Changes between Version 50 and Version 51 of SatelliteUseCases

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Timestamp:
2009/03/20 16:13:55 (15 years ago)
Author:
shuichi
Comment:

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  • SatelliteUseCases

    v50 v51  
    1313 * Keun-Joon Park 
    1414 * Yunsun Nam 
    15  * Arek Kasprzyk  
     15 * Arek Kasprzyk 
    1616 * Syed Haider 
    1717 * Shuichi Kawashima 
     
    4545== Notes == 
    4646 
    47 '''Data for testing''' 
     47=== Data for testing === 
    4848 
    49 1) SNPs data contain 262,338 SNPs (Stroke patient vs. normal) from Affymetrix SNP Chip (provided by Prof.Kim)[[BR]] 
    50 2) Amino acid sequences of 53 genes (multifasta format) which are located at disease map locus of one form of epilepsy (provided by Vachiranee)[[BR]] 
    51 3) Nucleotide sequences (multifasta format) (provided by Riu)[[BR]] 
    52 4) Genome data (provided by Takeshi)[[BR]] 
     49 * SNPs data contain 262,338 SNPs (Stroke patient vs. normal) from Affymetrix SNP Chip (provided by Prof.Kim) 
     50 * Amino acid sequences of 53 genes (multifasta format) which are located at disease map locus of one form of epilepsy (provided by Vachiranee) 
     51 * Nucleotide sequences (multifasta format) (provided by Riu) 
     52 * Genome data (provided by Takeshi) 
    5353 
    5454 
    55 '''Softwares'''  
     55=== Softwares === 
    5656 
    57 1) BioMart[[BR]] 
    58 2) Galaxy[[BR]] 
    59 3) jORCA[[BR]] 
    60 4) ANNOTATOR[[BR]] 
    61  
     57 * BioMart 
     58 * Galaxy 
     59 * jORCA 
     60 * ANNOTATOR 
    6261 
    6362== Meeting log == 
     
    122121== TODOs == 
    123122 
    124 1) How to combine the inhouse data into Public BioMart? => KAAS, blast2GO etc.[[BR]] 
    125 2) How easy to install the BioMart in local?[[BR]] 
    126 3) How modify the design of the interface of TogoDB?[[BR]] 
    127 4) User didn't have their own Data Repository site. (for TogoDB)[[BR]] 
     123 * How to combine the inhouse data into Public BioMart? => KAAS, blast2GO etc. 
     124 * How easy to install the BioMart in local? 
     125 * How modify the design of the interface of TogoDB? 
     126 * User didn't have their own Data Repository site. (for TogoDB) 
    128127 
    129128=== Requests from users to developper === 
    130129 
    131 ==== TO: [http://www.ebi.ac.uk/intact IntAct], Cytoscape) ==== 
     130==== TO: [http://www.ebi.ac.uk/intact IntAct], Cytoscape ==== 
    132131It would be nice if user can retrive PPIs which are expressed in any tissues by using option function. (From: Vachiranee)[[BR]] 
    133132 
    134    *At this moment the only way that Bruno@!IntAct knows of doing this is to get the list of proteins from a specific tissue (using [http://www.ebi.ac.uk/pride PRIDE]) and then using the list of proteins accessions to find PPIs in the molecular interaction databases, such as [http://www.ebi.ac.uk/intact IntAct]. If there is interest, we (!IntAct) could find a way to include this option in a future release. 
     133   * At this moment the only way that Bruno@!IntAct knows of doing this is to get the list of proteins from a specific tissue (using [http://www.ebi.ac.uk/pride PRIDE]) and then using the list of proteins accessions to find PPIs in the molecular interaction databases, such as [http://www.ebi.ac.uk/intact IntAct]. If there is interest, we (!IntAct) could find a way to include this option in a future release. 
    135134 
    136135==== TO: ANNOTATOR ====