User contributions
From WormBaseWiki
Jump to navigationJump to search- 16:04, 29 January 2014 diff hist +216 Website:WormMine Builds Added information about quick fix that handled a missing organisms.xml file.
- 16:02, 29 January 2014 diff hist +29 m Website:WormMine Builds
- 16:01, 29 January 2014 diff hist +1,144 Website:WormMine Builds Added information about InterMine WS240 build.
- 19:22, 25 January 2014 diff hist +229 Administration:Installing WormMine Added quick fix for missing organisms.xml file.
- 19:54, 23 January 2014 diff hist +141 Administration:Installing WormMine Added link to WormMine build wiki log.
- 19:40, 23 January 2014 diff hist +209 Administration:Installing WormMine Added comment about automatic intermine build.
- 19:42, 12 December 2013 diff hist +300 Coding standards Added guidelines to script naming/suffixes.
- 19:34, 12 December 2013 diff hist +253 Documentation and Communication Standards Added a section on fast communication.
- 19:27, 12 December 2013 diff hist +1,492 N Documentation and Communication Standards Basic steps to a doc/communication guideline document.
- 17:28, 12 December 2013 diff hist +90 m Developer documentation Added section about documentation and communication standards.
- 15:27, 12 December 2013 diff hist -9 m Developer documentation Renamed Web Site Development Guidelines to Development Guidelines.
- 23:09, 11 December 2013 diff hist +70 Website:Visualization with ggplot2 of the R-Project Starting R-serve on dev/staging.
- 18:42, 3 December 2013 diff hist +16 Website:WormMine Builds Changed ACeDB dump instructions for user "intermine".
- 16:57, 3 December 2013 diff hist -280 Administration:Installing WormMine Removed question for JD -- version update automated now.
- 16:24, 2 December 2013 diff hist +35 Website:WormMine Builds Added comment about output of prep step.
- 17:30, 29 November 2013 diff hist -210 m Administration:Installing WormMine Removed meaningless error. Has been fixed -- to the best of my knowledge.
- 17:27, 29 November 2013 diff hist -159 Administration:Installing WormMine Added pre-build disk space requirements for WS239, 240.
- 19:59, 27 November 2013 diff hist +347 Website:WormMine Builds Added preliminary pre-processing. instructions
- 17:05, 27 November 2013 diff hist +543 Software Life Cycle: 4. Updating The Production Servers Added instructions for getting an assemblies.json file for a particular release and committing it to the website's repo.
- 20:50, 18 November 2013 diff hist +1,670 Website:WormMine Builds WS240 output of ACeDB dump added.
- 16:27, 18 November 2013 diff hist +328 Website:WormMine Builds Added stub for WS240 ACeDB dump.
- 23:35, 15 November 2013 diff hist +255 Administration:Installing WormMine Added isntruction on how to run the automatic ACeDB dump script.
- 20:26, 13 November 2013 diff hist +35 Administration:Installing WormMine Updated section on starting/stopping Tomcat.
- 19:55, 13 November 2013 diff hist +135 Administration:Installing WormMine Added instruction on running the Tomcat installation script.
- 20:59, 12 November 2013 diff hist +232 Issues-11/12/2013 InterMine/WormMine progress current
- 15:57, 12 November 2013 diff hist +193 Administration:Installing WormMine Added information about the usage of VERSION and PATCH placeholders.
- 20:39, 11 November 2013 diff hist -1,885 Administration:Installing WormMine Added information about the InterMine installation script.
- 19:11, 8 November 2013 diff hist +152 Administration:Installing WormMine Added info that staging/production work should be done as "intermine" user.
- 18:57, 8 November 2013 diff hist +142 Administration:Installing WormMine Adding intermine user.
- 15:46, 8 November 2013 diff hist +28 Administration:Installing WormMine Updated launch command to it's spelled out version.
- 18:57, 6 November 2013 diff hist +142 Website:Visualization with ggplot2 of the R-Project Updated how to start Rserve on dev/staging.
- 15:39, 5 November 2013 diff hist +49 Issues-11/5/2013 Added link to Github ticket.
- 15:39, 5 November 2013 diff hist +267 Issues-11/5/2013 Summary of WormMine WS239-2 build progress.
- 15:36, 5 November 2013 diff hist +309 Issues-11/5/2013 Summary of R visualization progress.
- 20:15, 4 November 2013 diff hist +401 Website:WormMine Builds Added deployment information for WS239-2.
- 19:53, 1 November 2013 diff hist +248 Administration:Installing WormMine Added information about restoring a database build.
- 19:50, 1 November 2013 diff hist +6 m Administration:Installing WormMine Gave intermine_admin LOGIN privilege.
- 19:46, 1 November 2013 diff hist +105 Administration:Installing WormMine Added information about creating an intermine admin user.
- 19:23, 1 November 2013 diff hist -25 Administration:Installing WormMine Added information about the output of "project_build".
- 14:58, 1 November 2013 diff hist +985 N Website:WormMine Builds Added summary info of WS239 build.
- 14:55, 1 November 2013 diff hist +67 Developer documentation Added a sub-section for WormMine build stats.
- 18:10, 31 October 2013 diff hist +190 Administration:Installing WormMine Added TODO note regarding JAVA_OPTS.
- 16:36, 29 October 2013 diff hist +95 Administration:Installing WormMine Commented that keeping "-b" in conjunction with "-l" can take a long time before recovery.
- 16:13, 29 October 2013 diff hist +40 Administration:Installing WormMine Added information about explicit creation of a directory for storing Entrez data.
- 18:13, 28 October 2013 diff hist +163 Administration:Installing WormMine Added note about property files.
- 18:11, 28 October 2013 diff hist +190 Administration:Installing WormMine Note: "build-db" and following resumable actions unclear.
- 19:21, 25 October 2013 diff hist +5,568 Administration:Installing WormMine Reporting series of errors when restoring a DB dump.
- 19:20, 25 October 2013 diff hist +26 Administration:Installing WormMine Added parameters for DB creation when restoring a DB dump.
- 18:51, 25 October 2013 diff hist +122 Administration:Installing WormMine Request for a description of how staging is handled.
- 17:35, 24 October 2013 diff hist -62 Administration:Installing WormMine Added troubleshooting section to build.
- 20:04, 23 October 2013 diff hist +5,616 Administration:Installing WormMine Added question about integration exception.
- 19:25, 23 October 2013 diff hist +370 Administration:Installing WormMine Added development documentation request.
- 19:13, 23 October 2013 diff hist +101 Administration:Installing WormMine Added question about WormMine archives.
- 18:14, 23 October 2013 diff hist +306 Administration:Installing WormMine Added request for documenting AceDB converter.
- 17:27, 23 October 2013 diff hist +293 Administration:Installing WormMine Added questions about branches in the "intermine" repo.
- 17:08, 23 October 2013 diff hist +280 Administration:Installing WormMine Requested list of files that need updating when incrementing the version number.
- 14:44, 23 October 2013 diff hist +208 m Administration:Installing WormMine
- 14:37, 23 October 2013 diff hist +137 Administration:Installing WormMine Updated question with more information when running "../bio/scripts/project_build -b -v -a a_suum-gff3-gene localhost joachim_ws239_2" individually.
- 13:49, 23 October 2013 diff hist +12,444 Administration:Installing WormMine Added question about the build process and missing directory.
- 19:10, 22 October 2013 diff hist +268 Administration:Installing WormMine Added question about specific WormMine Java implementation.
- 18:52, 22 October 2013 diff hist +5,244 Administration:Installing WormMine Added information about executing just the a_suum-gff3-gene action that causes a build error.
- 17:22, 22 October 2013 diff hist +5,352 Administration:Installing WormMine Added question regarding WormMine build.
- 19:35, 21 October 2013 diff hist +136 Administration:Installing WormMine Added question about manual data dump generation and species specificity.
- 17:42, 21 October 2013 diff hist +200 Administration:Installing WormMine Added request that moving from one machine to another machine to continue the build is indicated better.
- 17:35, 21 October 2013 diff hist -1 m Administration:Installing WormMine →Manual queries
- 17:35, 21 October 2013 diff hist +251 Administration:Installing WormMine Added question about manual queries. Unclear what needs to be run.
- 13:55, 21 October 2013 diff hist +334 Administration:Installing WormMine Added questions about migrating to production.
- 19:34, 18 October 2013 diff hist +40 Administration:Installing WormMine Updated BUILD FAILED description with information about WormBase version used.
- 18:50, 18 October 2013 diff hist +147 Administration:Installing WormMine Added question regarding tace failure during dump.
- 18:38, 18 October 2013 diff hist +379 Administration:Installing WormMine →Quick Overview
- 18:32, 18 October 2013 diff hist +98 Administration:Installing WormMine →Quick Overview
- 18:11, 18 October 2013 diff hist +320 Administration:Installing WormMine Added question about ace_classes-test.txt again.
- 16:08, 18 October 2013 diff hist +167 Administration:Installing WormMine Added question about required disk space on a per-directory basis.
- 15:57, 18 October 2013 diff hist +625 Administration:Installing WormMine Added question about tace being killed during AceDB data dumping process.
- 14:32, 18 October 2013 diff hist +493 Administration:Installing WormMine Added troubleshooting section to redeployment build section.
- 20:07, 17 October 2013 diff hist +83 Administration:Installing WormMine →Build Steps (Preliminary Info)
- 19:26, 17 October 2013 diff hist +666 Administration:Installing WormMine Added comment about JSON error.
- 19:23, 17 October 2013 diff hist +244 Administration:Installing WormMine →Acquire and pre-process data files
- 17:59, 17 October 2013 diff hist +450 Administration:Installing WormMine Requesting a basic overflow of the complete mine life-cycle.
- 17:32, 17 October 2013 diff hist +1,904 Administration:Installing WormMine Added question about creating an AceDB dump.
- 16:30, 17 October 2013 diff hist +12 m Administration:Installing WormMine →Generate data files
- 16:30, 17 October 2013 diff hist +358 Administration:Installing WormMine Added question about build processes' hardcoded paths.
- 16:17, 17 October 2013 diff hist +125 Administration:Installing WormMine Added question regarding env vars.
- 15:49, 17 October 2013 diff hist +286 Administration:Installing WormMine Added questions about recovering from build failures.
- 14:48, 17 October 2013 diff hist +351 Administration:Installing WormMine Added questions about the build process.
- 17:51, 16 October 2013 diff hist +398 Administration:Installing WormMine Added information on copying an existing database.
- 16:44, 16 October 2013 diff hist +483 Administration:Installing WormMine Added information about configuring Tomcat port number.
- 16:29, 16 October 2013 diff hist +213 Administration:Installing WormMine Basic instructions on stopping/starting Tomcat.
- 16:04, 16 October 2013 diff hist +102 Administration:Installing WormMine Instructions added for working with the development version of WormBase InterMine.
- 15:40, 7 October 2013 diff hist +65 Administration:Installing WormMine Added not that origin "unmerged" is not defined where it is being used.
- 15:36, 7 October 2013 diff hist +4 Administration:Installing WormMine Changed repo URL on Github, so that everyone can checkout the code.
- 13:55, 7 October 2013 diff hist +285 Unit Testing Added description about required packages for GBrowse testing.
- 13:36, 7 October 2013 diff hist +2,316 Unit Testing Added output of reference set generation for WS239.
- 14:50, 26 September 2013 diff hist +435 Website:Visualization with ggplot2 of the R-Project Added ggplot2 installation instructions.
- 16:25, 19 September 2013 diff hist +148 m Website:GBrowse Set-up on dev.wormbase.org Added comment on replacing/keeping configuration files.
- 16:20, 19 September 2013 diff hist +2,083 N Website:GBrowse Set-up on dev.wormbase.org Instructions on building your own GBrowse installation.
- 15:48, 19 September 2013 diff hist +173 Developer documentation Added link-out to GBrowse installation page tailored to dev setup.
- 19:35, 9 September 2013 diff hist +104 Website:Visualization with ggplot2 of the R-Project Added information about starting Rserve.
- 19:32, 9 September 2013 diff hist -6 m Website:Visualization with ggplot2 of the R-Project
- 19:32, 9 September 2013 diff hist +643 N Website:Visualization with ggplot2 of the R-Project Installation instructions.
- 19:20, 9 September 2013 diff hist +165 m Developer documentation
- 18:49, 4 September 2013 diff hist +2 Unit Testing Bugfix. Documentation for running a particular API test was giving a wrong example.
- 17:08, 3 September 2013 diff hist -4 m Website:Genome Browser Survey
- 19:36, 29 August 2013 diff hist +3,724 GFF Release Data and Changes Added report on WS239. current
- 15:48, 27 August 2013 diff hist +30 m Website:Visualization Library Assessment Highlighted that only D3 can do all chart types.
- 15:44, 27 August 2013 diff hist +361 Website:Visualization Library Assessment Updated lib performance regarding heatmap plotting.
- 14:31, 27 August 2013 diff hist +526 m Website:Visualization Library Assessment Added table template for filling in status of scientific plotting on a per library basis.
- 13:35, 27 August 2013 diff hist +197 N Website:Visualization Library Assessment Created page with 'June 2012 blog post about various JavaScript visualization libraries: [http://kraskniga.blogspot.ca/2012/06/comparison-of-javascript-data.html Comparison of JavaScript Data Visua…'
- 13:33, 27 August 2013 diff hist +127 m Developer documentation Added link-out to visualization assessment.
- 14:54, 26 August 2013 diff hist +143 Unit Testing Added description about how to run individual unit tests.
- 19:25, 1 August 2013 diff hist +11 m Unit Testing
- 19:20, 1 August 2013 diff hist +74 Unit Testing Updated reference set generation output on staging.
- 14:53, 25 July 2013 diff hist +114 Unit Testing Added information about the logfile that is kept for GBrowse tests.
- 15:56, 24 July 2013 diff hist +2,097 Unit Testing Added current output from staging.
- 19:42, 19 July 2013 diff hist +129 Unit Testing Added explanation on how to create the GBrowse reference image set.
- 19:41, 19 July 2013 diff hist +376 Unit Testing Added GBrowse comparative test explanation.
- 13:20, 9 July 2013 diff hist +1,056 Website:Genome Browser Survey Added questions about data content. Added short header with summary of the discussion Todd and I had.
- 16:41, 8 July 2013 diff hist +324 Website:Genome Browser Survey
- 16:34, 8 July 2013 diff hist +177 Website:Genome Browser Survey
- 16:32, 8 July 2013 diff hist +14 Website:Genome Browser Survey
- 16:32, 8 July 2013 diff hist +81 Website:Genome Browser Survey
- 16:29, 8 July 2013 diff hist +696 Website:Genome Browser Survey
- 16:17, 8 July 2013 diff hist +181 Website:Genome Browser Survey
- 16:10, 8 July 2013 diff hist +637 Website:Genome Browser Survey
- 15:39, 8 July 2013 diff hist +222 Website:Genome Browser Survey
- 15:33, 8 July 2013 diff hist +2,263 N Website:Genome Browser Survey Created page with '== Worm Community Survey == This questionnaire will be send to the worm community via SurveyMonkey. '''Q:''' How frequent do you use the current WormBase genome browser? * ever…'
- 14:38, 8 July 2013 diff hist +161 m Developer documentation Added link to impending genome browser survey.
- 13:49, 18 June 2013 diff hist +1,889 Unit Testing Basic unit testing description.
- 20:42, 17 June 2013 diff hist +4 N Unit Testing Created page with 'TODO'
- 20:42, 17 June 2013 diff hist +17 Developer documentation
- 18:08, 30 May 2013 diff hist +252 GFF Release Data and Changes Added SQL commands that explain how I retrieve names from GFF2/GFF3 tables.
- 15:24, 29 May 2013 diff hist +160 GFF Release Data and Changes Format comparison: WS237 vs WS238.
- 14:15, 29 May 2013 diff hist +117 GFF Release Data and Changes Added overview of which datasets contain bioproject IDs as part of their landmark.
- 21:01, 28 May 2013 diff hist +1,051 N GFF Release Data and Changes Started a summary page for tracking data format changes.
- 20:35, 28 May 2013 diff hist +34 Developer documentation →Data Model and Data Development
- 17:45, 21 May 2013 diff hist +123 Issues-5/21/2013