Cytoscape SOFT Import PlugIn ------------------------------------- Table of Contents ================= 1. Introduction 2. PlugIn Installation Instructions 3. Using the SOFT PlugIn 4. Bugs / Feature Requests 5. Contacts 6. Release Notes 1. Introduction ================ This directory contains a copy of the Cytoscape SOFT Import PlugIn. This plugin enables Cytoscape to import data formatted in the GEO Simple Omnibus Format in Text (SOFT). SOFT is a text file format used to represent and exchange Gene Expression Data. Information is available online at: http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html. The plugin works by loading GEO data, and importing it into an existing Cytoscape network. You can load SOFT files from your local file system or from any arbitrary URL. Export functionality is not currently supported. Updates regarding this plugin will be posted to the Cytoscape-announce mailing list. You can subscribe to the mailing list or browse the archives at: http://groups-beta.google.com/group/cytoscape-announce. 2. PlugIn Installation Instructions ===================================== To use the SOFT PlugIn, you must first obtain a copy of Cytoscape, Version 2.0. You can download a copy from: http://cytoscape.org/. ------------------------------------------------------------------------------- | Important Note: This plugin only works with Cytoscape 2.0, and will not | | work with earlier version of Cytoscape. For a Cytoscape 1.1 compatible | | version of this plugin, please go to: http://cytoscape.org/plugins1.php, | | and download the DataServices plugin. | ------------------------------------------------------------------------------- Once you have downloaded Cytoscape and verified that it works, install the SOFT PlugIn: 1. Copy all the .jar files in the /plugin directory to your [Cytoscape_Home]/plugins directory. 2. Restart Cytoscape from the command line. For example, run: cytoscape.sh or cytoscape.bat. ------------------------------------------------------------------------------- | Warning: The SOFT PlugIn *cannot* be loaded dynamically from Cytoscape | | via the PlugIns menu. It can only be loaded by following the instructions | | above. | ------------------------------------------------------------------------------- 3. Using the SOFT PlugIn ============================= The SOFT PlugIn reads in expression data, and adds this data to an existing Cytoscape network. In order for the plugin to work correctly, the Cytoscape network and the GEO SOFT data must use common identifiers. For example, here is a sample SIF file: YLR331C pp YLR263W YLR333C pp YLR264W And, here is an excerpt from a matching SOFT data file: ID_REF IDENTIFIER GSM6219 GSM6220 10000_at YLR331C 268.8 141.4 10003_f_at YLR333C 4282 4003 Note that the second column contains IDENTIFIERS which match those in the SIF file. To try out the plugin: 1. Load a sample Interaction file. For example: Select File --> Load --> Interaction. Then, specify a sample SIF file, such as sampleData/GDS362.sif. 2. Load a sample SOFT file. For example: Select PlugIns --> GEO SOFT Import --> Import GEO SOFT Data from File. Then, specify a sample SOFT file, such as sampleData/GDS362.soft. After a few seconds, you will see a pop-up message showing the results of the import. For example, the message will say: Number of SOFT Entities Read: 7 Number of nodes in the current network: 116 Number of nodes which now contain expression data: 116 If the plugin is unable to determine any common identifiers, you will see an error message in the pop-up window. 3. View the Expression data within Cytoscape. For example: Select any node. Then, select Data --> Display Attribute Browser. Gene Expression data from the SOFT file will now appear within the attribute browser. Retrieving NCBI GEO Data via the Web: -------------------------------------- NCBI GEO provides a URL API that allows users to retrieve GEO SOFT files, among other data, via the web. The GEO SOFT reader plugin can retrieve SOFT files using this URL format. As of the release of this plugin, the URL to retrieve GDS SOFT files is: http://www.ncbi.nlm.nih.gov/projects/geo/gds/floader.fcgi?type=txt&relpath= gds/soft&fname=GDS438.soft&attach=GDS438.soft (Replace both instances of GDS438 with the accession number of interest) Note that the Cytoscape GEO SOFT PlugIn can only read GEO data set (GDS) SOFT files. All GEO accession numbers that start with GDS are valid input in SOFT format. E.g. GDS438.soft. 4. Bugs / Feature Requests ============================ If you encounter a bug with this plugin, or have a feature suggestion, we encourage you to use the Cytoscape Bug Tracker: http://www.cbio.mskcc.org/cytoscape/bugs/. If you log a bug, we will automatically email you when the bug is resolved. 5. Contacts ============= Sander Group, Computational Biology Center Memorial Sloan-Kettering Cancer Center, New York City http://www.cbio.mskcc.org/ For any questions concerning this plugin, please contact: Gary Bader: baderg AT mskcc.org Ethan Cerami: cerami AT cbio.mskcc.org This software is made available under the LGPL (Lesser General Public License). Until we develop a better source code distribution system, please email Gary or Ethan for a complete copy of the source code. This product includes software developed by the Apache Software Foundation (http://www.apache.org). 6. Release Notes ================= September, 2003 -- Initial Release of plugin. Available as part of the larger Data Services plugin. October, 2004 -- PlugIn updated to work with Cytoscape 2.0. -- Improved Error Handling, with more detailed error messages. June, 2006 -- Updated to Work with Cytoscape 2.3 (remains backward compatible to earlier Cytoscape versions).