Changes between Version 50 and Version 51 of SatelliteUseCases
- Timestamp:
- 2009/03/20 16:13:55 (16 years ago)
Legend:
- Unmodified
- Added
- Removed
- Modified
-
SatelliteUseCases
v50 v51 13 13 * Keun-Joon Park 14 14 * Yunsun Nam 15 * Arek Kasprzyk 15 * Arek Kasprzyk 16 16 * Syed Haider 17 17 * Shuichi Kawashima … … 45 45 == Notes == 46 46 47 '''Data for testing''' 47 === Data for testing === 48 48 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) 53 53 54 54 55 '''Softwares''' 55 === Softwares === 56 56 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 62 61 63 62 == Meeting log == … … 122 121 == TODOs == 123 122 124 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) 128 127 129 128 === Requests from users to developper === 130 129 131 ==== TO: [http://www.ebi.ac.uk/intact IntAct], Cytoscape )====130 ==== TO: [http://www.ebi.ac.uk/intact IntAct], Cytoscape ==== 132 131 It would be nice if user can retrive PPIs which are expressed in any tissues by using option function. (From: Vachiranee)[[BR]] 133 132 134 * 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. 135 134 136 135 ==== TO: ANNOTATOR ====
