Terry's compbio links
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| ===General programming stuff=== | ===General programming stuff=== | ||
| - | [http://www.python.org/doc www.python.org/doc]: Helpful links for '''Python''' programmers. | + | '''Unix shell:''' [[bash/tcsh syntax differences]] |
| - | [http://www.gnu.org/software/bash/manual/bashref.html '''Bash''' shell reference manual], [http://wiki.linuxquestions.org/wiki/Bash_tips Bash tips], [http://www.ibm.com/developerworks/library/l-bash-test.html Bash tests and comparators]. | + | '''Bash:''' [http://www.gnu.org/software/bash/manual/bashref.html Bash shell reference manual], [http://wiki.linuxquestions.org/wiki/Bash_tips Bash tips], [http://www.ibm.com/developerworks/library/l-bash-test.html Bash tests and comparators]. |
| - | [http://www.grymoire.com/Unix/Sed.html Nice '''sed''' (stream editor) reference] | + | '''Sed:''' [http://www.grymoire.com/Unix/Sed.html Nice sed (stream editor) reference] |
| [http://student.northpark.edu/pemente/sed/sed1line.txt sed one-liners] | [http://student.northpark.edu/pemente/sed/sed1line.txt sed one-liners] | ||
| - | [http://www.swaroopch.com/notes/Vim_en:Table_of_Contents A Byte of '''Vim'''], the text editor. [http://www.zinkwazi.com/unix/notes/vimtips.html Sweet little Vim recipes] | + | '''Vim:''' [http://www.swaroopch.com/notes/Vim_en:Table_of_Contents A Byte of Vim], the text editor. [http://www.zinkwazi.com/unix/notes/vimtips.html Sweet little Vim recipes.] |
| - | [http://www.troubleshooters.com/codecorn/littperl/ Steve Litt's '''Perl's''' of Wisdom], [http://perldoc.perl.org/index-tutorials.html Perl tutorials], and [http://www.cs.cf.ac.uk/Dave/PERL/ www.cs.cf.ac.uk/Dave/PERL/], another nice Perl reference. | + | '''Perl:''' [http://www.troubleshooters.com/codecorn/littperl/ Steve Litt's Perl's of Wisdom], [http://perldoc.perl.org/index-tutorials.html Perl tutorials], and [http://www.cs.cf.ac.uk/Dave/PERL/ www.cs.cf.ac.uk/Dave/PERL/], another nice Perl reference. |
| [http://www.cs.tut.fi/~jkorpela/perl/regexp.html Regular expressions in Perl] | [http://www.cs.tut.fi/~jkorpela/perl/regexp.html Regular expressions in Perl] | ||
| - | [http://svnbook.red-bean.com/en/1.5/svn-book.html One-page version of the subversion book.] | + | '''Python:''' [http://www.python.org/doc www.python.org/doc]: Helpful links for Python programmers. |
| - | [[bash/tcsh syntax differences]] | + | '''svn:''' [http://svnbook.red-bean.com/en/1.5/svn-book.html One-page version of the subversion book.] |
| ==A few other Links== | ==A few other Links== | ||
Revision as of 20:44, 25 March 2009
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.
