Terry's compbio links
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| ===Personal=== | ===Personal=== | ||
| + | [http://tinyurl.com/terry-activism Terry's Activism Page] | ||
| + | [https://nodapl.styrotopia.net/volunteers SR Legal DB] | ||
| - | 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.washington.edu/facilities/transportation/uwshuttles/slu/schedule SLU-UW schedule] |
| - | [http://www.industrymailout.com/Industry/Redirect.aspx?u=555740&q=490480490&lm=47920697&r=384020&qz=2d68889c931dc3fc88f91f4bc0b38e16 NEST volunteer portal] | + | [http://www.nestseattle.org/our-neighbors/volunteers/volunteer-calendar/ NEST volunteer portal] |
| + | [https://www.life360.com/circles/#/map Phone tracker] | ||
| - | ===ISB specific stuff=== | + | ===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/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://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] | ||
| - | ===Genomics stuff=== | + | [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://picard.sourceforge.net/explain-flags.html SAM flags decoder] | + | |
| - | [http://biobits.org/samtools_primer.html SAMtools Primer] revised July 2013 | + | [https://db.systemsbiology.net/devDC/sbeams/cgi/domybidding.cgi Be apache] on mimas |
| + | ===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] | ||
| + | |||
| + | ===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] | ||
| + | |||
| + | ===ISB: Inova & Family Genomics=== | ||
| + | [https://54.243.235.221/jira/secure JIRA] for reporting issues with ITMI | ||
| + | |||
| + | [http://ilyawiki.systemsbiology.net:8090/display/ISBInova/ISB-INOVA Confluence wiki] for Inova collaboration | ||
| + | |||
| + | [https://trello.com/b/kgG0tLkq/famgen-task-tracker Trello] task tracker | ||
| + | |||
| + | [https://itmi.signin.aws.amazon.com/console Amazon S3] | ||
| + | |||
| + | [https://docs.google.com/a/systemsbiology.org/document/d/1k6LMLPIp5JBSM38VuRsMotGFbwDrdofQtnLm38QL4Jk/edit#heading=h.tqo76n1fjy8z Gestalt user manual] | ||
| + | |||
| + | [http://db.systemsbiology.net/kaviar/ Kaviar] | ||
| + | [https://docs.google.com/document/d/1PCHWWVLl453x9ow76XgDrWVoFXKWJ1JXGhl6hf4d30k/edit How to build Kaviar] | ||
| + | |||
| + | [https://docs.google.com/document/d/1OLsShhl7TeMCBPk6Al6O9sH_n0sgL51OhExVtVwjXTQ/edit RCF specification] | ||
| + | |||
| + | 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 | [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] | [https://www.broadinstitute.org/gatk/about/#typical-workflows Intro to GATK] | ||
| + | [http://bedtools.googlecode.com/files/BEDTools-User-Manual.pdf BEDtools] | ||
| - | [http://supportres.illumina.com/documents/documentation/software_documentation/wgs/services_whole_genome_ug_15040892.pdf Illumina Whole-Genome Sequencing Services User Guide] | + | [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://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=== | ||
| - | ===General programming stuff=== | + | '''git:''' [http://git-scm.com/book/en/ introduction] |
| '''Unix shell:''' [[bash/tcsh syntax differences]] | '''Unix shell:''' [[bash/tcsh syntax differences]] | ||
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| '''Python:''' [http://www.python.org/doc www.python.org/doc]: Helpful links for Python programmers. | '''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. | 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] | '''Drawing Venn Diagrams:''' [http://code.google.com/apis/chart/docs/gallery/venn_charts.html] | ||
| Line 57: | Line 105: | ||
| '''Excel:''' [http://www.likeoffice.com/28057/excel-string String operations] | '''Excel:''' [http://www.likeoffice.com/28057/excel-string String operations] | ||
| - | ===General computational 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://pipe.systemsbiology.net The Pipe] Protein Information and Property Explorer, developed at ISB by Hector Ramos | ||
| Line 70: | Line 122: | ||
| 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. | 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 stuff=== | + | ===General biology=== |
| [http://www.youtube.com/watch?v=52dq2QOTdhs&feature=related Awesome animation of the inner life of the cell] | [http://www.youtube.com/watch?v=52dq2QOTdhs&feature=related Awesome animation of the inner life of the cell] | ||
| Line 105: | Line 157: | ||
| [http://informatics.systemsbiology.net/informatics/mspecLINE mspecLINE]: linking disease to PeptideAtlas | [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] | [http://pubs.acs.org/toc/jprobs/13/1 JPR Jan 2014 C-HPP special issue] | ||
Current revision
Contents |
Terry Farrah's Computational Biology Links
Personal
Terry's Activism Page SR Legal DB
NEST volunteer portal Phone tracker
ISB specific
Mail Intranet PubMed special link ISB library page ISB journal subscriptions Reservations paychexflex (terry.farrah 6char plus that year) ISB contacts
Price Lab wikiPrice Lab bioPrice Lab dropbox
Be apache on mimas
ISB: Metabolic Modeling
Running ProbAnno standalone at ISB (quite obsolete as of Sept. 2016) ProbAnno web server
ISB: BD Spoke grant
ISB: Inova & Family Genomics
JIRA for reporting issues with ITMI
Confluence wiki for Inova collaboration
Trello task tracker
GMS: local ITMI; need to be on ITMI network
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.
