Version 2 (modified by vachiranee, 15 years ago)

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Satellite meeting for Use-cases development and documentation

Topics

Participants

  • Raoul JP Bonnal
  • Toshiaki Katayama
  • Vachiranee Limviphuvadh
  • Tobias Gattermayer
  • Shuichi Kawashima
  • Takeshi Kawashima
  • Arek Kasprzyk
  • Syed Haider
  • Oswaldo Trelles
  • José M. Fernández
  • Paul Gordon
  • Keun-Joon Park
  • Yunsun Nam
  • Young Joo Kim
  • Tatsuya Nishizawa
  • Riu Yamashita
  • Fumikazu Konishi

Targets

Date

  • 2009/3/19 15:00-18:00

Room

  • 3F

Notes

Data -SNPs, Affy provided by Prof.Kim

SNPs data come from Affymatrix chip of stroke patients and normal people (contain 262,338 SNPs)

quality control, ancestry and case-control analysis

BioMart - have to know dataset, filter, attribute - can use Perl API,.. - Martview - DAS access - Martview - can set up server and use in-house

Question - Takeshi asked about how to annoate in-house data with comparing with public genome data using BioMart. - For example, how to annotate Halocynthia roretzi or Molgula tectiformis ESTs comparing with Ciona intestinalis and Ciona savigni using BioMart. Answer - Convert Halocynthia data into BioMart format. Install BioMart server locally. Then merge public DB and local data together. - BioMart format is simple.

Takeshi present - minor animal (closet animal Ciona) - how can analyze Halocynthia roretzi and M.tectiformis which are rare annotation. - type of data is ESTs, assembled EST cluster,etc - potential flow: BioMart -> ANNOTATOR -> TogoDB

DL ESTs of Halocynthia roretzi from NCBI/Taxonomy

TogoDB by Toshiaki - upload table format (table services for uploading data will be able to access using WS)

jORCA by Oswaldo

-mapped WABI services - jORCA: WABI WSDL application can run in local machine after installation - jORCA can tell which kind of analysis can do with our multifasta format file or anykind of format. For example, using Magallanes: INB*, if put "FASTA" in Find box, the result come up with 23 tools that can use for analysis. For analysis use myexperiment.org *Magallanes: INB (Services discovering that discover what kind of analysis can provide for your data format)

ANNOTATOR

- how different between ANNOTATOR and InterProscan? - how can I know the version of each DB use in Prim-seq-algorithm - it would be nice if user can save result in xml format

Results

TODOs

Attachments