Terry's compbio links
From SPCTools
Contents |
Terry Farrah's Computational Biology Links
ISB specific stuff
Terry's notes on how to perform a Peptide Atlas build
Notes on searching and TPP usage from the Unix command line at ISB
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
InsPecT sequence search engine
PRIDE PRoteomics IDEntification database
Terry's blog on improving proteomics peptide and protein identifications
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, updated every 3 weeks. UniProtKB/Swiss-Prot purportedly contains the canonical human proteome (The UniProt Consortium, "The Universal Protein Resource (UniProt) 2009, Nucleic Acids Research 2008 1-6) consisting of 20,325 entries for UniProt release 14.0. Swiss-Prot release 56.6 of 16-Dec-08 contains 20,333 human proteins.
[ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens: Download NCBI's UniGene human. Contains chromosomal information, among many other data.
http://www.broad.mit.edu/~mclamp/alpheus/ Gene content of human genome]: which Ensembl entries are real genes and which are not, according to Clamp et al, "Distinguishing protein-coding and noncoding genes in the human genome", PNAS December 4, 2007, 19428-19433, Vol. 104 No. 49.
General programming stuff
Unix shell: bash/tcsh syntax differences
Bash: Bash shell reference manual, Bash tips, Bash tests and comparators.
Sed: Nice sed (stream editor) reference sed one-liners
Vim: A Byte of Vim, the text editor. Sweet little Vim recipes.
Perl: Steve Litt's Perl's of Wisdom, Perl tutorials, and www.cs.cf.ac.uk/Dave/PERL/, another nice Perl reference.
Python: www.python.org/doc: Helpful links for Python programmers.
svn: One-page version of the subversion book.
A few other Links
ReligiousTolerance.org: I saw one intelligently written article there. Their purpose is to provide unbiased essays on various topics.
