Terry's compbio links
From SPCTools
Contents |
Terry Farrah's Computational Biology Links
ISB specific stuff
Peptide Atlas: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
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
Terry's notes on how to install and build the TPP under windows
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
X!Tandem parameters; X!Tandem home page
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.
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.
