Difference between revisions of "List of Software"
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| − | + | Please enter information about your core facility on the [[BioWiki:Community Portal]]. | |
| + | [[Category:Tools]] | ||
| + | <br> | ||
<hr> | <hr> | ||
<h2>Tools popular with biologists</h2> | <h2>Tools popular with biologists</h2> | ||
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<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://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> | </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> | ||
Latest revision as of 01:15, 26 July 2011
Please enter information about your core facility on the BioWiki:Community Portal.
Contents
- 1 Tools popular with biologists
- 1.1 Microarray data retrieval and basic analysis
- 1.2 Structure visualization and basic analysis
- 1.3 Visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data
- 1.4 Pipeline Tools
- 1.5 Looking for collaborations in Rosetta Resolver training
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.
- Galaxy This package is from Penn State: Experiences in a Core Facility
- 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
