User contributions for Vanessa

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9 March 2011

  • 20:2020:20, 9 March 2011 diff hist +2,952‎ N SNP Track QA ‎ New page: If you have any general questions about snps this is a good resource: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq. In addition to the SNP-specific checks on this page, b...
  • 20:1920:19, 9 March 2011 diff hist +26,213‎ N QAing UCSC Genes ‎ New page: == hgGene Page Source Information == Click on the following link to view a sample hgGene page annotated with the sources of the different components: [[Image:hg19uc002ypa.2.pdf|thumb=Imag...
  • 20:1820:18, 9 March 2011 diff hist +1,124‎ N Ensembl QA ‎ New page: There are periodic updates to all Ensembl Genes tracks in all dbs. Here is a list of things to do in addition to the regular QA you would do normally for a track: *Run qaEnsGenes.csh **Ru...
  • 20:1720:17, 9 March 2011 diff hist +8,047‎ N Conservation Track QA ‎ New page: ==Preparing to QA== The Conservation track will consist of one or more of the following subtracks: multiz#way, phyloP, phastCons and Most Conserved/Conserved Elements. Sometimes if there ...
  • 20:1120:11, 9 March 2011 diff hist +8,804‎ N Chains and Nets QA ‎ New page: Category:Browser QA tracks There are two components of chains/nets Chains_Nets: the actual chains/nets themselves and the liftOver directories/files. The liftOver [http://genome.u...
  • 20:0820:08, 9 March 2011 diff hist +2,399‎ N All.joiner problem ‎ New page: There is a problem with all.joiner rules and the -database parameter. This is taken from an email from Ann in 2007: Bob and I just ran into something sneaky with running joinerCheck or r...
  • 19:3019:30, 9 March 2011 diff hist +15,972‎ N New track checklist ‎ New page: This is the checklist for QA to follow when releasing Genome Browser tracks. General rule: stop testing when you come to the first non-trivial error, and bounce the track to the B queue ...
  • 19:2319:23, 9 March 2011 diff hist +72‎ N Category:Browser QA ‎ New page: Genome Browser QA procedures and tools Category:Browser Development
  • 19:1519:15, 9 March 2011 diff hist +1,136‎ N Search robot ‎ New page: One of the robots that runs automatically during the CGI Build Process, is the testSearch robot. The code is kent/src/hg/qa/testSearch.c. testSearch - test search functionality. usag...

8 March 2011

  • 00:2000:20, 8 March 2011 diff hist +3,384‎ N Windows testing machine ‎ New page: We now have remote access to a Windows machine! We can use this machine from the comfort of our own desks for testing CGIs, bug fixes, new features, etc on the win7 operating system. It ...
  • 00:1700:17, 8 March 2011 diff hist +7,702‎ N VI quick start ‎ New page: ==See also:== Graphical [http://www.viemu.com/a_vi_vim_graphical_cheat_sheet_tutorial.html vi/vim Cheat Sheet] ==Insert/Command States== vi is usually either in an 'insert' state, or in...
  • 00:1300:13, 8 March 2011 diff hist +2,755‎ N Updating blat servers ‎ New page: There are 3 places where blat servers are located. Assemblies that are important (eg. human or mouse) and are expected to get a lot of hits are hosted here at UCSC and will have a blat hos...

7 March 2011

  • 23:5023:50, 7 March 2011 diff hist +9,178‎ N UCSC Genes Staging Process ‎ New page: The UCSC Gene set is created at UCSC for three vertebrate organisms: human, mouse, and rat. It is built once during the initial release of a new assembly, then updated sporadically after ...
  • 22:2122:21, 7 March 2011 diff hist +1,408‎ N Training new Browser Staff ‎ New page: (see also: [http://genecats.cse.ucsc.edu/qa/newQaHire.html Getting Started for Browser QA Engineers] and [http://genecats.cse.ucsc.edu/eng/index.html Getting Started for Browser Dev Engin...
  • 22:1022:10, 7 March 2011 diff hist +4,003‎ N Static content for new assemblies ‎ New page: Category:Browser QA ==Static Doc changes for New and Updated Assemblies== After editing the docs for your assembly, test them in your sandbox ('''make user''' at the top of the browse...
  • 21:5621:56, 7 March 2011 diff hist +3,262‎ N Static Page Protocol ‎ New page: Category:Browser QACategory:Browser Development == Files Destined for the Round Robin and Mirrors (Public Documents) == *The made files are located in /usr/local/apache/htdocs (th...
  • 21:5321:53, 7 March 2011 diff hist +4,117‎ N Static Page JS Protocol ‎ New page: Category:Browser QACategory:Browser Development To solve some testing issues, there is a new procedure for hard coded links that go from hgwdev --> hgwbeta --> RR and for those t...
  • 21:2221:22, 7 March 2011 diff hist +3,999‎ N Running joinerCheck for all databases ‎ New page: == Overview == The joinerCheck program is run bi-monthly on all active databases on the hgwbeta machine. Errors that are found may be newly introduced or pre-existing. Corrections to data ...
  • 21:2021:20, 7 March 2011 diff hist +2,336‎ N Replacing old tables with new ones ‎ New page: When you are updating a track that already exists on the public site with new data or a new assembly, follow the steps below sequentially to make sure that the old data and new data are no...
  • 21:1621:16, 7 March 2011 diff hist +29,567‎ N Outdated instructions for releasing an assembly ‎ New page: ==Pre-staging of assembly on hgwbeta== ===Check if chromosome sizes have changed significantly=== * If you are releasing an update to an assembly, check to see if chromosome sizes have ch...
  • 21:1521:15, 7 March 2011 diff hist +1,796‎ N QA Checklist for Cancer Browser ‎ New page: ''This is a rough draft for now'' == QA checklist for tracks on the cancer browser == * Tracks can have both Chromosomes and Genesets as display options, check both ** Occasionally trac...
  • 21:1321:13, 7 March 2011 diff hist +2,589‎ N Pushing trackDb ‎ New page: '''a.k.a. "trackDb and friends"''' Starting with v243 CGIs and the release of the Track Search feature, every time we push the trackDb table, we need to also push the index files that go ...
  • 21:1321:13, 7 March 2011 diff hist +1,495‎ N Post-Release-Checklist ‎ New page: == Post Release Checklist for UCSC Genes == This page capture the things to remember after the release of UCSC Genes for the new assembly. * Update the metadata in hgcentral: ::set hgNea...
  • 21:1021:10, 7 March 2011 diff hist +2,831‎ N Patching a Branch ‎ New page: Edited to use Git and cherry-picking. '''How? ("Who" in parenthesis)''' * ('''QA'''): Find an error in the binaries, determine if it needs to be patched, and alert the Developer. * ('''...
  • 19:5519:55, 7 March 2011 diff hist +29,525‎ N New Assembly Release Process Details ‎ New page: Go to the Push Checklist ==Stage and test on hgwbeta== <ol> <li> If you are releasing an update assembly, check to see if chromosome sizes have changed significa...
  • 19:5319:53, 7 March 2011 diff hist +2,245‎ N Cherry-picking a change in git ‎ New page: Edited for Git and cherry-picking. (Need to ask Hiram about changing the title of the page to remove the cvs branch tag reference in the title of this article.) The CGIs are built onto h...
  • 19:4819:48, 7 March 2011 diff hist +1,592‎ N MakePushQSql.pl ‎ New page: This script was written by Angie. It is a script which assists developers in creating a [http://hgwbeta.cse.ucsc.edu/cgi-bin/qaPushQ qapushq table] for a new ge...
  • 19:3619:36, 7 March 2011 diff hist +4,923‎ N Make your own virtual space ‎ New page: ===So you want to have your own copies of the binaries and your own hgwdev-user.cse.ucsc.edu browser? Here is a walkthrough:=== ====Request a "virtual space" from the cluster-admins:===...
  • 19:3319:33, 7 March 2011 diff hist +1,113‎ N Internet browser testing ‎ New page: Category:Browser QA ==OS/Browser combinations QA has access to:== This is a list of the browser/OS combinations that QA has access to. The (h) annotation means that that person has t...
  • 19:0719:07, 7 March 2011 diff hist +1,618‎ N Genbank updates ‎ New page: To disable genbank updates to an assembly: In addition to removing the assembly name from the hgwbeta.dbs and rr.dbs files, the files here need to be removed: /cluster/data/genbank/data...
  • 19:0519:05, 7 March 2011 diff hist +5,417‎ N Frequently asked mailing list questions ‎ New page: This page is intended to be a collection of previously answered questions on the Genome and Genome-Mirror mailing lists that are useful for answering repeat questions. ==Genome== If a use...
  • 19:0219:02, 7 March 2011 diff hist +1,679‎ N Ensembl Links ‎ New page: ==Creating URL Links to Ensembl== * On the Ensembl details pages, there are links to the Ensembl Transcript ID and Ensembl Protein ID details pages. e.g. Ensembl Gene Link: ENST0000037...
  • 19:0119:01, 7 March 2011 diff hist +4,372‎ N ENCODE QA Checklist ‎ New page: ==Getting Started== # Check kent/src/hg/makeDb/doc/encodeDccHg18/*.txt to determine if/how the file diverges from reality. # Make a list of all tables (new & updated that need to be pushed...
  • 18:5718:57, 7 March 2011 diff hist +22,154‎ N ENCODE QA ‎ New page: ==Getting Started== * Choose a track from the encodePushQ (sub pushQ accessed from pushQ Gateway). * Also claim the [http://redmine.soe.ucsc.edu Redmine] Issue of that track & change statu...
  • 18:5318:53, 7 March 2011 diff hist +2,777‎ N Creating a pushQ Entry ‎ New page: After you have finished creating a track and it is ready for QA, you should add an entry to the qapushq table on hgwbeta. There is a [http://hgwbeta.cse.ucsc.edu/cgi-bin/qaPushQ CGI] for t...
  • 18:5018:50, 7 March 2011 diff hist +18,383‎ N Custom Track Examples ‎ New page: Return to: CGI_Testing All examples below can be pasted directly into the custom tracks input menu for hg18. ==RGB Item Example== <pre> browser position chr7:127471196-127495720 bro...
  • 18:4718:47, 7 March 2011 diff hist +13,130‎ N CGI Testing ‎ New page: Before testing your CGIs, check the [http://genecats.cse.ucsc.edu/builds/versions.html version notes] for recent changes particular to your CGIs. Pay extra attention to the changes when t...
  • 18:4418:44, 7 March 2011 diff hist +2,313‎ N CGI Build Schedule ‎ New page: Go to the CGI Build Process. == Three-week CGI Release Cycle == <TABLE BORDER CELLSPACING=0 CELLPADDING=5 VALIGN="top"> <TR> <TH>Monday</TH> <TH>Tuesda...
  • 18:4118:41, 7 March 2011 diff hist +15,172‎ N CGI Build Process ‎ New page: This page explains the process we use for building and releasing our CGIs. This is done on a three-week schedule. The builds are built into sandboxes which are ...
  • 18:3718:37, 7 March 2011 diff hist +2,717‎ N CBSE citation format ‎ New page: CBSE has requested that we standardise on the PubMed citation format throughout the genome browser. Here is a link to the PubMed Journal Article [http://www.nlm.nih.gov/bsd/policy/cit_for...
  • 18:2918:29, 7 March 2011 diff hist +8,857‎ N BlastTabs ‎ New page: ==When to update the blastTab tables== Update the blastTabs anytime the reference gene track for any of the following species is updated/changed: human, mouse, rat, zebrafish, fly, C. ele...
  • 18:2718:27, 7 March 2011 diff hist +563‎ N Big Bed/Wig QA ‎ New page: == Tools Available for QA of big* tracks == * bigWigToBedGraph — this program converts a bigWig file to ASCII bedGraph format. * bigWigSummary — this program extracts summary ...
  • 18:2218:22, 7 March 2011 diff hist +3,024‎ N Archived assemblies ‎ New page: Older assemblies are archived on the archives server, at [http://genome-archive.cse.ucsc.edu/ genome-archive.cse.ucsc.edu]. However, some metadata about the archived assemblies is kept in...

4 March 2011

1 March 2011

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