Difference between revisions of "List of Software"
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Revision as of 14:20, 28 July 2008
Ongoing Discussion for Bioinformatics Core Facilities
Tools popular with biologists
This is a list of the tools that were mentioned in our discussion on "bioinformatics for the biologists" on Feb 4th, 2008.
Microarray data retrieval and basic analysis
- <a href="http://base.thep.lu.se">BASE</a> from Lund University, Sweden (basic analysis and database)
- <a href="http://www.tm4.org/">Multiple Experiment Viewer from Quackenbush Group at Harvard Univ </a>
- <a href="http://bioinformatics.skcc.org/webarray/"> WebArray: Web interface, based on bioconductor and mySQL </a>
- <a href="https://carmaweb.genome.tugraz.at/carma">CarmaWeb </a>
- <a href="http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/">ChipMonk</a> for ChIP-on-chip data, e.g. from Nimblegen
- <A HREF="http://biosun1.harvard.edu/complab/dchip/">DChip</A>: basic analysis (e.g. get a list of differentially expressed genes)
- <A HREF="http://bioinfo.bgu.ac.il/bsu/microarrays/links/">A good links site</A> for multiple applications
Structure visualization and basic analysis
- <A HREF="http://pymol.sourceforge.net/">PyMOL</A>
- AutoDock for docking
- DiscoveryStudio (?)
- <a href="http://kinemage.biochem.duke.edu">Kinmage</a> for 3D Macromolecule analysis from Richardson Lab at Duke
- <a href="http://swissmodel.expasy.org/spdbv/">DeepView</a> for structure analysis and modeling from the Swiss Institute of Bioinformatics and GlaxoSmithKline R&D
- <a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</a> for structure veiwer from NCBI
Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data
- <A HREF="http://cytoscape.org/">Cytoscape</A>
- <A HREF="http://reactome.org/">Reactome</A> including <A HREF="http://www.reactome.org/cgi-bin/skypainter2?DB=gk_current">Skypainter</A> and the latest biomart interface <A HREF="http://brie8.cshl.org/cgi-bin/mart">Reactome Mart</A>
- <A HREF="http://www.bioinformatics.ed.ac.uk/epe/">EPE</A> Edinburgh Pathway Editor
Pipeline Tools
- <A HREF="http://taverna.sourceforge.net/">Tavera</a> Best uses in conjunction with in-house web services to ensure reliability. Most command line applications can be converted to a web service using <A HREF="http://wwww.ebi.ac.uk/soaplab/">Soaplab</A>. Version 2 of taverna should handle large file sizes a lot better.
- <A HREF="http://www.biomedcentral.com/1471-2105/8/208">Alternatives:</a> A paper highlighting Seahawk (<A HREF="http://biomoby.org/">Biomoby</A>) but also mentions both Taverna and Remora
