Difference between revisions of "List of Software"
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<h1>Ongoing Discussion for Bioinformatics Core Facilities</h1> | <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]. | |
| + | <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> | <hr> | ||
<h2>Tools popular with biologists</h2> | <h2>Tools popular with biologists</h2> | ||
| Line 8: | Line 13: | ||
<h3>Microarray data retrieval and basic analysis</h3> | <h3>Microarray data retrieval and basic analysis</h3> | ||
<ul> | <ul> | ||
| − | <li> | + | <li>[http://base.thep.lu.se BASE] from Lund University, Sweden (basic analysis and database) |
| − | <li> | + | <li>[http://www.tm4.org/ Multiple Experiment Viewer from Quackenbush Group at Harvard Univ] |
| − | <li> | + | <li>[http://bioinformatics.skcc.org/webarray/ WebArray: Web interface, based on bioconductor and mySQL] |
| − | <li> | + | <li>[https://carmaweb.genome.tugraz.at/carma CarmaWeb] |
| − | <li> | + | <li>[http://www.bioinformatics.bbsrc.ac.uk/projects/chipmonk/ ChipMonk] for ChIP-on-chip data, e.g. from Nimblegen |
| − | <li> | + | <li>[http://biosun1.harvard.edu/complab/dchip/ DChip]: basic analysis (e.g. get a list of differentially expressed genes) |
| − | <li> | + | <li>[http://bioinfo.bgu.ac.il/bsu/microarrays/links/ A good links site] for multiple applications |
</ul> | </ul> | ||
<h3>Structure visualization and basic analysis</h3> | <h3>Structure visualization and basic analysis</h3> | ||
<ul> | <ul> | ||
| − | <li> | + | <li>[http://pymol.sourceforge.net/ PyMOL] |
<li>AutoDock for docking | <li>AutoDock for docking | ||
<li>DiscoveryStudio (?) | <li>DiscoveryStudio (?) | ||
| − | <li> | + | <li>[http://kinemage.biochem.duke.edu Kinmage] for 3D Macromolecule analysis from Richardson Lab at Duke |
| − | <li> | + | <li>[http://swissmodel.expasy.org/spdbv/ DeepView] for structure analysis and modeling from the Swiss Institute of Bioinformatics and GlaxoSmithKline R&D |
| − | <li> | + | <li>[http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml Cn3D] for structure veiwer from NCBI |
</ul> | </ul> | ||
<h3>Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data</h3> | <h3>Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data</h3> | ||
<ul> | <ul> | ||
| − | <li> | + | <li>[http://cytoscape.org/ Cytoscape] |
| − | <li> | + | <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> | + | <li>[http://www.bioinformatics.ed.ac.uk/epe/ EPE] Edinburgh Pathway Editor |
</ul> | </ul> | ||
<h3>Pipeline Tools</h3> | <h3>Pipeline Tools</h3> | ||
<ul> | <ul> | ||
| − | <li> | + | <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> | + | <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> | </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, [mailto:erubin@bgu.ac.il erubin@bgu.ac.il] | ||
| + | <hr> | ||
| + | |||
| + | <hr> | ||
| + | <center>Return to [http://www.bioinfo-core.org Bioinfo-core wiki]</center> | ||
| − | |||
<hr> | <hr> | ||
Revision as of 09:53, 29 July 2008
Contents
- 1 Ongoing Discussion for Bioinformatics Core Facilities
- 1.1 Tools popular with biologists
- 1.1.1 Microarray data retrieval and basic analysis
- 1.1.2 Structure visualization and basic analysis
- 1.1.3 Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data
- 1.1.4 Pipeline Tools
- 1.1.5 Looking for collaborations in Rosetta Resolver training
- 1.1 Tools popular with biologists
Ongoing Discussion for Bioinformatics Core Facilities
Please enter information about your core facility on the Bioinfo-core main page.
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.
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
- BASE from Lund University, Sweden (basic analysis and database)
- Multiple Experiment Viewer from Quackenbush Group at Harvard Univ
- WebArray: Web interface, based on bioconductor and mySQL
- CarmaWeb
- ChipMonk for ChIP-on-chip data, e.g. from Nimblegen
- DChip: basic analysis (e.g. get a list of differentially expressed genes)
- A good links site for multiple applications
Structure visualization and basic analysis
- PyMOL
- AutoDock for docking
- DiscoveryStudio (?)
- Kinmage for 3D Macromolecule analysis from Richardson Lab at Duke
- DeepView for structure analysis and modeling from the Swiss Institute of Bioinformatics and GlaxoSmithKline R&D
- Cn3D for structure veiwer from NCBI
Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data
- Cytoscape
- Reactome including Skypainter and the latest biomart interface Reactome Mart
- EPE Edinburgh Pathway Editor
Pipeline Tools
- 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 Soaplab. Version 2 of taverna should handle large file sizes a lot better.
- Alternatives: A paper highlighting Seahawk (Biomoby) but also mentions both Taverna and Remora
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, erubin@bgu.ac.il
