Terry's compbio links
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| [ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete]: Download Swiss-Prot and other UniProt databases | [ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete]: Download Swiss-Prot and other UniProt databases | ||
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| + | [http://www.ebi.ac.uk/pride/ PRIDE PRoteomics IDEntification database] | ||
| [[Terry's blog | Terry's blog on improving proteomics peptide and protein identifications]] | [[Terry's blog | Terry's blog on improving proteomics peptide and protein identifications]] | ||
Revision as of 01:37, 6 December 2008
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
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
A few other Links
ReligiousTolerance.org: I saw one intelligently written article there. Their purpose is to provide unbiased essays on various topics.
