Satellite meeting for use-cases
Topics ¶
Participants¶
Date ¶
- 2009/3/19 15:00-18:00
Room ¶
- Chura Hall (3F)
Presentations ¶
Fill:
- Name of the presenter
o Title of the talk o Attachments (PPT or PDF slides etc.)
Notes ¶
Log of use-case workgroup
Data -SNPs, Affy provided by Prof.Kim
SNPs data come from Affymatrix chip of stroke patients and normal people (contain 262,338 SNPs)
- ANNOTATOR currently cannot analyse on SNPs data directly
- Galaxy ( http://galaxy.esphealth.org/) RGenetics
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
Results ¶
TODOs ¶
