galaxy-proteomics

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galaxy-proteomics@lists.galaxyproject.org

February 2015

3 participants
2 discussions

sqlite datatype
by Jorrit Boekel 13 Feb '15

13 Feb '15

Hi JJ and mailing list, I think it was John who mailed earlier about implementing an SQLite datatype for proteomics. I sort of like this, since I find myself using SQLite all the time for my own command line tool to do filtering, protein grouping, and relating quant output to ID data. https://github.com/glormph/msstitch — I basically wrote this to combine percolator, mzidentml, and openMS intermediate formats. It’s currently a bit of a mixture of different databases and tables for different operations, but maybe it would be a good idea to have one large proteomics experiment SQLite database. Note that this is nothing I want to push onto people like it would be the next PSI standard, more like a very convenient and fast intermediate datatype. I believe that the proteome discoverer msf files are also based on sqlite. While I’m not sure if it’s a good fit for a server environment since it can get locking/access problems when accessed by too many processes, it’s a very nice fit for a bioinformatic cli tool. Are you guys currently working on any standardized SQLite thing? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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galaxy community conference
by Jorrit Boekel 13 Feb '15

13 Feb '15

Hi all, Before I start planning my attendance, are Galaxy proteomics people going to be at the GCC in Norwich? cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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