List of Software

Ongoing Discussion for Bioinformatics Core Facilities

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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

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Looking for collaborations in Rosetta Resolver training

The National Institute of Biotechnology is experimenting with Rosetta in setting up a national test-bed for bioinformatics software. As a part of this collaboration, we are trying to develop a training strategy that would allow researchers, both industry and academia, figure out the value of Resolver for their research with minimal training.

We are looking for someone interested in developing together training material for people who understand microarray analysis, at least the basics of it, and wish to get rapidly started with Resolver.

Eitan Rubin, <a href="mailto:erubin@bgu.ac.il">erubin@bgu.ac.il</A>

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