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iPG2P Visual Analytics Meeting

October 15, 2009, 12pm EDT

Attendees: Nick Provart, Adam Kubach, Lenny Heath, Nirav Merchant, Ruth Grene, Tom Brutnell, Steve Welch, Eric Lyons, Chris Jordan

Action Items:

  1. Nick to research/compare/contrast what Eric Lyons does for ortholog finding
  2. Tom and Nick to look into MinSeq and see if it can be derived from SAM forma


Item 1: Nick presents tool

Nick gave a presentation about Bio_array Recourse DataViz Tools and slides can be found here .   Ortholog identification is done by themselves (might be nice to compare with what Eric does); Tom: getting ontologies is never ending; MinSeq: developed by NCBI for capturing info about mRNA datasets; can it be generated from a SAM file?  They have created another tool that shows protein interactions/co-expression (might present while at TACC)

Item 2: Tom presents PageMan

Tom gave a presentation of PageMan and slides can be found here ; looking at expression of genes along leaf development gradient.  Want to overlay metabolite data on transcription data; Working on GPML; Clustering methods are not worked out yet so don’t know what work bests; clustering algorithm needs to take into account biological information

Item 3:Mutual UnderstandingStart with basic underpinnings (remember CS will be there to learn vocabulary, will need to start far enough back, encourage to ask questions, people will have to tailor presentations on fly based on questions that are being asked, need to give them option to extend thoughts that we’ve had, provide them with opportunity to extend and innovated).  Ruth will do introduction into biology, little on plant biochemistry and morphology, Tom will start with photosynthesis

Tom chat with Nick about how do you want to view the data or other ways to view data before going to TACC


Homework/Action Items

  1. Nick presents his tool as applied to generating heat maps depicting sets of expressed genes.
  2. Tom presents PageMan, and his NGS work.
  3. Discussion of mutual education, if there is time


Topic: iPG2P Visual Analtyics Meeting
Date: Every Thursday, from Thursday, October 15, 2009 to no end date
Time: 9:00 am, Mountain Standard Time (GMT -07:00, Arizona)
Meeting Number: 754 536 751
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