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://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/journal-access/journal-access ISB journal subscriptions] [http:///intranet.systemsbiology.net/frs/ Reservations] [http://eservices.paychex.com paychex] (0495 w123 bar w/o hyphen + pilipina) [https://intranet.systemsbiology.net/Plone/contacts/first-name ISB contacts]
+[http://www.washington.edu/facilities/transportation/uwshuttles/slu/schedule SLU-UW schedule]
-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_6250 16] To ISB from home: [http://onebusaway.org/where/standard/stop.action?id=1_37980 64, 71, 76] @65th [http://onebusaway.org/where/standard/stop.action?id=1_10060 74] @55th To ISB from Trip: [http://onebusaway.org/where/standard/stop.action?id=1_16440 66] To ISB from Betsy: [http://onebusaway.org/where/standard/stop.action?id=1_82227 68, 73E]
+[http://www.nestseattle.org/our-neighbors/volunteers/volunteer-calendar/ NEST volunteer portal]
+[https://www.life360.com/circles/#/map Phone tracker]
-[http://www.industrymailout.com/Industry/Redirect.aspx?u=555740&q=490480490&lm=47920697&r=384020&qz=2d68889c931dc3fc88f91f4bc0b38e16 NEST volunteer portal]
+===ISB specific===
-===Genomics stuff===
+[http://mail.systemsbiology.org Mail] [http://intranet.systemsbiology.net Intranet] [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=waunkglib PubMed special link]
-[http://picard.sourceforge.net/explain-flags.html SAM flags decoder]
+[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]
-[http://biobits.org/samtools_primer.html SAMtools Primer] revised July 2013
+[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]
-[http://arxiv.org/abs/1403.7486 SAMBLASTER] duplicate marking and structural variant read extraction
+[https://db.systemsbiology.net/devDC/sbeams/cgi/domybidding.cgi Be apache] on mimas
-[https://www.broadinstitute.org/gatk/about/#typical-workflows Intro to GATK]
+===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]
-[http://supportres.illumina.com/documents/documentation/software_documentation/wgs/services_whole_genome_ug_15040892.pdf Illumina Whole-Genome Sequencing Services User Guide]
+===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]
-[http://www.completegenomics.com/customer-support/documentation/ Complete Genomics documentation]
+===ISB: Inova & Family Genomics===
+[https://54.243.235.221/jira/secure JIRA] for reporting issues with ITMI
-===General computational biology stuff===
+[http://ilyawiki.systemsbiology.net:8090/display/ISBInova/ISB-INOVA Confluence wiki] for Inova collaboration
-[http://pipe.systemsbiology.net The Pipe] Protein Information and Property Explorer, developed at ISB by Hector Ramos
-[http://www.expasy.org/sprot Swiss-Prot] curated protein sequence database
+[https://trello.com/b/kgG0tLkq/famgen-task-tracker Trello] task tracker
-[http://amigo.geneontology.org/cgi-bin/amigo/go.cgi Amigo]: browser for the Gene Ontology database
+[https://itmi.signin.aws.amazon.com/console Amazon S3]
-[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.
+[https://docs.google.com/a/systemsbiology.org/document/d/1k6LMLPIp5JBSM38VuRsMotGFbwDrdofQtnLm38QL4Jk/edit#heading=h.tqo76n1fjy8z Gestalt user manual]
-[[ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens]: Download NCBI's UniGene human. Contains chromosomal information, among many other data.
+[http://db.systemsbiology.net/kaviar/ Kaviar]
+[https://docs.google.com/document/d/1PCHWWVLl453x9ow76XgDrWVoFXKWJ1JXGhl6hf4d30k/edit How to build Kaviar]
-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.
+[https://docs.google.com/document/d/1OLsShhl7TeMCBPk6Al6O9sH_n0sgL51OhExVtVwjXTQ/edit RCF specification]
-===General programming stuff===
+GMS: [http://pedigree.bobama.systemsbiology.net/pedigrees local] [http://192.168.240.95 ITMI; need to be on ITMI network]
+===General genomics===
+[http://www.ncbi.nlm.nih.gov/snp/advanced Search dbSNP by hg38 coords]
+[https://www.biostars.org/p/93050/ Tabix api examples]
+[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://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
+[https://www.broadinstitute.org/gatk/about/#typical-workflows Intro to GATK]
+[http://bedtools.googlecode.com/files/BEDTools-User-Manual.pdf BEDtools]
+[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://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
+[http://blog.mlin.net/p/blogging-my-genome.html Mike Lin's blog] on analyzing his own Illumina genome
+[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]
+[http://archiv.ub.uni-heidelberg.de/volltextserver/15677/ Performance comparison of four human whole-genome sequencing technologies]
+===General programming===
+'''git:''' [http://git-scm.com/book/en/ introduction]
 '''Unix shell:''' [[bash/tcsh syntax differences]]
 '''Python:''' [http://www.python.org/doc www.python.org/doc]: Helpful links for Python programmers.
-'''svn:''' [http://svnbook.red-bean.com/en/1.5/svn-book.html One-page version of the subversion book.]
 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.
-'''IDL:''' [http://www.msi.umn.edu/software/idl/tutorial/]
 '''Drawing Venn Diagrams:''' [http://code.google.com/apis/chart/docs/gallery/venn_charts.html]
 '''Excel:''' [http://www.likeoffice.com/28057/excel-string String operations]
-===General biology stuff===
+'''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===
+[http://pipe.systemsbiology.net The Pipe] Protein Information and Property Explorer, developed at ISB by Hector Ramos
+[http://www.expasy.org/sprot Swiss-Prot] curated protein sequence database
+[http://amigo.geneontology.org/cgi-bin/amigo/go.cgi 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===
 [http://www.youtube.com/watch?v=52dq2QOTdhs&feature=related Awesome animation of the inner life of the cell]
 [http://informatics.systemsbiology.net/informatics/mspecLINE mspecLINE]: linking disease to PeptideAtlas
-===Proteomics stuff===
+===Proteomics===
 [http://pubs.acs.org/toc/jprobs/13/1 JPR Jan 2014 C-HPP special issue]

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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