Terry's compbio links
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Terry Farrah's Computational Biology Links
Personal
Bus home: 64 76 71 To Hearthstone: 16 To ISB from home: 64, 71, 76 @65th 74 @55th To ISB from Trip: 66 To ISB from Betsy: 68, 73E
NEST volunteer portal Mom & Aegis Phone tracker
ISB specific
Mail Intranet PubMed special link ISB library page ISB journal subscriptions Reservations paychex (0495 w123 bar w/o hyphen + pilipina) ISB contacts
Be apache on mimas
ISB: Inova & Family Genomics
JIRA for reporting issues with ITMI
Confluence wiki for Inova collaboration
Trello task tracker
General genomics
SAM flags decoder, SAM specification VCF 4.2 specification
SAMtools wiki, SAMtools Primer revised July 2013, SAMBLASTER duplicate marking and structural variant read extraction
isaac-align, used to create Inova BAM files, Isaac code
Illumina Whole-Genome Sequencing Services User Guide, gVCF documentation
Mike Lin's blog on analyzing his own Illumina genome
Complete Genomics documentation small variant assembler methods mapping and variant calling methods
Performance comparison of four human whole-genome sequencing technologies
General programming
git: introduction
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. Line terminator info.
Perl: Steve Litt's Perl's of Wisdom, Perl tutorials, and www.cs.cf.ac.uk/Dave/PERL/, another nice Perl reference.
PDL (Perl Data Language) quick start
Informative discussion of test module options
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: [1]
Excel: String operations
IDL: [2]
svn: One-page version of the subversion book.
General computational biology
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 biology
Awesome animation of the inner life of the cell
ISB proteomics informatics
Terry's notes on how to perform a Peptide Atlas build
Additional notes on PeptideAtlas software
Protein identification terminology
Using the PeptideAtlas SearchProteins tab
Dave Campbell's PABST peptide selector for targetted proteomics
Notes on searching and TPP usage from the Unix command line at ISB
Short TPP tutorial, Long TPP tutorial, TPP testimonials
Notes on database programming for SBEAMS
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
Joe Slagel's Oct. 2009 notes on scheduling on the regis cluster
mspecLINE: linking disease to PeptideAtlas
Proteomics
JPR Jan 2014 C-HPP special issue
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
NIST Peptide Mass Spectral Libraries
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
Specifications for protXML, pepXML, and more
UniMod database of amino acid modifications
How to use the mProphet SRM results processing/validation pipeline
A few other Links
ReligiousTolerance.org: I saw one intelligently written article there. Their purpose is to provide unbiased essays on various topics.
