Difference between revisions of "BioWiki:Community Portal"

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<h1>Ongoing Discussion for Bioinformatics Core Facilities</h1>
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<h2>Welcome to Bioinfo-Core.org</h2>
  
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Please enter information about your core facility on the <a href="http://www.bioinfo-core.org">Bioinfo-core main page</a>. 
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[Ongoing Discussions] | [Call Minutes] | [Wiki Help] | [Recent Changes] | [Core page template]
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<br><br>
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<h2> List of Bioinformatics Core Facilities</h2>
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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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<ol>
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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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<li> <h3><a href="http://jura.wi.mit.edu/bio/general.html">Bioinformatics and Research Computing (BaRC), Whitehead Institute</a> (USA)</H3>
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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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<li> <h3><a href="http://bsu.ncl.ac.uk/general.html">Newcastle University Bioinformatics Support Unit</a> (UK)</h3>
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<br><br>
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<li> <h3><a href="http://cbsu.tc.cornell.edu/cbsu_bioinfo_core.html">Computational Biology Service Unit, Cornell University</a> (USA)</h3>
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<hr>
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<li> <h3><a href="http://chgr.mc.vanderbilt.edu/page/computational-genomics-core">Computational Genomics Core, Center for Human Genetics Research, Vanderbilt University</a> (USA)</h3>
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<h2>Tools popular with biologists</h2>
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<li> <h3><a href="http://bioinformatics.unc.edu" target="_blank"> Center for Bioinformatics, University of North Carolina at Chapel Hill</a> (USA)</h3>
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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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<li> <h3> <a href="http://www.tufts.edu/sackler/neuroscience/CNR/bioinformatics.html" target="_blank"> Genomics Core, Center for Neuroscience Research, Tufts Univ School of Medicine</a> (USA)</h3>
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<br><br>
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<li> <h3><a class="wiki" href="?tag=Bioinformatics%20Group%2C%20Promega%20Corp.&" target="_top">Bioinformatics Group, Promega
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<h3>Microarray data retrieval and basic analysis</h3>
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Corp.</a> (USA)</h3>
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<ul>
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<li> <h3><a href="http://bioinformatics.ucdavis.edu">Bioinformatics Core, UC Davis Genome Center</a> (USA)</h3>
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<li><a href="http://base.thep.lu.se">BASE</a> from Lund University, Sweden (basic analysis and database)
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<li> <h3><a href="http://bifx1.bio.ed.ac.uk/wiki/index.php/Bioinformatics_Core_Facilities">Bioinformatics Core Facility, Wellcome Trust Centre for Cell Biology, University of Edinburgh</a> (UK)</h3>
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<li><a href="http://www.tm4.org/">Multiple Experiment Viewer from Quackenbush Group at Harvard Univ </a>
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<li> <h3><a href="http://www.radium.no/core/index.php?section=3">Bioinformatics Core, Rikshospitalet-Radiumhospitalet and University of Oslo</a> (Norway)</h3>
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<li><a href="http://bioinformatics.skcc.org/webarray/"> WebArray: Web interface, based on bioconductor and mySQL </a>
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<li> <h3><a href="http://bioinformatics.ualr.edu/mbc">MidSouth Bioinformatics Center, University of Arkansas at Little Rock</a> (USA)</h3>
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<li><a href="https://carmaweb.genome.tugraz.at/carma">CarmaWeb </a>
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<li> <h3><a href="http://bioinformatics.salk.edu/core.html">Salk Institute Bioinformatics, San Diego, CA</a> (USA)</h3>
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<li><a href="http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/">ChipMonk</a> for ChIP-on-chip data, e.g. from Nimblegen
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<li> <h3><a href="http://www.fmi.ch/html/technical_resources/bioinformatics/bioinformatics.html">Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel (Switzerland)</h3>
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<li><A HREF="http://biosun1.harvard.edu/complab/dchip/">DChip</A>: basic analysis (e.g. get a list of differentially expressed genes)
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<li> <h3><a href="http://bioinfo.bgu.ac.il">Bioinformatics Core Facility, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev</a> (Israel)</h3>
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<li><A HREF="http://bioinfo.bgu.ac.il/bsu/microarrays/links/">A good links site</A> for multiple applications
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<li> <h3><a href="http://bioinformatics.unl.edu/">Bioinformatics Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln</a> (USA)</h3>
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</ul>
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<li> <h3><a href="http://www.giga.ulg.ac.be/extranet/services.htm">Bioinformatics Facility, GIGA (Interdisciplinary Cluster for Applied Genoproteomics), University of Liege</a> (BE)</h3>
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<h3>Structure visualization and basic analysis</h3>
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<li> <h3><a href="?tag=babraham%20bioinformatics">Babraham Bioinformatics, The Babraham Institute, Cambridge</a> (UK)</h3>
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<ul>
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<li> <h3><a href="http://emboss.sf.net">EMBOSS</a>, European Bioinformatics Institute, Hinxton (UK)</h3>
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<li><A HREF="http://pymol.sourceforge.net/">PyMOL</A>
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Contact us at <a href='mailto:emboss-bug@emboss.open-bio.org'>emboss-bug@emboss.open-bio.org</a><li> <h3><a href="http://web.mit.edu/ccr/core/facilities/bioinformatics/">Bioinformatics and Computing Core Facility (BCC), Koch Institute - MIT</a> Cambridge, MA (USA)</H3>
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<li>AutoDock for docking
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</ol>
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<li>DiscoveryStudio (?)
 
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<li><a href="http://kinemage.biochem.duke.edu">Kinmage</a> for 3D Macromolecule analysis from Richardson Lab at Duke
 
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<li><a href="http://swissmodel.expasy.org/spdbv/">DeepView</a> for structure analysis and modeling from the Swiss Institute of Bioinformatics and GlaxoSmithKline R&D
 
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<li><a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</a> 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><A HREF="http://cytoscape.org/">Cytoscape</A>
 
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<li><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>
 
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<li><A HREF="http://www.bioinformatics.ed.ac.uk/epe/">EPE</A> 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><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.
 
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<li> <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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</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, <a href="mailto:erubin@bgu.ac.il">erubin@bgu.ac.il</A>
 
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<hr>
 

Revision as of 07:45, 25 July 2008

Contents

Welcome to Bioinfo-Core.org

[Ongoing Discussions] | [Call Minutes] | [Wiki Help] | [Recent Changes] | [Core page template]

List of Bioinformatics Core Facilities

  1. <a href="http://jura.wi.mit.edu/bio/general.html">Bioinformatics and Research Computing (BaRC), Whitehead Institute</a> (USA)

  2. <a href="http://bsu.ncl.ac.uk/general.html">Newcastle University Bioinformatics Support Unit</a> (UK)

  3. <a href="http://cbsu.tc.cornell.edu/cbsu_bioinfo_core.html">Computational Biology Service Unit, Cornell University</a> (USA)

  4. <a href="http://chgr.mc.vanderbilt.edu/page/computational-genomics-core">Computational Genomics Core, Center for Human Genetics Research, Vanderbilt University</a> (USA)

  5. <a href="http://bioinformatics.unc.edu" target="_blank"> Center for Bioinformatics, University of North Carolina at Chapel Hill</a> (USA)

  6. <a href="http://www.tufts.edu/sackler/neuroscience/CNR/bioinformatics.html" target="_blank"> Genomics Core, Center for Neuroscience Research, Tufts Univ School of Medicine</a> (USA)

  7. <a class="wiki" href="?tag=Bioinformatics%20Group%2C%20Promega%20Corp.&" target="_top">Bioinformatics Group, Promega Corp.</a> (USA)

  8. <a href="http://bioinformatics.ucdavis.edu">Bioinformatics Core, UC Davis Genome Center</a> (USA)

  9. <a href="http://bifx1.bio.ed.ac.uk/wiki/index.php/Bioinformatics_Core_Facilities">Bioinformatics Core Facility, Wellcome Trust Centre for Cell Biology, University of Edinburgh</a> (UK)

  10. <a href="http://www.radium.no/core/index.php?section=3">Bioinformatics Core, Rikshospitalet-Radiumhospitalet and University of Oslo</a> (Norway)

  11. <a href="http://bioinformatics.ualr.edu/mbc">MidSouth Bioinformatics Center, University of Arkansas at Little Rock</a> (USA)

  12. <a href="http://bioinformatics.salk.edu/core.html">Salk Institute Bioinformatics, San Diego, CA</a> (USA)

  13. <a href="http://www.fmi.ch/html/technical_resources/bioinformatics/bioinformatics.html">Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Basel (Switzerland)

  14. <a href="http://bioinfo.bgu.ac.il">Bioinformatics Core Facility, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev</a> (Israel)

  15. <a href="http://bioinformatics.unl.edu/">Bioinformatics Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln</a> (USA)

  16. <a href="http://www.giga.ulg.ac.be/extranet/services.htm">Bioinformatics Facility, GIGA (Interdisciplinary Cluster for Applied Genoproteomics), University of Liege</a> (BE)

  17. <a href="?tag=babraham%20bioinformatics">Babraham Bioinformatics, The Babraham Institute, Cambridge</a> (UK)

  18. <a href="http://emboss.sf.net">EMBOSS</a>, European Bioinformatics Institute, Hinxton (UK)

    Contact us at <a href='mailto:emboss-bug@emboss.open-bio.org'>emboss-bug@emboss.open-bio.org</a>

  19. <a href="http://web.mit.edu/ccr/core/facilities/bioinformatics/">Bioinformatics and Computing Core Facility (BCC), Koch Institute - MIT</a> Cambridge, MA (USA)

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