Terry's compbio links
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| ===ISB specific stuff=== | ===ISB specific stuff=== | ||
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| - | [http://www.peptideatlas.org Peptide Atlas]: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. | ||
| [[Building Peptide Atlas | Terry's notes on how to perform a Peptide Atlas build]] | [[Building Peptide Atlas | Terry's notes on how to perform a Peptide Atlas build]] | ||
| [[The ISB Unix user's expert guide to tandem MS sequence searching and TPP usage]] | [[The ISB Unix user's expert guide to tandem MS sequence searching and TPP usage]] | ||
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| - | [[Installing and building TPP on Windows | Terry's notes on how to install and build the TPP under windows]] | ||
| [http://www.sbeams.org SBeams]: SPC's experimental data storage system. Go here to run an SBeams test drive. | [http://www.sbeams.org SBeams]: SPC's experimental data storage system. Go here to run an SBeams test drive. | ||
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| [http://db.systemsbiology.net/devTF/sbeams/cgi/main.cgi db.systemsbiology.net/devTF/sbeams/cgi/main.cgi] Terry's SBeams software development sandbox | [http://db.systemsbiology.net/devTF/sbeams/cgi/main.cgi db.systemsbiology.net/devTF/sbeams/cgi/main.cgi] Terry's SBeams software development sandbox | ||
| - | [http://www.thegpm.org/TANDEM/api/ X!Tandem parameters]; [http://www.thegpm.org/TANDEM/ X!Tandem home page] | + | ===Proteomics stuff=== |
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| + | [http://www.peptideatlas.org Peptide Atlas]: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. | ||
| [http://groups.google.com/group/spctools-dev/ TPP developers' group], [http://groups.google.com/group/spctools-discuss/ TPP users' group] | [http://groups.google.com/group/spctools-dev/ TPP developers' group], [http://groups.google.com/group/spctools-discuss/ TPP users' group] | ||
| [http://prottools.ethz.ch/muellelu/web/LukasReiter/Mayu/ Mayu]: analysis of (large) mass spectrometry-based shotgun proteomics data sets. Mayu determines protein identification false discovery rates (protFDR), peptide identification false discovery rates (pepFDR) and peptide-spectrum match false discovery rates (mFDR) using a novel robust and fast strategy. Developed by Lukas Reiter. | [http://prottools.ethz.ch/muellelu/web/LukasReiter/Mayu/ Mayu]: analysis of (large) mass spectrometry-based shotgun proteomics data sets. Mayu determines protein identification false discovery rates (protFDR), peptide identification false discovery rates (pepFDR) and peptide-spectrum match false discovery rates (mFDR) using a novel robust and fast strategy. Developed by Lukas Reiter. | ||
| + | |||
| + | [http://www.thegpm.org/TANDEM/api/ X!Tandem parameters]; [http://www.thegpm.org/TANDEM/ X!Tandem home page] | ||
| ===General computational biology stuff=== | ===General computational biology stuff=== | ||
Revision as of 23:02, 16 December 2008
Contents |
Terry Farrah's Computational Biology Links
ISB specific stuff
Terry's notes on how to perform a Peptide Atlas build
The ISB Unix user's expert guide to tandem MS sequence searching and TPP usage
SBeams: SPC's experimental data storage system. Go here to run an SBeams test drive.
db.systemsbiology.org: Developer's back door into SBeams. Go here to contribute data.
db.systemsbiology.net/devTF/sbeams/cgi/main.cgi Terry's SBeams software development sandbox
Proteomics stuff
Peptide Atlas: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
TPP developers' group, TPP users' group
Mayu: analysis of (large) mass spectrometry-based shotgun proteomics data sets. Mayu determines protein identification false discovery rates (protFDR), peptide identification false discovery rates (pepFDR) and peptide-spectrum match false discovery rates (mFDR) using a novel robust and fast strategy. Developed by Lukas Reiter.
X!Tandem parameters; X!Tandem home page
General computational biology stuff
Swiss-Prot curated protein sequence database
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete: Download Swiss-Prot and other UniProt databases
PRIDE PRoteomics IDEntification database
Terry's blog on improving proteomics peptide and protein identifications
General programming stuff
www.python.org/doc: Helpful links for Python programmers.
Nice sed (stream editor) reference
Steve Litt's Perl's of Wisdom, and www.cs.cf.ac.uk/Dave/PERL/, another nice Perl reference.
A few other Links
ReligiousTolerance.org: I saw one intelligently written article there. Their purpose is to provide unbiased essays on various topics.
