List of Software - Revision history

Alastair.kerr at 09:15, 26 July 2011

2011-07-26T09:15:30Z

Rebhan at 09:48, 11 October 2008

2008-10-11T09:48:15Z

160.129.208.29 at 20:10, 1 August 2008

2008-08-01T20:10:18Z

Bgrichter: Software discussion moved to List of Software: rename

2008-07-30T02:59:27Z

Software discussion moved to List of Software: rename

Bgrichter at 02:54, 30 July 2008

2008-07-30T02:54:17Z

Bgrichter at 02:31, 30 July 2008

2008-07-30T02:31:10Z

Sexton at 17:53, 29 July 2008

2008-07-29T17:53:32Z

Lewitter at 22:20, 28 July 2008

2008-07-28T22:20:58Z

Lewitter: New page:

Ongoing Discussion for Bioinformatics Core Facilities

Please enter information about your core facility on the Bioinfo-core main page. ...

2008-07-28T22:19:37Z

New page: <h1>Ongoing Discussion for Bioinformatics Core Facilities</h1> Please enter information about your core facility on the <a href="http://www.bioinfo-core.org">Bioinfo-core main page</a>. ...

New page

<h1>Ongoing Discussion for Bioinformatics Core Facilities</h1>

Please enter information about your core facility on the <a href="http://www.bioinfo-core.org">Bioinfo-core main page</a>.
<br><br>
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
the new page and add a new wiki tag (the new page name enclosed in square brackets) for the new page. Hit save, then
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.
<br><br>
<hr>
<h2>Tools popular with biologists</h2>
<br>This is a list of the tools that were mentioned in our discussion on "bioinformatics for the biologists" on Feb 4th, 2008.
<br><br>
<h3>Microarray data retrieval and basic analysis</h3>
<ul>
<li><a href="http://base.thep.lu.se">BASE</a> from Lund University, Sweden (basic analysis and database)
<li><a href="http://www.tm4.org/">Multiple Experiment Viewer from Quackenbush Group at Harvard Univ </a>
<li><a href="http://bioinformatics.skcc.org/webarray/"> WebArray: Web interface, based on bioconductor and mySQL </a>
<li><a href="https://carmaweb.genome.tugraz.at/carma">CarmaWeb </a>
<li><a href="http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/">ChipMonk</a> for ChIP-on-chip data, e.g. from Nimblegen
<li><A HREF="http://biosun1.harvard.edu/complab/dchip/">DChip</A>: basic analysis (e.g. get a list of differentially expressed genes)
<li><A HREF="http://bioinfo.bgu.ac.il/bsu/microarrays/links/">A good links site</A> for multiple applications
</ul>
<h3>Structure visualization and basic analysis</h3>
<ul>
<li><A HREF="http://pymol.sourceforge.net/">PyMOL</A>
<li>AutoDock for docking
<li>DiscoveryStudio (?)
<li><a href="http://kinemage.biochem.duke.edu">Kinmage</a> for 3D Macromolecule analysis from Richardson Lab at Duke
<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
<li><a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</a> for structure veiwer from NCBI
</ul>
<h3>Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data</h3>
<ul>
<li><A HREF="http://cytoscape.org/">Cytoscape</A>
<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>
<li><A HREF="http://www.bioinformatics.ed.ac.uk/epe/">EPE</A> Edinburgh Pathway Editor
</ul>
<h3>Pipeline Tools</h3>
<ul>
<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.
<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
</ul>

<hr>
<h3>Looking for collaborations in Rosetta Resolver training</h3>
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>
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>
Eitan Rubin, <a href="mailto:erubin@bgu.ac.il">erubin@bgu.ac.il</A>
<hr>

<hr>
<center>Return to <a href="http://www.bioinfo-core.org">Bioinfo-core wiki</a></center>
<hr>

@@ Line 36: / Line 36: @@
 <ul>
 <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.
-<li>[http://galaxy.psu.edu/ Galaxy] This package is from Penn State and is very good.
+<li>[http://galaxy.psu.edu/ Galaxy] This package is from Penn State: [[Galaxy Experiences|Experiences in a Core Facility]]
 <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
 </ul>

← Older revision		Revision as of 09:48, 11 October 2008
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	Please enter information about your core facility on the [[BioWiki:Community Portal]].		Please enter information about your core facility on the [[BioWiki:Community Portal]].
		+
		+	[[Category:Tools]]

	<br>		<br>

@@ Line 34: / Line 34: @@
 <ul>
 <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.
 <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
 </ul>

← Older revision	Revision as of 02:59, 30 July 2008
(No difference)

@@ Line 1: / Line 1: @@
 Please enter information about your core facility on the [[BioWiki:Community Portal]].
-<br><br>
+<br>
 <hr>
 <h2>Tools popular with biologists</h2>

@@ Line 1: / Line 1: @@
 <h1>Ongoing Discussion for Bioinformatics Core Facilities</h1>
+Please enter information about your core facility on the [http://www.bioinfo-core.org Bioinfo-core main page].
 <hr>
 <h2>Tools popular with biologists</h2>
@@ Line 8: / Line 13: @@
 <h3>Microarray data retrieval and basic analysis</h3>
 <ul>
-<li><a href="http://base.thep.lu.se">BASE</a> from Lund University, Sweden (basic analysis and database)
+<li>[http://base.thep.lu.se BASE] from Lund University, Sweden (basic analysis and database)
-<li><a href="http://www.tm4.org/">Multiple Experiment Viewer from Quackenbush Group at Harvard Univ </a>
+<li>[http://www.tm4.org/ Multiple Experiment Viewer from Quackenbush Group at Harvard Univ]
-<li><a href="http://bioinformatics.skcc.org/webarray/"> WebArray: Web interface, based on bioconductor and mySQL </a>
+<li>[http://bioinformatics.skcc.org/webarray/  WebArray: Web interface, based on bioconductor and mySQL]
-<li><a href="https://carmaweb.genome.tugraz.at/carma">CarmaWeb </a>
+<li>[https://carmaweb.genome.tugraz.at/carma CarmaWeb]
-<li><a href="http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/">ChipMonk</a> for ChIP-on-chip data, e.g. from Nimblegen
+<li>[http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ ChipMonk] for ChIP-on-chip data, e.g. from Nimblegen
-<li><A HREF="http://biosun1.harvard.edu/complab/dchip/">DChip</A>: basic analysis (e.g. get a list of differentially expressed genes)
+<li>[http://biosun1.harvard.edu/complab/dchip/ DChip]: basic analysis (e.g. get a list of differentially expressed genes)
-<li><A HREF="http://bioinfo.bgu.ac.il/bsu/microarrays/links/">A good links site</A> for multiple applications
+<li>[http://bioinfo.bgu.ac.il/bsu/microarrays/links/ A good links site] for multiple applications
 </ul>
 <h3>Structure visualization and basic analysis</h3>
 <ul>
-<li><A HREF="http://pymol.sourceforge.net/">PyMOL</A>
+<li>[http://pymol.sourceforge.net/ PyMOL]
 <li>AutoDock for docking
 <li>DiscoveryStudio (?)
-<li><a href="http://kinemage.biochem.duke.edu">Kinmage</a> for 3D Macromolecule analysis from Richardson Lab at Duke
+<li>[http://kinemage.biochem.duke.edu Kinmage] for 3D Macromolecule analysis from Richardson Lab at Duke
-<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
+<li>[http://swissmodel.expasy.org/spdbv/ DeepView] for structure analysis and modeling from the Swiss Institute of Bioinformatics and GlaxoSmithKline R&D
-<li><a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</a> for structure veiwer from NCBI
+<li>[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D] for structure veiwer from NCBI
 </ul>
 <h3>Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data</h3>
 <ul>
-<li><A HREF="http://cytoscape.org/">Cytoscape</A>
+<li>[http://cytoscape.org/ Cytoscape]
-<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>
+<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]
-<li><A HREF="http://www.bioinformatics.ed.ac.uk/epe/">EPE</A> Edinburgh Pathway Editor
+<li>[http://www.bioinformatics.ed.ac.uk/epe/ EPE] Edinburgh Pathway Editor
 </ul>
 <h3>Pipeline Tools</h3>
 <ul>
-<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.
+<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.
-<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
+<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
 </ul>
 <hr>