITMprobe</i> allows Cytoscape users to manipulate and visualize context-specific information in a manner more flexible than its web predecessor. It also enables seamless integration of <i>ITM Probe</i> results with other <i>Cytoscape</i> plugins having complementary functionality for data analysis.</p>Network generation1.42.72.82011-11-30Aleksandar StojmirovicNCBI/NLM/NIHAlexander BliskovskyNCBI/NLM/NIHhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=443jar262CytoITMprobe<p>Earlier, we developed a network information flow framework and implemented it as a web application, called <i>ITM Probe</i>. Given a context consisting of one or more user-selected nodes, <i>ITM Probe</i> retrieves other network nodes most related to that context. Although <i>ITM Probe</i> has several desirable features such a requiring neither restriction to subnetwork of interest nor additional and possibly noisy information, it still has a few limitations. For example, users can only query pre-compiled protein interaction networks. Also, manipulating the layout of significant subnetworks is non-trivial. Most importantly, it is difficult to integrate the results of <i>ITM Probe</i> within workflows involving other analysis methods. To resolve these difficulties. we thus developed <i>CytoITMprobe</i>, a <i>Cytoscape</i> plugin.</p><br><p><i>CytoITMprobe</i> provides access to <i>ITM Probe</i> either through a web server or locally. The input, consisting of desired origins and/or destinations of information and a dissipation coefficient, is specified through a query form. The results are shown as a subnetwork of significant nodes and several summary tables. Users can control the composition and appearance of the subnetwork.</p><br><p>Saving results as node and network attributes, <i>CytoITMprobe</i> allows Cytoscape users to manipulate and visualize context-specific information in a manner more flexible than its web predecessor. It also enables seamless integration of <i>ITM Probe</i> results with other <i>Cytoscape</i> plugins having complementary functionality for data analysis.</p>Network generation1.52.72.82012-03-12Aleksandar StojmirovicNCBI/NLM/NIHAlexander BliskovskyNCBI/NLM/NIHhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=463jar214CytomclA wrapper for the MCL clustering algorithm.<br> CytoMCL allows users to cluster networks by using the markov clustering by Van Dongen. (http://micans.org/mcl)<p>Clusters, i.e. strongly connected subnetworks, may represent protein complexes.<p>Other1.02.6GPL2010-06-01Pietro Hiram Guzzi Mario CannataroUMGErnesto PuleoUMG Studenthttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=291zip214CytomclA wrapper for the MCL clustering algorithm.<br> CytoMCL allows users to cluster networks by using the markov clustering by Van Dongen. (http://micans.org/mcl)<p>Clusters, i.e. strongly connected subnetworks, may represent protein complexes.<p>Other1.12.52.62.7GPL2010-06-05Pietro Hiram Guzzi Mario CannataroMAGNA GRAECIA UNIVERSITY OF CATANZAROErnesto PuleoUMG STUDENThttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=294zip214CytomclA wrapper for the MCL clustering algorithm.<br> CytoMCL allows users to cluster networks by using the markov clustering by Van Dongen. (http://micans.org/mcl)<p>Clusters, i.e. strongly connected subnetworks, may represent protein complexes.<p>Other1.12.52.62.7GPL2010-08-13Pietro Hiram Guzzi Mario CannataroMAGNA GRAECIA UNIVERSITY OF CATANZAROErnesto PuleoUMG STUDENThttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=320zip154CytoprophetCytoprophet is a Cytoscape plugin that helps researchers infer new potential protein (PPI) and domain (DDI) interactions. Users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score.Other1.02.6GNU General Public License2008-04-18Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesus IzaguirreUniversity of Notre Damehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=119jar259CytoSaddleSum<p><i>CytoSaddleSum</i> is a <i>Cytoscape</i> functional enrichment plugin that provides interface to <i>SaddleSum</i> functionality. It works by querying <i>SaddleSum</i> either locally (using the standalone version) or remotely, through an HTTP request to a web server. The results of a functional enrichment query are shown as a term relationship network, where nodes represent terms linked by edges showing term relationships. The statistics and other query details for each term are written as node attributes, allowing easy integration into network-based data analysis workflows.</p>Ontology analysis1.42.72.8Public Domain2011-09-19Aleksandar StojmirovicNCBI/NLM/NIHAlexander BliskovskyNCBI/NLM/NIHhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=431jar259CytoSaddleSum<p><i>CytoSaddleSum</i> is a <i>Cytoscape</i> functional enrichment plugin that provides interface to <i>SaddleSum</i> functionality. It works by querying <i>SaddleSum</i> either locally (using the standalone version) or remotely, through an HTTP request to a web server. The results of a functional enrichment query are shown as a term relationship network, where nodes represent terms linked by edges showing term relationships. The statistics and other query details for each term are written as node attributes, allowing easy integration into network-based data analysis workflows.</p>Ontology analysis1.52.72.8Public Domain2011-12-14Aleksandar StojmirovicNCBI/NLM/NIHAlexander BliskovskyNCBI/NLM/NIHhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=445jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.02.62.72010-08-16Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=322jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.12.62.72010-09-21Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=331jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.22.62.72010-09-21Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=336jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.32.62.72011-02-04Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=369jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.42.82011-04-04Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=383jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.52.82011-04-04Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=388jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.62.82011-05-09Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=396jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.72.82011-10-05Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=438jar225CytoscapeRPC"A plug-in which allows users to query and modify networks trough an XML-RPC connection."Scripting1.82.82012-03-27Jan BotDelft Bioinformatics Lab, Delft University of Technologyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=465jar260CytoSEEDThe CytoSEED plugin enables viewing, manipulating and analyzing metabolic models created by the Model SEED (http://www.theseed.org/models)Network generation1.02.8.12.8.22011-09-09Matthew DeJongh, Benjamin Bockstege, Paul Frybarger, Nicholas Hazekamp, Joshua Kammeraad, Travis McGeehanHope Collegehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=433jar260CytoSEEDThe CytoSEED plugin enables viewing, manipulating and analyzing metabolic models created by the Model SEED (http://www.theseed.org/models)Network generation1.12.8.12.8.22011-10-27Matthew DeJongh, Benjamin Bockstege, Paul Frybarger, Nicholas Hazekamp, Joshua Kammeraad, Travis McGeehanHope Collegehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=435jar266CytoSeVisVisualizing networks by semantic similaritiesClustering1.02.7GPL2012-02-06Pietro Hiram GuzziUniczFrancesco TafuriUniczhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=455jar190CytoSQLA plugin to execute SQL SELECT statements against relational databases, and convert the results table to Cytoscape network elements. It can be used to create new networks, extend existing networks or load extra attributes for selected network elements from any accessible relational database. Check the website (<a href="http://www.ptools.ua.ac.be/CytoSQL">http://www.ptools.ua.ac.be/CytoSQL</a>)for common use cases.Online data import0.92.52.62009-08-18Kris Laukens and Koen Van Leemput University of Antwerp - Intelligent Systems Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=224jar190CytoSQLA plugin to execute SQL SELECT statements against relational databases, and convert the results table to Cytoscape network elements. It can be used to create new networks, extend existing networks or load extra attributes for selected network elements from any accessible relational database. Check the website (<a href="http://www.ptools.ua.ac.be/CytoSQL">http://www.ptools.ua.ac.be/CytoSQL</a>)for common use cases.Online data import1.02.52.62.72010-06-28Kris Laukens, Thanh Hai Dang and Koen Van Leemput University of Antwerp - Intelligent Systems Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=304jar239DisplayNetworkFromFlatFileIt displays a Network From a Flat FileOther1.02.72010-11-03http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=341zip160DomainGraphThe main functionality of the DomainGraph plugin is the<br>visual analysis of the effects of alternative splicing<br>on genes, protein isoforms, molecular interactions,<br>pathways and miRNA binding sites. Statistical results<br>of Exon Array data computed with AltAnalyze can be<br>imported into DomainGraph and affected genes, pathways and<br>miRNA binding sites are automatically annotated. From<br>these annotations, genes, gene products, and pathways<br>can directly be loaded and visualized via DomainGraph and<br>occurrences of alternative splicing are highlighted. Therefore,<br> an in-depth analysis of Exon Array data regarding<br>alternative splicing events and their biological impact<br>is easily possible without the need of prior knowledge.<br>Furthermore, the detailed analysis of interaction networks<br>and pathways is possible. Given a gene interaction<br>network, DomainGraph visualizes the genes together with<br>all known encoded protein isoforms and their respective<br>domain compositions. Given a protein interaction network,<br>DomainGraph decomposes the proteins into their domains and<br>visualizes the domain interactions underlying the protein<br>interactions. These networks can be integrated with<br>exon expression data produced by the Affymetrix Exon<br>Array. Genes, protein isoforms and domains are highlighted<br>according to potentially occurring alternative splicing<br>events or differential expression in different groups of samples.Network generation2.012.52.62008-12-12Dorothea Emig,Thomas Lengauer,Mario AlbrechtMax Planck Institute for InformaticsMelissa S. ClineUCSCAnne Kunert,Karsten Klein,Petra MutzelUniversity of DortmundNathan SalomonisThe Gladstone Instituteshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=180jar160DomainGraphThe main functionality of the DomainGraph plugin is the<br>visual analysis of the effects of alternative splicing<br>on genes, protein isoforms, molecular interactions,<br>pathways and miRNA binding sites. Statistical results<br>of Exon Array data computed with AltAnalyze can be<br>imported into DomainGraph and affected genes, pathways and<br>miRNA binding sites are automatically annotated. From<br>these annotations, genes, gene products, and pathways<br>can directly be loaded and visualized via DomainGraph and<br>occurrences of alternative splicing are highlighted. Therefore,<br> an in-depth analysis of Exon Array data regarding<br>alternative splicing events and their biological impact<br>is easily possible without the need of prior knowledge.<br>Furthermore, the detailed analysis of interaction networks<br>and pathways is possible. Given a gene interaction<br>network, DomainGraph visualizes the genes together with<br>all known encoded protein isoforms and their respective<br>domain compositions. Given a protein interaction network,<br>DomainGraph decomposes the proteins into their domains and<br>visualizes the domain interactions underlying the protein<br>interactions. These networks can be integrated with<br>exon expression data produced by the Affymetrix Exon<br>Array. Genes, protein isoforms and domains are highlighted<br>according to potentially occurring alternative splicing<br>events or differential expression in different groups of samples.Network generation2.02.52.62008-11-17Dorothea Emig,Thomas Lengauer,Mario AlbrechtMax Planck Institute for InformaticsMelissa S. ClineUCSCAnne Kunert,Karsten Klein,Petra MutzelUniversity of DortmundNathan SalomonisThe Gladstone Instituteshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=179jar160DomainGraphThe main functionality of the DomainGraph plugin is the<br>visual analysis of the effects of alternative splicing<br>on genes, protein isoforms, molecular interactions,<br>pathways and miRNA binding sites. Statistical results<br>of Exon Array data computed with AltAnalyze can be<br>imported into DomainGraph and affected genes, pathways and<br>miRNA binding sites are automatically annotated. From<br>these annotations, genes, gene products, and pathways<br>can directly be loaded and visualized via DomainGraph and<br>occurrences of alternative splicing are highlighted. Therefore,<br> an in-depth analysis of Exon Array data regarding<br>alternative splicing events and their biological impact<br>is easily possible without the need of prior knowledge.<br>Furthermore, the detailed analysis of interaction networks<br>and pathways is possible. Given a gene interaction<br>network, DomainGraph visualizes the genes together with<br>all known encoded protein isoforms and their respective<br>domain compositions. Given a protein interaction network,<br>DomainGraph decomposes the proteins into their domains and<br>visualizes the domain interactions underlying the protein<br>interactions. These networks can be integrated with<br>exon expression data produced by the Affymetrix Exon<br>Array. Genes, protein isoforms and domains are highlighted<br>according to potentially occurring alternative splicing<br>events or differential expression in different groups of samples.Network generation3.012.62009-12-01Dorothea Emig,Thomas Lengauer,Mario AlbrechtMax Planck Institute for InformaticsNathan SalomonisThe Gladstone Instituteshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=278jar148DroIDDroID plugin provides access to DroID (DROsophila Interaction Database).Interaction database1.02.52.62008-03-24Russ FinleyWSU CMMGSvetlana PacificoWSU CMMG Finley Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=98jar188DualLayoutLayout Network Comparison Toolkit output file. Still an experimental version.Other0.012.62009-08-06Ryan KelleyUCSDKeiichiro OnoUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=222jar150dynamicXprA Plug-In that colors nodes according to their expression across many conditions, as in a movieIntegrated analysis1.22.62008-03-18Iliana Avila-CompilloISBJohn "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=103jar150dynamicXprA Plug-In that colors nodes according to their expression across many conditions, as in a movieIntegrated analysis1.32.62008-09-18Iliana Avila-CompilloISBJohn \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=154jar151edgeLengthPluginThis plugin calculates edge lengths and stores them in an edge attributeOther1.02.62008-01-14John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=104jar151edgeLengthPluginThis plugin calculates edge lengths and stores them in an edge attributeOther1.12.62008-09-14John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=148jar119EnhancedSearchPerform search on multiple attributes using logical operators and wildcards. Locate nodes and edges of interest based on their attributes and highlight them on the network. Reference to the simple query syntax is provided through right-click menu.Utility1.12.52.62008-02-01Maital AshkenaziHUJIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=85jar119EnhancedSearchPerform search on multiple attributes using logical operators and wildcards. Locate nodes and edges of interest based on their attributes and highlight them on the network. Reference to the simple query syntax is provided through right-click menu.Utility1.22.52.62.72.82010-10-30Maital AshkenaziEvogenehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=343jar245EnrichmentMapEnrichment Map is a network-based method to visualize and interpret gene-set enrichment results.Ontology analysis1.02.62.72.82010-11-16Gary Bader, Daniele Merico, Ruth Isserlin, Oliver StuekerUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=354jar245EnrichmentMapEnrichment Map is a network-based method to visualize and interpret gene-set enrichment results.Ontology analysis1.12.62.72.82011-02-07Gary Bader, Daniele Merico, Ruth Isserlin, Oliver StuekerUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=370jar245EnrichmentMapEnrichment Map is a network-based method to visualize and interpret gene-set enrichment results.Ontology analysis1.22.62.72.82011-04-14Gary Bader, Daniele Merico, Ruth Isserlin, Oliver StuekerUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=404jar248ExprEssence<i>ExprEssence</i> condenses a network using gene expression data.<br/><br/><a href="http://www.biomedcentral.com/qc/1752-0509/4/164">Click for more information</a>.<br/><a href="https://sourceforge.net/projects/expressence/">Get the latest version</a>.Integrated analysis1.202.82011-01-05Gregor WarsowInstitute for Biostatistics and Informatics in Medicine and Ageing - University of Rostock, Germanyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=362jar171ExpressionCorrelationExpressionCorrelation plugin computes a similarity network from<br> either the genes or conditions in an expression matrix.Network generation1.012.52.62008-10-07Elena Potylitsine, Weston Whitaker and Gary BaderMemorial Sloan-Kettering Cancer Center Chris SanderMemorial Sloan-Kettering Cancer Center Shirley Hui and Laetitia MorrisonUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=166jar171ExpressionCorrelationExpressionCorrelation plugin computes a similarity network from<br> either the genes or conditions in an expression matrix.Network generation1.02.52.62008-09-24Elena Potylitsine, Weston Whitaker and Gary BaderMSKCC Shirley Hui and Laetitia MorrisonUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=159jar205FluxVizCytoscape Plugin for the visualisation of fluxes in biochemical networks.Network generation0.092.62010-01-28Matthias KoenigComputational Systems Biochemistry Berlinhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=264jar205FluxVizCytoscape Plugin for the visualisation of fluxes in biochemical networks.Network generation0.122.62010-02-05Matthias KoenigComputational Systems Biochemistry Berlinhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=267jar233FM3one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul(2005).Other1.12.62010-10-13Di ChangUniversity of Dortmund, Germanyhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=334zip203FunNetVizFunNetViz is a Cytoscape plug-in associated to FunNet tool for transcriptional interaction analysis. It provides important additional functionalities, including the selection of annotation systems as well as various parameters required for the analysis of networks and modules. Furthermore, it allows for interactional centrality assessment to facilitate exploration and visualization of important transcripts in co-expression networks. It is built upon the powerful Cytoscape open-source platform that includes other tools for biological network analysis and visualization, readily available to the scientific community.Other1.02.6.3 ---- FunNetViz LICENSE AGREEMENT ---- GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation\'s software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author\'s protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors\' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone\'s free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The \"Program\", below, refers to any such program or work, and a \"work based on the Program\" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term \"modification\".) Each licensee is addressed as \"you\". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and \"any later version\", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM \"AS IS\" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 2010-07-01Edi Prifti, Karine Clement, Shakti Rielland, Corneliu Henegar and Jean-Daniel ZuckerINSERM, UMR-S 872, Les Cordeliers, Eq. 7 Nutriomique, Paris - France;http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=260zip227GeneMANIAGeneMANIA helps you predict the function of your favourite genes and gene sets.<br>The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.Network generation1.02.62.72010-08-27GeneMANIA TeamUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=324jar227GeneMANIAGeneMANIA helps you predict the function of your favourite genes and gene sets.<br>The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.Network generation2.02.62.72.82010-12-01GeneMANIA TeamUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=344jar227GeneMANIAGeneMANIA helps you predict the function of your favourite genes and gene sets.<br>The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.Network generation2.12.62.72.82011-03-16GeneMANIA TeamUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=379jar227GeneMANIAGeneMANIA helps you predict the function of your favourite genes and gene sets.<br>The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.Network generation2.22.62.72.82011-07-21GeneMANIA TeamUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=410jar227GeneMANIAGeneMANIA helps you predict the function of your favourite genes and gene sets.<br>The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.Network generation2.32.62.72.82011-12-20GeneMANIA TeamUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=446jar227GeneMANIAGeneMANIA helps you predict the function of your favourite genes and gene sets.<br>The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.Network generation2.42.62.72.82012-01-31GeneMANIA TeamUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=454jar227GeneMANIAGeneMANIA helps you predict the function of your favourite genes and gene sets.<br>The interface is backed by powerful analysis software and a large data warehouse containing extensive amounts of existing functional genomics data. The data warehouse supporting our interface will be kept current using low-maintenance, automated data collection software that we have developed.Network generation2.52.62.72.82012-05-10GeneMANIA TeamUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=476jar186GenoscapeGenoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments. <br>Other1.12.02.12.22.32.42.52.62.6.12009-07-01M.Clement-ZizaTU-DresdenC.MalabatPasteur instituteC.WeberPasteur instituteT.AittokallioC.LetondalPasteur institute and LRIS.RousseauPasteur institutehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=213jar186GenoscapeGenoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments. <br>Other1.112.42.52.62009-08-05M.Clement-ZizaTU-DresdenC.MalabatPasteur instituteC.WeberPasteur instituteT.AittokallioC.LetondalPasteur institute and LRIS.RousseauPasteur institutehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=219jar186GenoscapeGenoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments. <br>Other1.22.42.52.62009-10-10M.Clement-ZizaTU-DresdenC.MalabatPasteur instituteC.WeberPasteur instituteT.AittokallioC.LetondalPasteur institute and LRIS.RousseauPasteur institutehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=245jar228GoogleChartFunctionsFunctions that create image URLs from attribute values using the Google Chart API.Data visualization1.12.82011-08-05Mike SmootUC San Diegohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=327jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.12.52008-01-08Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=54jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.42.62008-08-21Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=135jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.22.52.62008-02-20Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=75jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.32.52.62008-05-27Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=123jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.52.62008-10-09Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=167jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.62.62008-11-14Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=177jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.72.62009-03-13Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=186jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.82.62009-06-04Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=208jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import0.92.62009-09-11Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=232jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import1.02.62010-02-05Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=266jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import1.12.62.72010-06-23Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=299jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import1.22.82011-02-11Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=372jar127GPML-PluginThe GPML plugin for Cytoscape is a converter between Cytoscape networks and the GPML (GenMAPP Pathway Markup Language) pathway format.<p>This plugin makes it possible open and save GPML pathways from Cytoscape. You can also copy/paste bits of pathways or networks between PathVisio, WikiPathways and Cytoscape. The plugin provides a webservice client to directly search and open pathways on WikiPathways<br>See http://www.pathvisio.org/Cytoscape_plugin for more information and http://www.wikipathways.org for a collection of GPML pathways.Online data import1.32.72.82012-01-13Thomas KelderMaastricht Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=450jar208GraMoFoNePlugin to resolve the GRAPH MOTIF problem : find connected occurrences of a motif (i.e. set or multiset of proteins) in a Protein Protein Interaction networks.Other0.122.62010-03-10Blin,Sikora,VialetteUniversity Paris-Est LIGMhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=273jar234GraphletCounterGraphletCounter is a software tool for computing the graphlet signatures of nodes and motifs in biological networks. GraphletCounter can operate on its own or as a plugin to the network analysis environment Cytoscape. GraphletCounter computes the graphlet signatures of individual nodes or of motifs, which can be specified by files generated by the motif-finding tool mfinder. It displays graphlet signatures visually within Cytoscape, and can output graphlet data for integration with larger workflows. Graphlet signatures were introduced by the Przulj group at the University of California at Irvine; please see the following references:<p>Przulj, N. (2007) Biological network comparison using graphlet degree distribution. <i>Bioinformatics</i>, 23(2), e177-e183.<p>Milenkovic, T. and Przulj, N. (2008) Uncovering Biological Network Function via Graphlet Degree Signatures. <i>Cancer Informatics</i>, 6, 257-273.<p>Also refer to the <a href="http://www.weizmann.ac.il/mcb/UriAlon/groupNetworkMotifSW.html">mfinder home page</a> for information on motif finding and a description of its output file format.Graph analysis1.02.62.7 GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. 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You may convey a Combined Work under terms of your choice that, taken together, effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications, if you also do each of the following: a) Give prominent notice with each copy of the Combined Work that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the Combined Work with a copy of the GNU GPL and this license document. c) For a Combined Work that displays copyright notices during execution, include the copyright notice for the Library among these notices, as well as a reference directing the user to the copies of the GNU GPL and this license document. d) Do one of the following: 0) Convey the Minimal Corresponding Source under the terms of this License, and the Corresponding Application Code in a form suitable for, and under terms that permit, the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work, in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source. 1) Use a suitable shared library mechanism for linking with the Library. 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You may place library facilities that are a work based on the Library side by side in a single library together with other library facilities that are not Applications and are not covered by this License, and convey such a combined library under terms of your choice, if you do both of the following: a) Accompany the combined library with a copy of the same work based on the Library, uncombined with any other library facilities, conveyed under the terms of this License. b) Give prominent notice with the combined library that part of it is a work based on the Library, and explaining where to find the accompanying uncombined form of the same work. 6. Revised Versions of the GNU Lesser General Public License. The Free Software Foundation may publish revised and/or new versions of the GNU Lesser General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. 2010-05-01Christopher Whelan and Kemal SonmezOregon Health & Science Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=335jar234GraphletCounterGraphletCounter is a software tool for computing the graphlet signatures of nodes and motifs in biological networks. GraphletCounter can operate on its own or as a plugin to the network analysis environment Cytoscape. GraphletCounter computes the graphlet signatures of individual nodes or of motifs, which can be specified by files generated by the motif-finding tool mfinder. It displays graphlet signatures visually within Cytoscape, and can output graphlet data for integration with larger workflows. Graphlet signatures were introduced by the Przulj group at the University of California at Irvine; please see the following references:<p>Przulj, N. (2007) Biological network comparison using graphlet degree distribution. <i>Bioinformatics</i>, 23(2), e177-e183.<p>Milenkovic, T. and Przulj, N. (2008) Uncovering Biological Network Function via Graphlet Degree Signatures. <i>Cancer Informatics</i>, 6, 257-273.<p>Also refer to the <a href="http://www.weizmann.ac.il/mcb/UriAlon/groupNetworkMotifSW.html">mfinder home page</a> for information on motif finding and a description of its output file format.Graph analysis1.22.62.72.8 GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. An "Application" is any work that makes use of an interface provided by the Library, but which is not otherwise based on the Library. Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library. A "Combined Work" is a work produced by combining or linking an Application with the Library. The particular version of the Library with which the Combined Work was made is also called the "Linked Version". 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If you modify a copy of the Library, and, in your modifications, a facility refers to a function or data to be supplied by an Application that uses the facility (other than as an argument passed when the facility is invoked), then you may convey a copy of the modified version: a) under this License, provided that you make a good faith effort to ensure that, in the event an Application does not supply the function or data, the facility still operates, and performs whatever part of its purpose remains meaningful, or b) under the GNU GPL, with none of the additional permissions of this License applicable to that copy. 3. Object Code Incorporating Material from Library Header Files. The object code form of an Application may incorporate material from a header file that is part of the Library. You may convey such object code under terms of your choice, provided that, if the incorporated material is not limited to numerical parameters, data structure layouts and accessors, or small macros, inline functions and templates (ten or fewer lines in length), you do both of the following: a) Give prominent notice with each copy of the object code that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the object code with a copy of the GNU GPL and this license document. 4. Combined Works. You may convey a Combined Work under terms of your choice that, taken together, effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications, if you also do each of the following: a) Give prominent notice with each copy of the Combined Work that the Library is used in it and that the Library and its use are covered by this License. b) Accompany the Combined Work with a copy of the GNU GPL and this license document. c) For a Combined Work that displays copyright notices during execution, include the copyright notice for the Library among these notices, as well as a reference directing the user to the copies of the GNU GPL and this license document. d) Do one of the following: 0) Convey the Minimal Corresponding Source under the terms of this License, and the Corresponding Application Code in a form suitable for, and under terms that permit, the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work, in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source. 1) Use a suitable shared library mechanism for linking with the Library. A suitable mechanism is one that (a) uses at run time a copy of the Library already present on the user's computer system, and (b) will operate properly with a modified version of the Library that is interface-compatible with the Linked Version. e) Provide Installation Information, but only if you would otherwise be required to provide such information under section 6 of the GNU GPL, and only to the extent that such information is necessary to install and execute a modified version of the Combined Work produced by recombining or relinking the Application with a modified version of the Linked Version. (If you use option 4d0, the Installation Information must accompany the Minimal Corresponding Source and Corresponding Application Code. If you use option 4d1, you must provide the Installation Information in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source.) 5. Combined Libraries. You may place library facilities that are a work based on the Library side by side in a single library together with other library facilities that are not Applications and are not covered by this License, and convey such a combined library under terms of your choice, if you do both of the following: a) Accompany the combined library with a copy of the same work based on the Library, uncombined with any other library facilities, conveyed under the terms of this License. b) Give prominent notice with the combined library that part of it is a work based on the Library, and explaining where to find the accompanying uncombined form of the same work. 6. Revised Versions of the GNU Lesser General Public License. The Free Software Foundation may publish revised and/or new versions of the GNU Lesser General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. 2011-11-11Christopher Whelan and Kemal SonmezOregon Health & Science Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=440jar244GraphMLReaderGraphML reader plugin. You can load basic information (network and attributes) from GraphML files. Experimental GraphML export function is also available for testing.Other0.112.82010-12-11Kozo NishidaNAISTKeiichiro OnoUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=352jar255GroovyEngine<p>Groovy engine v1.8.1.</p>Scripting1.02.82011-08-01Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=415jar172GroovyScriptingEngine<p>Scripting Engine based on Groovy 1.6.7 implementation.Scripting0.112.62.72009-12-07Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=254jar107GroupToolThis plugin provides a generic interface to CyGroupsOther1.02.52007-07-07John \"Scooter\" MorrisUCSF Resource for Biocomputing, Visualization, and Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=13jar107GroupToolThis plugin provides a generic interface to CyGroupsOther1.12.62008-03-18John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=106jar107GroupToolThis plugin provides a generic interface to CyGroupsOther1.22.62008-09-08John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=145jar107GroupToolThis plugin provides a generic interface to CyGroupsOther1.32.82011-09-15John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=420jar180HiderSlider<br> The HiderSlider allows a user to interactively explore a network by hiding/showing nodes or edges with attribute values above an adjustable threshold using a slider bar. The user may choose to slide over any numeric (floating point or integer) attribute for edges or nodes. <br><p>Utility1.02.6GNU Lesser General Public License (LGPLv3) 2009-03-16Ronald SchuylerUniversity of Colorado Health Sciences Centerhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=195jar105HyperEdgeEditorAdd, remove, and modify HyperEdges in a Cytoscape Network.Other2.612.62008-03-28Allan Kuchinsky and Aditya VailayaAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=99jar105HyperEdgeEditorAdd, remove, and modify HyperEdges in a Cytoscape Network.Other2.622.62008-04-03Allan Kuchinsky and Aditya VailayaAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=111jar105HyperEdgeEditorAdd, remove, and modify HyperEdges in a Cytoscape Network.Other2.662.6.32009-07-01Allan Kuchinsky and Aditya VailayaAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=236jar105HyperEdgeEditorAdd, remove, and modify HyperEdges in a Cytoscape Network.Other2.682.82011-05-25Allan Kuchinsky and Aditya VailayaAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=401jar270iCTNetintegrated Complex Traits Network (iCTNet) is a large-scale network, assembling human disease-gene association, tissue-gene association, disease-tissue associations, protein-DNA interactions, protein-protein interactions and drug-target information. This network provides a new and comprehensive perspective for human genetic diseasesOnline data import0.12.62011-09-26Lili Wang, Parvin MousaviQueen's University, CanadaPouya Khankhanian, Sergio E. BaranziniUniversity of California, San Francisco, USAhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=459zip257IgraphPluginThis plugin brings some of igraph's features into Cytoscape.Other0.12.8.12.8.2GPL version 3.2011-09-13Gerardo HuckGoogle Summer of Code 2011http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=423jar125IntActWSClient<html><body>Web Service Client for IntAct Database. <p>Users can import network data from IntAct interaction database. This is a web service client and accessible from other plugins through WebServiceClientManager. This is minor update (bug fix only).</p></body></html>Interaction database0.662.62009-08-05Keiichiro OnoUCSD Bioengineering Ideker Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=221jar258Interference<P ALIGN=JUSTIFY>Interference is a Cytoscape plug-in for virtual experimental network topological analysis allowing virtual knock-out experiments on complex networks<BR><BR>Centrality indexes allow categorizing nodes in complex networks according to their topological relevance (see CentiScaPe plugin). In a node-oriented perspective, centralities are very useful topological parameters to compute in order to quantify the effect of individual node(s) alteration. We have introduced the notion of interference and developed the Cytoscape plugin Interference to evaluate the topological effects of single or multiple nodes removal from a network. In this perspective, interference allows virtual node knock-out experiments: it is possible to remove one or more nodes from a network and analyze the consequences on network structure, by looking to the variations of the node centralities values. As the centrality value of a node is strictly dependent on the network structure and on the properties of other nodes in the network, the consequences of a node deletion are well captured by the variation on the centrality values of all the other nodes.<BR><BR>Potential Applications<BR><BR>The interference approach can model common situations where real nodes are removed or added from/to a physical network:<BR><BR>-Biological networks, where one or more nodes (genes, proteins, metabolites) are possibly removed from the network because of gene deletion, pharmacological treatment or protein degradation. Interference can be used to:<BR><BR>-Simulate pharmacological treatment: one can potentially predict side effects of the drug by looking at topological properties of nodes in a drug-treated network, meaning with that a network in which a drug-targeted node (protein) was removed. To inhibit a protein (for instance a kinases) corresponds to removing the node from the network<BR><BR>-Simulate gene deletion: gene deletion implies losing encoded proteins, thus resulting in the corresponding removal of one or more nodes from a protein network<BR><BR>-Social and financial networks, where the structure of the network is naturally modified over time<BR><BR>-Power grid failures<BR><BR>-Traffic jam or work in progress in a road network<BR><BR>-Temporary closure of an airport in an airline network<BR></P>Graph analysis1.02.8.20000-00-00Giovanni Scardoni Center for Biomedical Computing (CBMC), University of Veronahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=426jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database0.822.62010-04-27Ian Donaldson and Sabry RazickBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=289jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database0.872.62010-06-21Ian Donaldson and Sabry RazickBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=297jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database0.862.62010-06-18Ian Donaldson and Sabry RazickBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=296jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database0.882.62010-06-22Ian Donaldson and Sabry RazickBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=298jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database0.892.62010-06-23Ian Donaldson and Sabry RazickBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=300jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database0.902.72010-06-23Ian Donaldson and Sabry RazickBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=301jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database1.162.72.82011-06-28Ian Donaldson and Sabry RazickBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=406jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database1.172.72.82011-10-10Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie and Ian M DonaldsonBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=429jar212iRefScapeiRefScape:More information frompluginDescription=http://www.biomedcentral.com/1471-2105/12/388pluginDescription=.<br>http://irefindex.uio.no/wiki/iRefScape<p>Interaction database1.182.72.82011-11-18Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie and Ian M DonaldsonBiotechnology Centre of Oslo, University of Oslohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=442jar101jActiveModulesActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks, i.e., modules.Integrated analysis2.22.52007-03-23Ryan M. KelleyUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=5jar101jActiveModulesActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks, i.e., modules.Integrated analysis2.212.52.62008-03-31Ryan KelleyUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=101jar101jActiveModulesActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks, i.e., modules.Integrated analysis2.222.52.62008-06-10Ryan KelleyUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=125jar101jActiveModulesActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks, i.e., modules.Integrated analysis2.232.52.62008-08-13Ryan KelleyUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=133jar153JavaScriptEngine<p>Default JavaScript engine in Java SE 6. You can run JavaScript on Cytoscape. <strong>To use this plugin, you need to install Java SE 6 AND ScriptEngineManager Plugin 1.0 or later</strong>.</p>Scripting0.112.62.72009-12-07Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=255jar153JavaScriptEngine<p>Default JavaScript engine in Java SE 6. You can run JavaScript on Cytoscape. <strong>To use this plugin, you need to install Java SE 6 AND ScriptEngineManager Plugin 1.0 or later</strong>.</p>Scripting1.02.82011-08-01Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=413jar254KeyPathwayMinerA plugin for the combined analysis of differential expression data and biological networks.Data visualization1.02.82011-07-10Nicolas Alcaraz and Hande KucukMPIIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=407jar254KeyPathwayMinerA plugin for the combined analysis of differential expression data and biological networks.Data visualization2.02.82011-09-16Nicolas AlcarazMPIIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=425jar254KeyPathwayMinerA plugin for the combined analysis of differential expression data and biological networks.Data visualization2.12.82011-10-13Nicolas AlcarazMPIIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=430jar254KeyPathwayMinerA plugin for the combined analysis of differential expression data and biological networks.Data visualization3.02.82012-01-26Nicolas AlcarazMPIIJoachim MuellerMPIIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=452jar224KGMLReaderReader plugin for KEGG pathway datasets in KGML format. Visit <a href="http://code.google.com/p/kgmlreader/">Google Code Site</a> for more information. If you have questions or feature request, please send them to <a href="http://groups-beta.google.com/group/cytoscape-discuss">cytoscape-discuss</a> mailing list.Other0.062.72010-08-18Kozo NishidaNara Institute of Science and TechnologyKeiichiro OnoUC, San Diego Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=321jar224KGMLReaderReader plugin for KEGG pathway datasets in KGML format. Visit <a href="http://code.google.com/p/kgmlreader/">Google Code Site</a> for more information. If you have questions or feature request, please send them to <a href="http://groups-beta.google.com/group/cytoscape-discuss">cytoscape-discuss</a> mailing list.Other0.102.82011-04-27Kozo NishidaNara Institute of Science and TechnologyKeiichiro OnoUC, San Diego Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=392jar224KGMLReaderReader plugin for KEGG pathway datasets in KGML format. Visit <a href="http://code.google.com/p/kgmlreader/">Google Code Site</a> for more information. If you have questions or feature request, please send them to <a href="http://groups-beta.google.com/group/cytoscape-discuss">cytoscape-discuss</a> mailing list.Other0.112.82011-04-27Kozo NishidaNara Institute of Science and TechnologyKeiichiro OnoUC, San Diego Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=462jar224KGMLReaderReader plugin for KEGG pathway datasets in KGML format. Visit <a href="http://code.google.com/p/kgmlreader/">Google Code Site</a> for more information. If you have questions or feature request, please send them to <a href="http://groups-beta.google.com/group/cytoscape-discuss">cytoscape-discuss</a> mailing list.Other0.152.82012-04-10Kozo NishidaNara Institute of Science and TechnologyKeiichiro OnoUC, San Diego Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=466jar263KNIMEConnector<p>This plug-in allows networks to be sent and received to and from <a href="http://knime.org">KNIME</a> (Konstanz Information Miner) a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform.<br>Click <a href="http://knime.org/knime">here</a> for a detailed description of KNIME.</p><p>KNIME enables large attributed graphs to be processed via the <a href="http://tech.knime.org/node/36031">Network Mining</a> plug-in. For a detailed description on how to send and receive networks see the <a href="http://tech.knime.org/node/36081">Network Visualization</a> section.</p><p>You can access the KNIME Connector from the Cytoscape menu (Plugins->KNIME Connector).</p>Online data import1.02.8GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. <one line to give the program's name and a brief idea of what it does.> Copyright (C) <year> <name of author> This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. <signature of Ty Coon>, 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License.2012-01-10Tobias KoetterUniversity of Konstanzhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=449jar273LayoutSaverPluginA simple plugin that saves the X/Y positions of nodes in one network so that the positions can be applied to other networks that share the same nodes. Click on the <b>Layout&rarr;Save Node Positions</b> to save the node positions in the current network and the Click on the <b>Layout&rarr;Cytoscape Layouts&rarr;Apply Saved Layout</b> to apply the saved node positions to the current network.Utility1.02.82012-04-24Mike SmootUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=467jar111MCODEMCODE finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.Clustering1.22.52007-02-15Gary BaderMSKCChttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=4jar111MCODEMCODE finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.Clustering1.32.52007-12-07Gary Bader, Vuk PavlovicUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=47jar111MCODEMCODE finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.Clustering1.312.62009-05-22Gary Bader, Vuk PavlovicUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=206jar111MCODEMCODE finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.Clustering1.322.62.72.82011-06-28Gary Bader, Vuk PavlovicUniversity of Torontohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=403jar117MetaNetterPlugin for the inference of metabolic networks based on high resolution metabolomic data.Network generation2.12.52007-07-24Fabien JourdanINRAhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=40jar108MetaNodePlugin2This plugin provides a viewer for groups that implements a collapse/expand abstractionOther1.02.52007-07-07John \"Scooter\" MorrisUCSF Resource for Biocomputing, Visualization, and Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=14jar108MetaNodePlugin2This plugin provides a viewer for groups that implements a collapse/expand abstractionOther1.012.52007-07-07John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=35jar108MetaNodePlugin2This plugin provides a viewer for groups that implements a collapse/expand abstractionOther1.12.62008-03-18John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=107jar108MetaNodePlugin2This plugin provides a viewer for groups that implements a collapse/expand abstractionOther1.22.62008-09-18John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=146jar108MetaNodePlugin2This plugin provides a viewer for groups that implements a collapse/expand abstractionOther1.62.82011-09-15John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=422jar179MetScape<p>MetScape provides a bioinformatics framework for the visualization and interpretation of metabolomic data using Cytoscape. MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. Gene expression and/or compound concentration data can be loaded from file(s) (in CSV, TSV, or Excel formats), or the user can simply enter individual compounds/genes/pathways (using KEGG, EHMN, or Entrez Gene IDs) to build metabolic networks without loading a file. MetScape uses an internal relational database stored at NCIBI that integrates data from KEGG and EHMN.</p><p>For more information contact the MetScape development team: metscape-help@umich.edu</p><p>This work developed at the University of Michigan, National Center for Integrative Biomedical Informatics (NCIBI), under National Institutes of Health Grant #U54DA021519..</p>Data visualization0.82.62009-03-13Jing Gao, Alla Karnovsky, Glenn Tarcea, James Cavalcoli and H. V. Jagadish CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=194jar179MetScape<p>MetScape provides a bioinformatics framework for the visualization and interpretation of metabolomic data using Cytoscape. MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. Gene expression and/or compound concentration data can be loaded from file(s) (in CSV, TSV, or Excel formats), or the user can simply enter individual compounds/genes/pathways (using KEGG, EHMN, or Entrez Gene IDs) to build metabolic networks without loading a file. MetScape uses an internal relational database stored at NCIBI that integrates data from KEGG and EHMN.</p><p>For more information contact the MetScape development team: metscape-help@umich.edu</p><p>This work developed at the University of Michigan, National Center for Integrative Biomedical Informatics (NCIBI), under National Institutes of Health Grant #U54DA021519..</p>Data visualization1.02.62009-09-01Jing Gao, Alla Karnovsky, Glenn Tarcea, Barbara Mirel, Terry Weymouth, James Cavalcoli, H.V. Jagadish CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=229jar179MetScape<p>MetScape provides a bioinformatics framework for the visualization and interpretation of metabolomic data using Cytoscape. MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. Gene expression and/or compound concentration data can be loaded from file(s) (in CSV, TSV, or Excel formats), or the user can simply enter individual compounds/genes/pathways (using KEGG, EHMN, or Entrez Gene IDs) to build metabolic networks without loading a file. MetScape uses an internal relational database stored at NCIBI that integrates data from KEGG and EHMN.</p><p>For more information contact the MetScape development team: metscape-help@umich.edu</p><p>This work developed at the University of Michigan, National Center for Integrative Biomedical Informatics (NCIBI), under National Institutes of Health Grant #U54DA021519..</p>Data visualization1.012.72010-04-29Jing Gao, Alla Karnovsky, Glenn Tarcea, Barbara Mirel, Terry Weymouth, James Cavalcoli, H.V. Jagadish CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=259jar179MetScape<p>MetScape provides a bioinformatics framework for the visualization and interpretation of metabolomic data using Cytoscape. MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. Gene expression and/or compound concentration data can be loaded from file(s) (in CSV, TSV, or Excel formats), or the user can simply enter individual compounds/genes/pathways (using KEGG, EHMN, or Entrez Gene IDs) to build metabolic networks without loading a file. MetScape uses an internal relational database stored at NCIBI that integrates data from KEGG and EHMN.</p><p>For more information contact the MetScape development team: metscape-help@umich.edu</p><p>This work developed at the University of Michigan, National Center for Integrative Biomedical Informatics (NCIBI), under National Institutes of Health Grant #U54DA021519..</p>Data visualization2.32.82011-10-03Tim Hull, V. Glenn Tarcea, Alla Karnovsky and Terry E. Weymouth University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=427jar179MetScape<p>MetScape provides a bioinformatics framework for the visualization and interpretation of metabolomic data using Cytoscape. MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. Gene expression and/or compound concentration data can be loaded from file(s) (in CSV, TSV, or Excel formats), or the user can simply enter individual compounds/genes/pathways (using KEGG, EHMN, or Entrez Gene IDs) to build metabolic networks without loading a file. MetScape uses an internal relational database stored at NCIBI that integrates data from KEGG and EHMN.</p><p>For more information contact the MetScape development team: metscape-help@umich.edu</p><p>This work developed at the University of Michigan, National Center for Integrative Biomedical Informatics (NCIBI), under National Institutes of Health Grant #U54DA021519..</p>Data visualization2.312.82011-10-05Tim Hull, V. Glenn Tarcea, Alla Karnovsky and Terry E. Weymouth University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=428jar113MiMIplugin<p>MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching.</p>Interaction database2.02.52007-08-31Jing Gao, Alex Adehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=31jar113MiMIplugin<p>MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching.</p>Interaction database2.12.52007-10-08Jing Gao, Alex Ade and David StatesUniversity of Michigan CCMB/NCIBIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=39jar113MiMIplugin<p>MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching.</p>Interaction database2.22.52.62008-04-14Jing Gao, Alex Ade, David States CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=59jar113MiMIplugin<p>MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching.</p>Interaction database3.02.62008-07-01Jing Gao, Alex Ade, David States CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=124jar113MiMIplugin<p>MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching.</p>Interaction database3.012.72010-04-29Jing Gao, Alex Ade, David States CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=132jar113MiMIplugin<p>MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching.</p>Interaction database3.12.72.82011-02-24Jing Gao, Alex Ade, David States CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=375jar113MiMIplugin<p>MiMI Cytoscape plugin retrieves molecular interactions from Michigan Molecular Interactions (MiMI) database and displays the interaction network with Cytoscape. MiMI gathers and merges data from well-known protein interaction databases including BIND, DIP, HPRD, RefSeq, SwissProt, IPI and CCSB-HI1 etc. A provenance model has been developed that tracks the source of each data element and what processes have been performed upon it. The plugin also integrates with other NCIBI tools for literature information, document summarization and pathway matching.</p>Interaction database3.112.72.82011-04-05Jing Gao, Alex Ade, David States CCMB/NCIBI University of Michiganhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=386jar235MINEMINE is an agglomerative clustering method that is able to identify highly modular sets of gene products within dense molecular interaction networks. It was created in response to the challenge of discovering high quality modules of gene products from dense biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters.<p>Clustering1.02.62010-10-18Kahn RhrissorrakraiNYU Kristin C. GunsalusNYUhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=338jar235MINEMINE is an agglomerative clustering method that is able to identify highly modular sets of gene products within dense molecular interaction networks. It was created in response to the challenge of discovering high quality modules of gene products from dense biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters.<p>Clustering1.52.62010-10-18Kahn RhrissorrakraiNYU Kristin C. GunsalusNYUhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=368jar123MiSinkNetwork interface to MiSink-enabled Web sites, including DIP (The Database of Interacting Proteins: http://dip.doe-mbi.ucla.edu).Scripting2.002.52007-07-24Lukasz SalwinskiUCLA-DOE Institute for Genomics and Proteomicshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=24zip123MiSinkNetwork interface to MiSink-enabled Web sites, including DIP (The Database of Interacting Proteins: http://dip.doe-mbi.ucla.edu).Scripting2.032.52007-11-21Lukasz SalwinskiUCLAhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=51zip123MiSinkNetwork interface to MiSink-enabled Web sites, including DIP (The Database of Interacting Proteins: http://dip.doe-mbi.ucla.edu).Scripting2.042.62008-05-28Lukasz SalwinskiUCLAhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=122zip126MONET<i><b>Motivation:</b></i> Although gene expression data has been continuously accumulated and meta-analysis approaches have been developed to integrate independent expression profiles into larger datasets, the amount of information is still insufficient to infer large scale genetic networks. In addition, global optimization such as Bayesian network inference, one of the most representative techniques for genetic network inference, requires tremendous computational load far beyond the capacity of moderate workstations. <br><br><i><b>Results:</b></i> MONET is a Cytoscape plugin to infer genome-scale networks from gene expression profiles. It alleviates the shortage of information by incorporating pre-existing annotations. The current version of MONET utilizes thousands of parallel computational cores in the supercomputing center in KISTI, Korea, to cope with the computational requirement for large scale genetic network inference.<br><br><i><b>Reference:</b></i> Lee et al., Modularized learning of genetic interaction networks from biological annotations and mRNA expression data. <i>Bioinformatics</i> (2005) 21, 2739-2747Network generation2.12.32.42.52.62.72010-09-13Younghoon Kim, Yongseong Cho, Doheon LeeKAISThttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=328jar261MosaicNetwork partition, layout and color based on Gene Ontology or other annotationsOntology analysis1.02.82011-11-15Chao ZhangUniversity of Missouri & GSoCAlexander PicoGladstone Institutes, UCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=441jar128MultilevelLayoutPluginThe plug-in generates network layouts using the multilevel node placement framework introduced by C. Walshaw (2003).The multilevel approach is relative fast and it provides visually pleasant layouts also for larger networks.Utility0.412.52008-01-16Pekka SalmelaUniversity of Turku, Finland Olli S. NevalainenUniversity of Turku, Finland Tero aittokallioUniversity of Turku, Finlandhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=56jar128MultilevelLayoutPluginThe plug-in generates network layouts using the multilevel node placement framework introduced by C. Walshaw (2003).The multilevel approach is relative fast and it provides visually pleasant layouts also for larger networks.Utility0.62.52008-07-06Pekka SalmelaUniversity of Turku, Finland Olli S. NevalainenUniversity of Turku, Finland Tero aittokallioUniversity of Turku, Finlandhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=129jar109NamedSelectionThis plugin provides the ability to "remember" a group of selected nodesUtility1.02.52007-07-07John \"Scooter\" MorrisUCSF Resource for Biocomputing, Visualization, and Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=15jar109NamedSelectionThis plugin provides the ability to "remember" a group of selected nodesUtility1.12.62008-03-18John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=108jar109NamedSelectionThis plugin provides the ability to "remember" a group of selected nodesUtility1.22.62008-09-18John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=147jar109NamedSelectionThis plugin provides the ability to "remember" a group of selected nodesUtility1.52.82011-09-15John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=421jar138NCBIClient<p>Web Service client module for <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html">NCBI Entrez Utilities Web Service</a>.</p><p>For more information, please visit the following pages:</p><ul><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients">Sample clients</a></li><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/WebServiceWorkflow">Sample workflow</a></li></ul><p><strong><font color="red">To use this function from Cytoscape Desktop, <u>NCBI Entrez Gene User Interface</u> plugin is required. This plugin works with Cytoscape 2.7.0 or later.</font></strong>Online data import0.702.62008-10-24Keiichiro OnoUCSD Bioengineeringhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=174jar138NCBIClient<p>Web Service client module for <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html">NCBI Entrez Utilities Web Service</a>.</p><p>For more information, please visit the following pages:</p><ul><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients">Sample clients</a></li><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/WebServiceWorkflow">Sample workflow</a></li></ul><p><strong><font color="red">To use this function from Cytoscape Desktop, <u>NCBI Entrez Gene User Interface</u> plugin is required. This plugin works with Cytoscape 2.7.0 or later.</font></strong>Online data import0.922.72009-11-06Keiichiro OnoUCSD Dept. of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=246jar139NCBIEntrezGeneUserInterface<p>This plugin provides user interface for <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html">NCBI Entrez Utilities Web Service</a>.</p><p>For more information, please visit the following pages:</p><ul><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/SampleWebServiceClients">Sample clients</a></li><li><a href="http://www.cytoscape.org/cgi-bin/moin.cgi/WebServiceWorkflow">Sample workflow</a></li></ul><p><strong><font color="red">To use this plugin, <u>NCBIClient</u> is required.</font></strong>Online data import0.522.62008-03-14Keiichiro OnoUCSD Bioengineeringhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=91jar161NeighborHighlightThe plugin highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.Utility1.02.62008-08-26Dorothea Emig, Mario AlbrechtMax Planck Institute for Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=136jar195NeMoNeMo is a network community-finding plugin for cytoscape. This plugin has the unique ability to find both densely connected networks and densely connected bipartite structures in a unified approach. The quick performance of the plugin allows it to be used interactively for network analysis. The plugin is easy to use because it is free of tunable parameters.Clustering1.32.62009-10-12Corban G. Rivera, Rachit Vakil, Joel S. BaderDepartment of Biomedical Engineering, Johns Hopkins Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=242jar195NeMoNeMo is a network community-finding plugin for cytoscape. This plugin has the unique ability to find both densely connected networks and densely connected bipartite structures in a unified approach. The quick performance of the plugin allows it to be used interactively for network analysis. The plugin is easy to use because it is free of tunable parameters.Clustering1.42.62.72010-02-26Corban G. Rivera, Rachit Vakil, Joel S. BaderDepartment of Biomedical Engineering, Johns Hopkins Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=271jar145NetAtlasInformation about the plugin that will be displayed to users.<br>Please use html tags for all formatting and do not add newlines.<p>Integrated analysis1.12.42.52007-11-20Russell S. ThomasThe Hamner Institutes for Health SciencesLonglong YangThe Hamner Institutes for Health Scienceshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=74zip145NetAtlasInformation about the plugin that will be displayed to users.<br>Please use html tags for all formatting and do not add newlines.<p>Integrated analysis1.22.72.82010-05-01Longlong Yang and Russell S. Thomas The Hamner Institutes for Health Scienceshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=395jar213NetCirChroNetCirChro is a Cytoscape plug-in for network visualization on circular chromosomes. It enables mapping of interaction networks and node/edge attributes on circular genomes. This plug-in allows users to dynamically analyze the association between gene interactions and gene organization on chromosomes.<p>Web: <a href="http://exon.niaid.nih.gov/netcirchro">http://exon.niaid.nih.gov/netcirchro</a> <br>Email: <a href="mailto:NetCirChroSupport@niaid.nih.gov">NetCirChroSupport@niaid.nih.gov</a>Data visualization1.02.6.12.6.3GNU General Public License2009-11-25Jie Li, Qina Tan, Vijayaraj Nagarajan, Mariam Quinones, Yasmin Mohamoud, Yentram HuyenBioinformatics and Computational Biosciences Branch (BCBB) / The Office of Cyber Infrastructure and Computational Biology (OCICB) / National Institutehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=286jar155NetLinkLinks network nodes or edges to other networks via the right-click menu based on an attribute (called netlink.connection) that maps the node/edge id to a network name.Utility0.12.62008-04-30Mike SmootUC San Diegohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=120jar124netMatchNetMatch is a Cytoscape plugin that finds user defined network motifs in any Cytoscape network. Node and edge attributes of any type and paths of unknown length can be specified in the search.Graph analysis2.12.52.62008-11-07A. FerroUniversity of CataniaR. GiugnoUniversity of CataniaG. PigolaUniversity of CataniaA. PulvirentiUniversity of CataniaD. SkripinUniversity of CataniaG.D. BaderUniversity of TorontoD. ShashaNew York Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=176jar124netMatchNetMatch is a Cytoscape plugin that finds user defined network motifs in any Cytoscape network. Node and edge attributes of any type and paths of unknown length can be specified in the search.Graph analysis2.22.72.8.12011-05-02A. FerroUniversity of CataniaR. GiugnoUniversity of CataniaG. PigolaUniversity of CataniaA. PulvirentiUniversity of CataniaD. SkripinUniversity of CataniaG.D. BaderUniversity of TorontoD. ShashaNew York Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=394jar209NetworkEvolutionThe plugin allows the user to map selected network regions to interactomes of evolutionary predecessors and descendants, making it possible to interactively inspect evolutionary changes and observe both conservation and diversification of specific network components.Other2.12.6.32010-03-05Michal WozniakUniversity of WarsawJanusz DutkowskiUniversity of Warsawhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=275jar247nodeChartsPaint a chart on a nodeData visualization0.912.82010-12-17http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=356jar247nodeChartsPaint a chart on a nodeData visualization0.922.82010-12-21http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=360jar247nodeChartsPaint a chart on a nodeData visualization0.942.82011-02-25http://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=380jar241OrthoNetsProtein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. OrthoNets is a Cytoscape plugin that displays PPI networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors. Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism.Other1.02.72.82010-12-06Wodak Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=345jar269OWLPluginThis plugin builds a cyto-network from OWL/RDF ontologies. Using OWL-API library and Pellet Reasoner, OWLPlugin generates the graph of each ontology elements with some extra-information: the type of relationships, individuals, classes,... We are working in including new extra features and user dialogs. In next versions, we make public the source repository and more relevant information. For any thing, please do not hesitate to contact me.Network generation1.02.8.22013-02-28Isaac LeraUniversitat de les Illes Balearshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=458zip243PanGIAPanGIA (Physical and Genetic Interaction Alignment) is a plugin designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies "modules" as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules.Integrated analysis1.02.82010-12-09Gregory Hannum, Rohith Srivas, Johannes Ruscheinski, Kei Ono, Peng-Liang Wang, Michael Smoot, Trey IdekerUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=350jar243PanGIAPanGIA (Physical and Genetic Interaction Alignment) is a plugin designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies "modules" as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules.Integrated analysis1.12.82011-02-24Gregory Hannum, Rohith Srivas, Johannes Ruscheinski, Kei Ono, Peng-Liang Wang, Michael Smoot, Trey IdekerUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=376jar238PathintegratorPathintegrator obtains a list of pathways from different sources (Pathway Commons, NetPath, Wikipathways and KEGG) in which a protein of interest has a role, merges the information contained in the networks and displays it.Online data import1.02.72010-11-01Juan Ramón Meneu Hernández Università degli Studi di Bologna Paolo Tieri Università degli Studi di Bolognahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=340jar181PerturbationAnalyzerThe PerturbationAnalyzer is an open source java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network. Source code is avaliable at http://code.google.com/p/perturbation-analyzer/Integrated analysis0.12.52.6.12009-03-23Fei LiNUDT/BMIWenjian XuBMIPeng LiBMIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=197jar181PerturbationAnalyzerThe PerturbationAnalyzer is an open source java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network. Source code is avaliable at http://code.google.com/p/perturbation-analyzer/Integrated analysis0.22.52.62009-05-24Fei LiNUDT/BMIWenjian XuBMIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=207jar181PerturbationAnalyzerThe PerturbationAnalyzer is an open source java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network. Source code is avaliable at http://code.google.com/p/perturbation-analyzer/Integrated analysis1.02.52.62009-06-18Fei LiNUDT/BMIhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=209jar181PerturbationAnalyzerThe PerturbationAnalyzer is an open source java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network. Source code is avaliable at http://code.google.com/p/perturbation-analyzer/Integrated analysis1.12.52009-08-14Fei LiBMI NUDThttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=223jar181PerturbationAnalyzerThe PerturbationAnalyzer is an open source java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network. Source code is avaliable at http://code.google.com/p/perturbation-analyzer/Integrated analysis1.22.52.6.32009-10-04Fei LiBMI NUDThttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=238jar252PhyloTreeThis plugin provides the ability to read phylogenetic tree formats and display them in Cytoscape as treesNetwork generation0.12.82011-04-19Chinmoy Bhatiyahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=390jar147PICRClient<html><body>Web Service Client for PICR protein ID cross reference service. <p>Users can import protein synonyms from PICR RESTful service.</p><p><strong>Caution: Since PICR is a beta service, if you send a lot of query to their server, you may be blocked from their service.</strong></p></body></html>Other0.22.62008-04-10Keiichiro OnoUCSD Bioengineering Ideker Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=97jar223PiNGOPiNGO is a plugin to find candidate genes in a network that are associated with user-defined target Gene Ontology (GO) categories.Ontology analysis1.002.62.72010-08-01Steven MaereVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=319jar223PiNGOPiNGO is a plugin to find candidate genes in a network that are associated with user-defined target Gene Ontology (GO) categories.Ontology analysis1.102.72.82010-12-06Steven MaereVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=346jar223PiNGOPiNGO is a plugin to find candidate genes in a network that are associated with user-defined target Gene Ontology (GO) categories.Ontology analysis1.112.82011-01-18Steven MaereVIBhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=365jar156PinnacleZ<html>An implementation of the PinnacleZ algorithm as specified in Chuang, H. Y. and Lee, E., et al., "Network-based classification of breast cancer metastasis," <i>Molecular Systems Biology</i> 3:140 (2007).</html>Integrated analysis1.02.52.62008-06-16Samad Lotia and Han-Yu ChuangUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=127jar156PinnacleZ<html>An implementation of the PinnacleZ algorithm as specified in Chuang, H. Y. and Lee, E., et al., "Network-based classification of breast cancer metastasis," <i>Molecular Systems Biology</i> 3:140 (2007).</html>Integrated analysis1.12.52.62008-10-10Samad Lotia and Han-Yu ChuangUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=170jar202PSICQUICUniversalClientPSICQUIC Web Service Universal Client. You can perform meta-search in PSICQUIC-compliant databases. This plugin works with Cytoscape 2.7.0 or later.Interaction database0.252.72010-07-29Keiichiro OnoUC San Diego Department of Medicine Trey Ideker Labhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=313jar170PythonScriptingEngine<p>Scripting engine based on Jython 2.5.1 implementation. This plugin uses JyConsole library by Artenum OpenSource project.Scripting0.212.62.72009-12-07Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=253jar166RandomNetworksThe plugin is used to generate random networks, randomize existing networks and compare existing networks to random models.Network generation1.02.62008-09-19Patrick J. McSweeneySyracuse Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=143jar251RemainingDegreeDistributionThis plugin calculates the remaining degree distribution of a networkGraph analysis1.02.52.62.72011-02-25Isuru Udana University of Moratuwahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=377jar175ReOrientPlugin<br>Applies node positions from a network in any stored Cytoscape session file to the currently selected network.<br><p> A network can be created, laid out, and stored with an existing data set. When new data becomes available, a new network can be created and easily compared to the old network by placing nodes in the same positions. <br><p> To use the plugin, select "from Saved Session" from the Layout menu. <br><p> The current version allows the user to select any network from a saved session as the source network.<br><p>Other0.32.52.6GNU Lesser General Public License (LGPLv3) 2009-01-22Ronald SchuylerUniversity of Colorado Health Sciences Centerhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=183jar175ReOrientPlugin<br>Applies node positions from a network in any stored Cytoscape session file to the currently selected network.<br><p> A network can be created, laid out, and stored with an existing data set. When new data becomes available, a new network can be created and easily compared to the old network by placing nodes in the same positions. <br><p> To use the plugin, select "from Saved Session" from the Layout menu. <br><p> The current version allows the user to select any network from a saved session as the source network.<br><p>Other1.02.52.6GNU Lesser General Public License (LGPLv3) 2009-01-22Ronald SchuylerUniversity of Colorado Health Sciences Centerhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=191jar141RubyScriptingEngine<p>Script Engine based on JRuby 1.6.3 implementation.Scripting0.212.62.72009-12-07Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=252jar141RubyScriptingEngine<p>Script Engine based on JRuby 1.6.3 implementation.Scripting1.02.82011-08-01Keiichiro OnoUC San Diego Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=417jar140ScriptEngineManagerThis plugin manages scripting engines for Cytoscape. Supports Java Scripting Framework available from Java 6 (JSR-223)Scripting0.082.62.72009-12-07Keiichiro OnoUCSD Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=251jar140ScriptEngineManagerThis plugin manages scripting engines for Cytoscape. Supports Java Scripting Framework available from Java 6 (JSR-223)Scripting1.02.82011-08-01Keiichiro OnoUC San Diego Department of Medicinehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=412jar132SessionForWebSaves the current Cytoscape session as a web page with images thumbnails, and legends of each network, or as zip file compatible with the CellCircuit website. For zip file for CellCircuits website, publication information can also be included in the Zip file. Please look at this page (http://www.cellcircuits.org/search/zipFormatDefinition.html) for the directory structure of ZIP file.Other3.02.52008-01-30Samad LotiaUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=65jar132SessionForWebSaves the current Cytoscape session as a web page with images thumbnails, and legends of each network, or as zip file compatible with the CellCircuit website. For zip file for CellCircuits website, publication information can also be included in the Zip file. Please look at this page (http://www.cellcircuits.org/search/zipFormatDefinition.html) for the directory structure of ZIP file.Other3.12.52.62008-10-15Samad LotiaUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=139jar132SessionForWebSaves the current Cytoscape session as a web page with images thumbnails, and legends of each network, or as zip file compatible with the CellCircuit website. For zip file for CellCircuits website, publication information can also be included in the Zip file. Please look at this page (http://www.cellcircuits.org/search/zipFormatDefinition.html) for the directory structure of ZIP file.Other3.22.52.62009-09-30Peng-Liang WangUCSDhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=235jar110SFLDLoaderThis plugin provides an interface to the Structure-Function Linkage DatabaseOnline data import1.02.52007-07-07John \"Scooter\" MorrisUCSF Resource for Biocomputing, Visualization, and Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=16jar110SFLDLoaderThis plugin provides an interface to the Structure-Function Linkage DatabaseOnline data import1.22.62008-03-18John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=110jar110SFLDLoaderThis plugin provides an interface to the Structure-Function Linkage DatabaseOnline data import1.32.62008-09-18John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=149jar112ShortestPath PluginShortestPath is a plugin for Cytoscape 2.1 to show the shortest path between 2 selected nodes in the current network. It supports both directed and undirected networks and it gives the user the possibility to choose which node (of the selected ones) should be used as source and target (useful for directed networks). The plugin API makes possible to use its functionality from another plugin.Graph analysis1.12.42.52007-07-25Marcio Rosa da Silvahttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=23jar178StringWSClientProvides connectivity to the STRING database (http://www.string-db.org).This version supports only import of interaction networks; upcoming versions will be ableto extend existing networks, filter them using STRING specific criteria, etc.Interaction database1.02.6.12009-02-27Milan SimonovicUniversity of Zurich Christian von MeringUniversity of Zurichhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=190jar178StringWSClientProvides connectivity to the STRING database (http://www.string-db.org).This version supports only import of interaction networks; upcoming versions will be ableto extend existing networks, filter them using STRING specific criteria, etc.Interaction database1.12.62009-07-17Milan SimonovicUniversity of Zurich Christian von MeringUniversity of Zurichhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=217jar178StringWSClientProvides connectivity to the STRING database (http://www.string-db.org).This version supports only import of interaction networks; upcoming versions will be ableto extend existing networks, filter them using STRING specific criteria, etc.Interaction database1.22.72010-08-29Milan SimonovicUniversity of Zurich Christian von MeringUniversity of Zurichhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=325jar106structureVizThis plugin provides an interface to UCSF Chimera from within Cytoscape, providing a linkage between the network view and the structural view.Other1.02.52007-05-01John \"Scooter\" MorrisUCSF Resource for Biocomputing, Visualization, and Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=12jar106structureVizThis plugin provides an interface to UCSF Chimera from within Cytoscape, providing a linkage between the network view and the structural view.Other1.22.62008-03-18John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=109jar106structureVizThis plugin provides an interface to UCSF Chimera from within Cytoscape, providing a linkage between the network view and the structural view.Other1.32.62008-09-18John \"Scooter\" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=155jar106structureVizThis plugin provides an interface to UCSF Chimera from within Cytoscape, providing a linkage between the network view and the structural view.Other1.92.82011-01-15John "Scooter" MorrisUCSFhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=363jar265SubnetworkCreatorCytoscape Plugin to create subnetworks for disconnected graphs.Utility1.02.82012-02-02Tim te BeekNetherlands Bioinformatics Centre, Bioinformatics Research Supporthttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=453jar191Superpathways-PluginThe Superpathways plugin for Cytoscape is to help merge multiple pathways into a single Cytoscape network.<p>This plugin makes it possible to select multiple pathways from Wiki Pathways and load them in a single network. The plugin would merge nodes that represent the same biological entity (e.g. gene, protein or molecule).</p>Online data import1.02.62009-08-31Xuemin LiuIowa State Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=226jar191Superpathways-PluginThe Superpathways plugin for Cytoscape is to help merge multiple pathways into a single Cytoscape network.<p>This plugin makes it possible to select multiple pathways from Wiki Pathways and load them in a single network. The plugin would merge nodes that represent the same biological entity (e.g. gene, protein or molecule).</p>Online data import1.22.62010-07-10Xuemin LiuIowa State Universityhttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=308jar183TransClustThis plugin clusters a given similarity graph by using transitivity clustering, i.e. solving the weighted transitive graph projection problem.<br><br> Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.Clustering1.02.62009-04-28Jan BaumbachInternational Computer Science Institute, BerkeleyTobias WittkopBielefeld UniversityDorothea EmigMax Planck Institute for Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=202jar183TransClustThis plugin clusters a given similarity graph by using transitivity clustering, i.e. solving the weighted transitive graph projection problem.<br><br> Please contact Jan Baumbach (jbaumbac@ICSI.Berkeley.EDU) if you have further questions.Clustering1.012.72009-04-28Jan BaumbachInternational Computer Science Institute, BerkeleyTobias WittkopBielefeld UniversityDorothea EmigMax Planck Institute for Informaticshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=316jar229VennDiagramGeneratorThis plugin generates a Venn/Euler diagram of shared nodes for a selection of networks. The diagram generation algorithm is described in <a href=http://www.computer.org/portal/web/csdl/doi/10.1109/TVCG.2011.56>Exact and Approximate Area-proportional Circular Venn and Euler Diagrams</a> by Leland Wilkinson.Other1.02.52.62.72010-09-15Leland WilkinsonUniversity of Illinois, ChicagoMike SmootUC San Diegohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=329jar229VennDiagramGeneratorThis plugin generates a Venn/Euler diagram of shared nodes for a selection of networks. The diagram generation algorithm is described in <a href=http://www.computer.org/portal/web/csdl/doi/10.1109/TVCG.2011.56>Exact and Approximate Area-proportional Circular Venn and Euler Diagrams</a> by Leland Wilkinson.Other1.022.52.62.72.82011-01-03Leland WilkinsonUniversity of Illinois, ChicagoMike SmootUC San Diegohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=361jar229VennDiagramGeneratorThis plugin generates a Venn/Euler diagram of shared nodes for a selection of networks. The diagram generation algorithm is described in <a href=http://www.computer.org/portal/web/csdl/doi/10.1109/TVCG.2011.56>Exact and Approximate Area-proportional Circular Venn and Euler Diagrams</a> by Leland Wilkinson.Other1.42.52.62.72.82012-02-09Leland WilkinsonUniversity of Illinois, ChicagoMike SmootUC San Diegohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=418jar250VennDiagramsCytoscape plugin for venn diagrams.<p>This plugin is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.</p><p>This plugin has dependencies on libraries released under other free and/or open source licenses, see website for details.</p><p><a href="http://www.dishevelled.org/venn-cytoscape-plugin">http://www.dishevelled.org/venn-cytoscape-plugin</a></p>Other0.32.72.8This plugin is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This plugin has dependencies on libraries released under other free and/or open source licenses, see website for details.2011-02-22Michael Heuerdishevelled.orghttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=374jar144VistaClaraPluginA visualization plugin using an extended permutation matrix for exploratory data analysis of multi-experiment microarray studies.Data visualization1.02.6AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW. TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENTS SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. Software. Software means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format. License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilents third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the applicable license, you may store or run one copy of the Software on one machine or instrument. If the Software is otherwise licensed for concurrent or network use, you may not allow more than the maximum number of authorized users to access and use the Software concurrently. License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network. Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Such services may be purchased separately. Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement. No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification. High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer. Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software. Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations. U.S. Government Restricted Rights. Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Computer Software Documentation). NO WARRANTY. TO THE EXTENT ALLOWED BY LOCAL LAW, AND EXCEPT TO THE EXTENT AGILENT HAS PROVIDED A SPECIFIC WRITTEN WARRANTY APPLICABLE TO THIS PRODUCT, THIS SOFTWARE IS PROVIDED TO YOU \\\\\\\"AS IS\\\\\\\" WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN, EXPRESS OR IMPLIED. AGILENT SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE RISK AND COST RESULTING FROM OR RELATING TO THE DEFECT. SOME JURISDICTIONS DO NOT ALLOW EXCLUSIONS OF IMPLIED WARRANTIES OR CONDITIONS, SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. YOU MAY HAVE OTHER RIGHTS THAT VARY ACCORDING TO LOCAL LAW. LIMITATION OF LIABILITY. TO THE EXTENT ALLOWED BY LOCAL LAW, IN NO EVENT WILL AGILENT OR ITS SUBSIDIARIES, AFFILIATES OR SUPPLIERS BE LIABLE FOR DIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR OTHER DAMAGES (INCLUDING LOST PROFIT, LOST DATA, OR DOWNTIME COSTS), ARISING OUT OF THE USE, INABILITY TO USE, OR THE RESULTS OF USE OF THE SOFTWARE, WHETHER BASED IN WARRANTY, CONTRACT, TORT OR OTHER LEGAL THEORY, AND WHETHER OR NOT ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. YOUR USE OF THE SOFTWARE IS ENTIRELY AT YOUR OWN RISK. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. Applicable Law. Disputes arising in connection with this Agreement will be governed by the laws of the United States and of the State of New York, without regard to choice of law provisions. The United Nations Convention for Contracts for the International Sale of Goods will not apply to this Agreement. Unenforceability. To the extent that any provision of this Agreement is determined to be illegal or unenforceable, the remainder of this Agreement will remain in full force and effect. Entire Agreement. This Agreement constitutes the entire agreement between you and Agilent, and supersedes any previous communications, representations or agreements between the parties, whether oral or written, regarding transactions hereunder except for a specific warranty issued by Agilent with regard to this product. Your additional or different terms and conditions will not apply. This Agreement may not be changed except by an amendment signed by an authorized representative of each party. 2008-04-09Robert Kincaid and Allan KuchinskyAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=112jar144VistaClaraPluginA visualization plugin using an extended permutation matrix for exploratory data analysis of multi-experiment microarray studies.Data visualization1.012.6AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW. TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENTS SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. Software. Software means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format. License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilents third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the applicable license, you may store or run one copy of the Software on one machine or instrument. If the Software is otherwise licensed for concurrent or network use, you may not allow more than the maximum number of authorized users to access and use the Software concurrently. License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network. Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Such services may be purchased separately. Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement. No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification. High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer. Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software. Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations. U.S. Government Restricted Rights. Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Computer Software Documentation). NO WARRANTY. TO THE EXTENT ALLOWED BY LOCAL LAW, AND EXCEPT TO THE EXTENT AGILENT HAS PROVIDED A SPECIFIC WRITTEN WARRANTY APPLICABLE TO THIS PRODUCT, THIS SOFTWARE IS PROVIDED TO YOU \\\\\\\"AS IS\\\\\\\" WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN, EXPRESS OR IMPLIED. AGILENT SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE RISK AND COST RESULTING FROM OR RELATING TO THE DEFECT. SOME JURISDICTIONS DO NOT ALLOW EXCLUSIONS OF IMPLIED WARRANTIES OR CONDITIONS, SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. YOU MAY HAVE OTHER RIGHTS THAT VARY ACCORDING TO LOCAL LAW. LIMITATION OF LIABILITY. TO THE EXTENT ALLOWED BY LOCAL LAW, IN NO EVENT WILL AGILENT OR ITS SUBSIDIARIES, AFFILIATES OR SUPPLIERS BE LIABLE FOR DIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR OTHER DAMAGES (INCLUDING LOST PROFIT, LOST DATA, OR DOWNTIME COSTS), ARISING OUT OF THE USE, INABILITY TO USE, OR THE RESULTS OF USE OF THE SOFTWARE, WHETHER BASED IN WARRANTY, CONTRACT, TORT OR OTHER LEGAL THEORY, AND WHETHER OR NOT ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. YOUR USE OF THE SOFTWARE IS ENTIRELY AT YOUR OWN RISK. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. Applicable Law. Disputes arising in connection with this Agreement will be governed by the laws of the United States and of the State of New York, without regard to choice of law provisions. The United Nations Convention for Contracts for the International Sale of Goods will not apply to this Agreement. Unenforceability. To the extent that any provision of this Agreement is determined to be illegal or unenforceable, the remainder of this Agreement will remain in full force and effect. Entire Agreement. This Agreement constitutes the entire agreement between you and Agilent, and supersedes any previous communications, representations or agreements between the parties, whether oral or written, regarding transactions hereunder except for a specific warranty issued by Agilent with regard to this product. Your additional or different terms and conditions will not apply. This Agreement may not be changed except by an amendment signed by an authorized representative of each party. 2008-07-28Robert Kincaid and Allan KuchinskyAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=130jar144VistaClaraPluginA visualization plugin using an extended permutation matrix for exploratory data analysis of multi-experiment microarray studies.Data visualization1.052.8AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE AGREEMENT ATTENTION: DOWNLOADING, COPYING, PUBLICLY DISTRIBUTING, OR USING THIS SOFTWARE IS SUBJECT TO THE AGREEMENT SET FORTH BELOW. TO DOWNLOAD, STORE, INSTALL, OR RUN THE SOFTWARE, YOU MUST FIRST AGREE TO AGILENTS SOFTWARE LICENSE AGREEMENT BELOW. IF YOU HAVE PURCHASED THE SOFTWARE FROM AGILENT, YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. Software. Software means one or more computer programs in object code format, whether stand-alone or bundled with other products, and related documentation. It does NOT include programs in source code format. License Grant. Agilent grants you a non-exclusive license to download one copy of the Software, and to store or run that copy of the Software for internal use and purposes in accordance with this Agreement and the documentation provided with the Software. Such documentation may include license terms provided by Agilents third party suppliers, which will apply to the use of the Software and take precedence over these license terms. In the absence of documentation specifying the applicable license, you may store or run one copy of the Software on one machine or instrument. If the Software is otherwise licensed for concurrent or network use, you may not allow more than the maximum number of authorized users to access and use the Software concurrently. License Restrictions. You may make copies or adaptations of the Software for archival purposes or when copying or adaptation is an essential step in the authorized use of the Software, but for no other purpose. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not copy the Software onto any public or distributed network. Upgrades. This license does not entitle you to receive upgrades, updates or technical support. Such services may be purchased separately. Ownership. The Software is owned and copyrighted by Agilent or its third party suppliers. Agilent and its third party suppliers retain all right, title and interest in the Software. Agilent and its third party suppliers may protect their respective rights in the Software in the event of any violation of this Agreement. No Disassembly. You may not disassemble or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly or modification. High Risk Activities. The Software is not specifically written, designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. Transfer. You may transfer the license granted to you here provided that you deliver all copies of the Software to the transferee along with this Agreement. The transferee must accept this Agreement as a condition to any transfer. Your license to use the Software will terminate upon transfer. Termination. Agilent may terminate this license upon notice for breach of this Agreement. Upon termination, you must immediately destroy all copies of the Software. Export Requirements. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations. U.S. Government Restricted Rights. Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Computer Software Documentation). NO WARRANTY. TO THE EXTENT ALLOWED BY LOCAL LAW, AND EXCEPT TO THE EXTENT AGILENT HAS PROVIDED A SPECIFIC WRITTEN WARRANTY APPLICABLE TO THIS PRODUCT, THIS SOFTWARE IS PROVIDED TO YOU \\\\\\\"AS IS\\\\\\\" WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, WHETHER ORAL OR WRITTEN, EXPRESS OR IMPLIED. AGILENT SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE ENTIRE RISK AND COST RESULTING FROM OR RELATING TO THE DEFECT. SOME JURISDICTIONS DO NOT ALLOW EXCLUSIONS OF IMPLIED WARRANTIES OR CONDITIONS, SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. YOU MAY HAVE OTHER RIGHTS THAT VARY ACCORDING TO LOCAL LAW. LIMITATION OF LIABILITY. TO THE EXTENT ALLOWED BY LOCAL LAW, IN NO EVENT WILL AGILENT OR ITS SUBSIDIARIES, AFFILIATES OR SUPPLIERS BE LIABLE FOR DIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL OR OTHER DAMAGES (INCLUDING LOST PROFIT, LOST DATA, OR DOWNTIME COSTS), ARISING OUT OF THE USE, INABILITY TO USE, OR THE RESULTS OF USE OF THE SOFTWARE, WHETHER BASED IN WARRANTY, CONTRACT, TORT OR OTHER LEGAL THEORY, AND WHETHER OR NOT ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. YOUR USE OF THE SOFTWARE IS ENTIRELY AT YOUR OWN RISK. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF LIABILITY FOR DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. Applicable Law. Disputes arising in connection with this Agreement will be governed by the laws of the United States and of the State of New York, without regard to choice of law provisions. The United Nations Convention for Contracts for the International Sale of Goods will not apply to this Agreement. Unenforceability. To the extent that any provision of this Agreement is determined to be illegal or unenforceable, the remainder of this Agreement will remain in full force and effect. Entire Agreement. This Agreement constitutes the entire agreement between you and Agilent, and supersedes any previous communications, representations or agreements between the parties, whether oral or written, regarding transactions hereunder except for a specific warranty issued by Agilent with regard to this product. Your additional or different terms and conditions will not apply. This Agreement may not be changed except by an amendment signed by an authorized representative of each party. 2011-03-01Robert Kincaid and Allan KuchinskyAgilent LabsMichael CreechBlue Oak Softwarehttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=391jar236WordCloudWhen biological networks are studied, it is common to look for clusters, i.e. sets of nodes that are highly inter-connected. To understand the \\\\\\\"biological meaning\\\\\\\" of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities. The WordCloud Cytoscape plugin generates a visual summary of these annotations by displaying them as a ‘tag cloud’, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network. These visualizations provide a concise visual summary of annotations which is helpful for network analysis and interpretation.Ontology analysis1.02.62011-04-07Layla OesperBrown UniversityDaniele Merico, Ruth Isserlin, Gary D. Bader University of Toronotohttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=397zip1Cytoscape Tutorial ThemeThis collection of plugins provides all the functionality2.61136NatureProtocolsWorkflowGroups all of the plugins required for the Nature Protocols workflow.Other1.02.52.62007-11-12Allan KuchinskyAgilent Technologieshttp://chianti.ucsd.edu/cyto_web/plugins/pluginjardownload.php?id=66jar1111.31032.551042.11012.22WebServiceClientPackThis bundle of plugins provides access to several different external data sources for importing network and attribute data. Data sources include NCBI, Biomart, IntAct and Pathway Commons. Please contact the individual plugin authors with any questions.2.61.21310.801380.701390.52