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| − | <h1>Ongoing Discussion for Bioinformatics Core Facilities</h1>
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| − | Please enter information about your core facility on the [http://www.bioinfo-core.org Bioinfo-core main page].
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| − | <br><br>
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| − | To get started, create a New Account and then edit the main page to add a link for your core facility. To create a new page, edit the page from which you'd like to link to
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| − | the new page and add a new wiki tag (the new page name enclosed in square brackets) for the new page. Hit save, then
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| − | the tag you added will display as underlined with a question mark next to it. Click the question mark to create that page. Save that page and you should be all set.
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| − | <br><br>
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| − | <hr>
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| − | <h2>Tools popular with biologists</h2>
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| − | <br>This is a list of the tools that were mentioned in our discussion on "bioinformatics for the biologists" on Feb 4th, 2008.
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| − | <br><br>
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| − | <h3>Microarray data retrieval and basic analysis</h3>
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| − | <ul>
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| − | <li>[http://base.thep.lu.se BASE] from Lund University, Sweden (basic analysis and database)
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| − | <li>[http://www.tm4.org/ Multiple Experiment Viewer from Quackenbush Group at Harvard Univ]
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| − | <li>[http://bioinformatics.skcc.org/webarray/ WebArray: Web interface, based on bioconductor and mySQL]
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| − | <li>[https://carmaweb.genome.tugraz.at/carma CarmaWeb]
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| − | <li>[http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ ChipMonk] for ChIP-on-chip data, e.g. from Nimblegen
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| − | <li>[http://biosun1.harvard.edu/complab/dchip/ DChip]: basic analysis (e.g. get a list of differentially expressed genes)
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| − | <li>[http://bioinfo.bgu.ac.il/bsu/microarrays/links/ A good links site] for multiple applications
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| − | </ul>
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| − | <h3>Structure visualization and basic analysis</h3>
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| − | <ul>
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| − | <li>[http://pymol.sourceforge.net/ PyMOL]
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| − | <li>AutoDock for docking
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| − | <li>DiscoveryStudio (?)
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| − | <li>[http://kinemage.biochem.duke.edu Kinmage] for 3D Macromolecule analysis from Richardson Lab at Duke
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| − | <li>[http://swissmodel.expasy.org/spdbv/ DeepView] for structure analysis and modeling from the Swiss Institute of Bioinformatics and GlaxoSmithKline R&D
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| − | <li>[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D] for structure veiwer from NCBI
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| − | </ul>
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| − | <h3>Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data</h3>
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| − | <ul>
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| − | <li>[http://cytoscape.org/ Cytoscape]
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| − | <li>[http://reactome.org/ Reactome] including [http://www.reactome.org/cgi-bin/skypainter2?DB=gk_current Skypainter] and the latest biomart interface [http://brie8.cshl.org/cgi-bin/mart Reactome Mart]
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| − | <li>[http://www.bioinformatics.ed.ac.uk/epe/ EPE] Edinburgh Pathway Editor
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| − | </ul>
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| − | <h3>Pipeline Tools</h3>
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| − | <ul>
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| − | <li>[http://taverna.sourceforge.net/ Taverna] Best uses in conjunction with in-house web services to ensure reliability. Most command line applications can be converted to a web service using [http://wwww.ebi.ac.uk/soaplab/ Soaplab]. Version 2 of taverna should handle large file sizes a lot better.
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| − | <li> [http://www.biomedcentral.com/1471-2105/8/208 Alternatives:] A paper highlighting Seahawk ([http://biomoby.org/ Biomoby]) but also mentions both Taverna and Remora
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| − | </ul>
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| − | <hr>
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| − | <h3>Looking for collaborations in Rosetta Resolver training</h3>
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| − | 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.<p>
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| − | 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.<p>
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| − | Eitan Rubin, [mailto:erubin@bgu.ac.il erubin@bgu.ac.il]
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| − | <hr>
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| − | <hr>
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| − | <center>Return to [http://www.bioinfo-core.org Bioinfo-core wiki]</center>
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| − | <hr>
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