Terry's compbio links
Terry Farrah's Computational Biology Links
ISB specific stuff
SBeams: SPC's experimental data storage system. Go here to run an SBeams test drive.
db.systemsbiology.net: 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
mspecLINE: linking disease to PeptideAtlas
Peptide Atlas: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
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.
InsPecT sequence search engine
General computational biology stuff
The Pipe Protein Information and Property Explorer, developed at ISB by Hector Ramos
Swiss-Prot curated protein sequence database
Amigo: browser for the Gene Ontology 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
PDL (Perl Data Language) quick start
Python: www.python.org/doc: Helpful links for Python programmers.
gnu screen: One-page ref manual. Screen allows you to run several terminal sessions from one window, and allows sessions to persist after you close the window. Very handy if you want to take your work home with you -- close windows, then resume screen from your home computer.
Drawing Venn Diagrams: 
Excel: String operations
General biology stuff
A few other Links
ReligiousTolerance.org: I saw one intelligently written article there. Their purpose is to provide unbiased essays on various topics.