Hi Guys, Looking really good. Two quick questions on a skim 1) Are you not going to include point mutations/replacements along with insertions/deletions (given the increasing use of MAGE, etc), 2) In the data file info on media would seem to need to be quantitative so the amount of glucose, etc. should be noted. If there is a time series this might be measured in time. This would seem to be important to the analysis where will that data be kept? Adam From: Christopher Henry <[email protected]> Date: Wed, 4 Apr 2012 16:49:37 -0500 To: 'KBase Microbes List' <[email protected]>, <[email protected]> Subject: [Kbase-devel] Phenotype data format proposal
Hello all,
Attached is the proposal for phenotype data in KBase that was discussed in the developers call today. This is geared towards microbes, but probably works for other cases as well. This is a draft, so modification can certainly be made.
Also, after discussing this with Paramvir and Ben, it¹s been decided that we will also introduce a data format for ³growth phenotypes², which Ben is in charge of formulating. ³Growth Phenotypes² will be highly derived datasets (basically knockouts/fitness pairs). ³Growth Phenotypes² will ultimately be computed from the experimental data-structure described in the attached file, and ³Growth phenotypes² will be used as direct inputs into FBA and Growmatch algorithms.
Chris _______________________________________________ Kbase-devel mailing list [email protected] https://lists.kbase.us/mailman/listinfo/kbase-devel