Difference between revisions of "WebDev 2009.10.21-Agenda and Minutes"

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== 1. Administration (Todd, 5 minutes) ==
 
== 1. Administration (Todd, 5 minutes) ==
WS207 - in production <br>
+
WS207 - in production  
- some hardware problems with production notes -> will resolve shortly <br>
+
* some hardware problems with production nodes -> will resolve shortly  
- working on things for Friday meeting (postponed) <br>
+
* working on things for Friday meeting (postponed)
  
 
== 2. WS207 Development progress, paralog display (Norie; 10 minutes) ==
 
== 2. WS207 Development progress, paralog display (Norie; 10 minutes) ==
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* Paralog sections to the orthology page
 
* Paralog sections to the orthology page
 
* Table of paralogs:
 
* Table of paralogs:
gathered biological processes annotations<br>
+
** gathered biological processes annotations<br>
listed in terms of diff/similarities to the gene
+
** listed in terms of diff/similarities to the gene
  
 
* Search algorithm for ontologies - diseases
 
* Search algorithm for ontologies - diseases
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== 3. nBrowse, pathway visualization progress (Xiaoqi; 10 minutes) ==
 
== 3. nBrowse, pathway visualization progress (Xiaoqi; 10 minutes) ==
 +
* Created pathway page w/ related reactome & nemapath info
 +
** linked through function section on gene page
 +
** Bannon site still blocked by firewall
 +
** LS: beta test Cytoscape lite along with nBrowse
 +
** ND: will install nBrowse 1 since no installation package for nBrowse2
 +
* Updated bitbucket issues - TH will look at them
  
 
== 4. modENCODE migration progress (Abby; 10 minutes) ==
 
== 4. modENCODE migration progress (Abby; 10 minutes) ==
 +
* SAM/BAM data is displayed, using track sharing to show multiple tracks since each BAM file needs a separate config file
 +
* However, shared tracks always zoomed in
 +
** LS: will be fixed
 +
* TH: will move to GB2 for WS209 early Dec
 +
* Goal: have all modENCODE tracks on WormBase by data freeze via track sharing
  
 
== 5. WormMart status and timeline (Zheng; 10 minutes) ==
 
== 5. WormMart status and timeline (Zheng; 10 minutes) ==
 +
* 195 - most recent build of WormMart
 +
* Will manually create 200 and 2004, will try scripting 205 to be fully automated
 +
* will put code for bioMart build in svn
 +
* TH: setting up machine for Mart - ZZ will send appropriate config info
 +
* Working on Chado migration

Latest revision as of 10:19, 22 October 2009

Agenda

1. Administration (Todd, 5 minutes)

WS207 - in production

  • some hardware problems with production nodes -> will resolve shortly
  • working on things for Friday meeting (postponed)

2. WS207 Development progress, paralog display (Norie; 10 minutes)

  • Paralog sections to the orthology page
  • Table of paralogs:
    • gathered biological processes annotations
    • listed in terms of diff/similarities to the gene
  • Search algorithm for ontologies - diseases
  • TH: incorporate obj to disease: search by these terms
  • LS: Add treefam picture - link to txt (maybe mouseover to highlight paragraph)

3. nBrowse, pathway visualization progress (Xiaoqi; 10 minutes)

  • Created pathway page w/ related reactome & nemapath info
    • linked through function section on gene page
    • Bannon site still blocked by firewall
    • LS: beta test Cytoscape lite along with nBrowse
    • ND: will install nBrowse 1 since no installation package for nBrowse2
  • Updated bitbucket issues - TH will look at them

4. modENCODE migration progress (Abby; 10 minutes)

  • SAM/BAM data is displayed, using track sharing to show multiple tracks since each BAM file needs a separate config file
  • However, shared tracks always zoomed in
    • LS: will be fixed
  • TH: will move to GB2 for WS209 early Dec
  • Goal: have all modENCODE tracks on WormBase by data freeze via track sharing

5. WormMart status and timeline (Zheng; 10 minutes)

  • 195 - most recent build of WormMart
  • Will manually create 200 and 2004, will try scripting 205 to be fully automated
  • will put code for bioMart build in svn
  • TH: setting up machine for Mart - ZZ will send appropriate config info
  • Working on Chado migration