Terry's compbio links

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.

[edit]

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.

[edit]

General biology

Awesome animation of the inner life of the cell

[edit]

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

Processing glycopeptide data

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

Raw MS file conversion

Joe Slagel's Oct. 2009 notes on scheduling on the regis cluster

mspecLINE: linking disease to PeptideAtlas

[edit]

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

Tranche downloader

SpectraST spectrum viewer

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

[edit]

A few other Links

ReligiousTolerance.org: I saw one intelligently written article there. Their purpose is to provide unbiased essays on various topics.

Comic of the observable universe, from top to bottom

Peace Pilgrim

Links on mindfulness, meditation, and Buddhism

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Terry%27s_compbio_links"

 ==Terry Farrah's Computational Biology Links==
-===ISB specific stuff===
+===Personal===
+[http://tinyurl.com/terry-activism Terry's Activism Page]
+[https://nodapl.styrotopia.net/volunteers SR Legal DB]
+[http://www.washington.edu/facilities/transportation/uwshuttles/slu/schedule SLU-UW schedule]
+[http://www.nestseattle.org/our-neighbors/volunteers/volunteer-calendar/ NEST volunteer portal]
+[https://www.life360.com/circles/#/map Phone tracker]
+===ISB specific===
 [http://mail.systemsbiology.org Mail] [http://intranet.systemsbiology.net Intranet] [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=waunkglib PubMed special link]
+[https://intranet.systemsbiology.net/Plone/community/library ISB library page] [https://intranet.systemsbiology.net/Plone/community/library/journal-access/journal-access ISB journal subscriptions] [http:///intranet.systemsbiology.net/frs/ Reservations] [http://www.paychexflex.com paychexflex] (terry.farrah 6char plus that year) [https://intranet.systemsbiology.net/Plone/contacts/first-name ISB contacts]
-Bus home: [http://onebusaway.org/where/standard/stop.action?id=1_1050&route=1_64 64] [http://onebusaway.org/where/standard/stop.action?id=1_1192&route=1_76 76] [http://onebusaway.org/where/standard/stop.action?id=1_10305&route=1_71 71] To Hearthstone: [http://onebusaway.org/where/standard/stop.action?id=1_18390&route=1_16 16] [http://onebusaway.org/where/standard/stop.action?id=1_18390&route=1_26 26]
+[https://pricewiki.systemsbiology.net/ Price Lab wiki][https://price.systemsbiology.org/bio/terry-farrah/ Price Lab bio][https://www.dropbox.com/home/price%20lab Price Lab dropbox]
-[[Building Peptide Atlas | Terry's notes on how to perform a Peptide Atlas build]]
+[https://db.systemsbiology.net/devDC/sbeams/cgi/domybidding.cgi Be apache] on mimas
-[[PeptideAtlas software | Additional notes on PeptideAtlas software]]
+===ISB: Metabolic Modeling===
+[https://docs.google.com/document/d/1qsYYMgGTYOWpgTAPMG72wh7aNiuU8xLI15M-i-A181k/edit Running ProbAnno standalone] at ISB (quite obsolete as of Sept. 2016)
+[https://probanno.systemsbiology.org ProbAnno web server]
-[[Protein identification terminology]]
+===ISB: BD Spoke grant===
+[http://tfarrah.github.io/Genome-Peptide-Structure Workshop website]
+[https://drive.google.com/a/systemsbiology.org/folderview?id=0Bz3pOYghbQpgSGU3eEpEd1lNdVk&usp=sharing_eid&ts=56942828 Google drive]
-[[SearchProteins | Using the PeptideAtlas SearchProteins tab]]
+===ISB: Inova & Family Genomics===
+[https://54.243.235.221/jira/secure JIRA] for reporting issues with ITMI
-[[PABST_peptide_examples | Dave Campbell's PABST peptide selector for targetted proteomics]]
+[http://ilyawiki.systemsbiology.net:8090/display/ISBInova/ISB-INOVA Confluence wiki] for Inova collaboration
-[[Expert search and TPP usage | Notes on searching and TPP usage from the Unix command line at ISB]]
+[https://trello.com/b/kgG0tLkq/famgen-task-tracker Trello] task tracker
-[[TPP_Demo2009 | Short TPP tutorial]], [[TPP_Tutorial | Long TPP tutorial]], [[TPP testimonials]]
+[https://itmi.signin.aws.amazon.com/console Amazon S3]
-[[Using SBEAMS | Notes on database programming for SBEAMS]]
+[https://docs.google.com/a/systemsbiology.org/document/d/1k6LMLPIp5JBSM38VuRsMotGFbwDrdofQtnLm38QL4Jk/edit#heading=h.tqo76n1fjy8z Gestalt user manual]
-[[Processing glycopeptide data]]
+[http://db.systemsbiology.net/kaviar/ Kaviar]
+[https://docs.google.com/document/d/1PCHWWVLl453x9ow76XgDrWVoFXKWJ1JXGhl6hf4d30k/edit How to build Kaviar]
-[http://www.sbeams.org SBeams]: SPC's experimental data storage system. Go here to run an SBeams test drive.
+[https://docs.google.com/document/d/1OLsShhl7TeMCBPk6Al6O9sH_n0sgL51OhExVtVwjXTQ/edit RCF specification]
-[http://db.systemsbiology.net db.systemsbiology.net]: Developer's back door into SBeams. Go here to contribute data.
+GMS: [http://pedigree.bobama.systemsbiology.net/pedigrees local] [http://192.168.240.95 ITMI; need to be on ITMI network]
-[http://db.systemsbiology.net/devTF/sbeams/cgi/main.cgi db.systemsbiology.net/devTF/sbeams/cgi/main.cgi] Terry's SBeams software development sandbox
+===General genomics===
+[http://www.ncbi.nlm.nih.gov/snp/advanced Search dbSNP by hg38 coords]
-[[Raw MS file conversion]]
+[https://www.biostars.org/p/93050/ Tabix api examples]
-[[Scheduling on regis cluster | Joe Slagel's Oct. 2009 notes on scheduling on the regis cluster]]
+[http://picard.sourceforge.net/explain-flags.html SAM flags decoder],
+[http://samtools.sourceforge.net/SAMv1.pdf SAM specification]
+[http://samtools.github.io/hts-specs/VCFv4.2.pdf VCF 4.2 specification]
-[http://informatics.systemsbiology.net/informatics/mspecLINE mspecLINE]: linking disease to PeptideAtlas
+[http://davetang.org/wiki/tiki-index.php?page=SAMTools SAMtools wiki],
+[http://biobits.org/samtools_primer.html SAMtools Primer] revised July 2013,
+[http://arxiv.org/abs/1403.7486 SAMBLASTER] duplicate marking and structural variant read extraction
-===Proteomics stuff===
+[https://www.broadinstitute.org/gatk/about/#typical-workflows Intro to GATK]
+[http://bedtools.googlecode.com/files/BEDTools-User-Manual.pdf BEDtools]
-[http://www.peptideatlas.org Peptide Atlas]: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
+[https://github.com/sequencing/isaac_aligner/blob/master/src/markdown/manual.md#isaac-align isaac-align], used to create Inova BAM files,
+[https://github.com/sequencing Isaac code]
-[http://groups.google.com/group/spctools-dev/ TPP developers' group], [http://groups.google.com/group/spctools-discuss/ TPP users' group]
+[http://supportres.illumina.com/documents/documentation/software_documentation/wgs/services_whole_genome_ug_15040892.pdf Illumina Whole-Genome Sequencing Services User Guide], [https://support.basespace.illumina.com/knowledgebase/articles/147078-gvcf-file gVCF] documentation
-[[Software:SpectraST#Plotspectrast | SpectraST spectrum viewer]]
+[http://blog.mlin.net/p/blogging-my-genome.html Mike Lin's blog] on analyzing his own Illumina genome
-[http://peptide.nist.gov/ NIST Peptide Mass Spectral Libraries]
+[http://www.completegenomics.com/customer-support/documentation/ Complete Genomics documentation]
+[http://media.completegenomics.com/documents/Small_Variant_Assembler_Methods.pdf small variant assembler methods]
+[http://www.completegenomics.com/FAQs/Assembly-Mapping-and-Variant-Calling/ mapping and variant calling methods]
-[[Software:Mayu | 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.
+[http://archiv.ub.uni-heidelberg.de/volltextserver/15677/ Performance comparison of four human whole-genome sequencing technologies]
-[http://www.thegpm.org/TANDEM/api/ X!Tandem parameters]; [http://www.thegpm.org/TANDEM/ X!Tandem home page]
+===General programming===
-[http://bix.ucsd.edu/InspectDocs/Database.html InsPecT] sequence search engine
+'''git:''' [http://git-scm.com/book/en/ introduction]
-[http://www.ebi.ac.uk/pride/ PRIDE PRoteomics IDEntification database]
+'''Unix shell:''' [[bash/tcsh syntax differences]]
-[[Terry's blog | Terry's blog on improving proteomics peptide and protein identifications]]
+'''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://tools.proteomecenter.org/formats.php Specifications for protXML, pepXML, and more]
+'''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://www.unimod.org UniMod database of amino acid modifications]
+'''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://vim.wikia.com/wiki/File_format Line terminator info.]
+'''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://pdl.perl.org/?docs=QuickStart&title=PDL::QuickStart PDL] (Perl Data Language) quick start
+[http://www.perlmonks.org/?node_id=469927 Informative discussion of test module options]
+[http://www.cs.tut.fi/~jkorpela/perl/regexp.html Regular expressions in Perl]
+'''Python:''' [http://www.python.org/doc www.python.org/doc]: Helpful links for Python programmers.
+gnu '''screen''': [http://www.gnu.org/software/screen/manual/screen.html.gz 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:''' [http://code.google.com/apis/chart/docs/gallery/venn_charts.html]
+'''Excel:''' [http://www.likeoffice.com/28057/excel-string String operations]
+'''IDL:''' [http://www.msi.umn.edu/software/idl/tutorial/]
+'''svn:''' [http://svnbook.red-bean.com/en/1.5/svn-book.html One-page version of the subversion book.]
-===General computational biology stuff===
+===General computational biology===
 [http://pipe.systemsbiology.net The Pipe] Protein Information and Property Explorer, developed at ISB by Hector Ramos
 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===
+===General biology===
+[http://www.youtube.com/watch?v=52dq2QOTdhs&feature=related Awesome animation of the inner life of the cell]
-'''Unix shell:''' [[bash/tcsh syntax differences]]
+===ISB proteomics informatics===
-'''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].
+[[Building Peptide Atlas | Terry's notes on how to perform a Peptide Atlas build]]
-'''Sed:''' [http://www.grymoire.com/Unix/Sed.html Nice sed (stream editor) reference]
+[[PeptideAtlas software | Additional notes on PeptideAtlas software]]
-[http://student.northpark.edu/pemente/sed/sed1line.txt sed one-liners]
-'''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.]
+[[Protein identification terminology]]
-'''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.
+[[SearchProteins | Using the PeptideAtlas SearchProteins tab]]
-[http://pdl.perl.org/?docs=QuickStart&title=PDL::QuickStart PDL] (Perl Data Language) quick start
+[[PABST_peptide_examples | Dave Campbell's PABST peptide selector for targetted proteomics]]
-[http://www.perlmonks.org/?node_id=469927 Informative discussion of test module options]
+[[Expert search and TPP usage | Notes on searching and TPP usage from the Unix command line at ISB]]
-[http://www.cs.tut.fi/~jkorpela/perl/regexp.html Regular expressions in Perl]
+[[TPP_Demo2009 | Short TPP tutorial]], [[TPP_Tutorial | Long TPP tutorial]], [[TPP testimonials]]
-'''Python:''' [http://www.python.org/doc www.python.org/doc]: Helpful links for Python programmers.
+[[Using SBEAMS | Notes on database programming for SBEAMS]]
-'''svn:''' [http://svnbook.red-bean.com/en/1.5/svn-book.html One-page version of the subversion book.]
+[[Processing glycopeptide data]]
-gnu '''screen''': [http://www.gnu.org/software/screen/manual/screen.html.gz 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.
+[http://www.sbeams.org SBeams]: SPC's experimental data storage system. Go here to run an SBeams test drive.
-'''IDL:''' [http://www.msi.umn.edu/software/idl/tutorial/]
+[http://db.systemsbiology.net db.systemsbiology.net]: Developer's back door into SBeams. Go here to contribute data.
-'''Drawing Venn Diagrams:''' [http://code.google.com/apis/chart/docs/gallery/venn_charts.html]
+[http://db.systemsbiology.net/devTF/sbeams/cgi/main.cgi db.systemsbiology.net/devTF/sbeams/cgi/main.cgi] Terry's SBeams software development sandbox
+[[Raw MS file conversion]]
-===General biology stuff===
+[[Scheduling on regis cluster | Joe Slagel's Oct. 2009 notes on scheduling on the regis cluster]]
-[http://www.youtube.com/watch?v=52dq2QOTdhs&feature=related Awesome animation of the inner life of the cell]
-==ISB (not computational biology)==
+[http://informatics.systemsbiology.net/informatics/mspecLINE mspecLINE]: linking disease to PeptideAtlas
-[http:///intranet.systemsbiology.net/frs/ Room and communications equipment reservations]
+===Proteomics===
+[http://pubs.acs.org/toc/jprobs/13/1 JPR Jan 2014 C-HPP special issue]
+[http://www.peptideatlas.org Peptide Atlas]: a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.
+[http://groups.google.com/group/spctools-dev/ TPP developers' group], [http://groups.google.com/group/spctools-discuss/ TPP users' group]
+[http://www.proteomecommons.org/tranche/data-downloader.jsp Tranche downloader]
+[[Software:SpectraST#Plotspectrast | SpectraST spectrum viewer]]
+[http://peptide.nist.gov/ NIST Peptide Mass Spectral Libraries]
+[[Software:Mayu | 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.
+[http://www.thegpm.org/TANDEM/api/ X!Tandem parameters]; [http://www.thegpm.org/TANDEM/ X!Tandem home page]
+[http://bix.ucsd.edu/InspectDocs/Database.html InsPecT] sequence search engine
+[http://www.ebi.ac.uk/pride/ PRIDE PRoteomics IDEntification database]
+[[Terry's blog | Terry's blog on improving proteomics peptide and protein identifications]]
+[http://tools.proteomecenter.org/formats.php Specifications for protXML, pepXML, and more]
+[http://www.unimod.org UniMod database of amino acid modifications]
+[[Using mProphet at ISB | How to use the mProphet SRM results processing/validation pipeline]]
 ==A few other Links==
 [http://xkcd.com/482/ Comic of the observable universe, from top to bottom]
+[http://www.peacepilgrim.com/htmfiles/mdppbio.htm Peace Pilgrim]
+[[Links on mindfulness, meditation, and Buddhism]]

Terry's compbio links

From SPCTools

Current revision

Contents

Terry Farrah's Computational Biology Links

Personal

ISB specific

ISB: Metabolic Modeling

ISB: BD Spoke grant

ISB: Inova & Family Genomics

General genomics

General programming

General computational biology

General biology

ISB proteomics informatics

Proteomics

A few other Links

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