April 2012 - Microbe - mailman3.cels.anl.gov

Limited scope phenotype document
by Christopher Henry 09 Apr '12

09 Apr '12

Limited scope phenotype document

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Re: [Microbe] meeting today! 11am Pacific / 1pm Central / 2pm Eastern
by Paramvir Dehal 09 Apr '12

09 Apr '12

Whoops! I forgot the most important part of the reminder email: 866-740-1260 Code: 4958182# On Mon, Apr 9, 2012 at 8:15 AM, Matt DeJongh <dejongh(a)hope.edu> wrote: > Please send the phone number/passcode. Thanks, > > Matt > > On Mon, Apr 9, 2012 at 11:13 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > > Hi guys, don't forget our call today. Please send me anything that you'd > > like to add to the agenda. Here's what we have so far: > > > > 1) Phenotype data update > > 2) Quarterly Report & Milestone update (due end of April) > > 3) May 2nd/3rd Science Review > > 4) ? > > > > Paramvir > > > > _______________________________________________ > > Microbe mailing list > > Microbe(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/microbe > > > > > > -- > Matt DeJongh, Ph.D. > Computer Science Department > Hope College, Holland, MI 49423 > (616) 395-7429 >

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meeting today! 11am Pacific / 1pm Central / 2pm Eastern
by Paramvir Dehal 09 Apr '12

09 Apr '12

Hi guys, don't forget our call today. Please send me anything that you'd like to add to the agenda. Here's what we have so far: 1) Phenotype data update 2) Quarterly Report & Milestone update (due end of April) 3) May 2nd/3rd Science Review 4) ? Paramvir

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Re: [Microbe] [Kbase-devel] Phenotype data format proposal
by Christopher Henry 04 Apr '12

04 Apr '12

Hi Adam, Great comments. 1.) Nathan's people requested this as well. So yes, I believe we will have a third type called "mutation" where this will be handled. 2.) Media species concentrations collected over time is a very important dataset we need to handle. In the proposed structure, this would be handled in the "Metabolite measures" object, which will be able to handle uptake rates, media concentrations, and intracellular metabolite concentrations collected over time. In fact, I believe we will introduce algorithms that compute average uptake rates based on media concentrations collected over time, as uptake is not actually a directly measureable quantity. In these cases, I think the concentrations listed in the media formulation would be "starting concentrations". Alternatively, it's arguable that we shouldn't put concentrations in the media formulation at all, as these will vary too much. No hard and fast decisions here. Just explaining the thinking behind the proposed structure. Chris From: Adam Paul Arkin [mailto:[email protected]] Sent: Wednesday, April 04, 2012 8:10 PM To: Christopher Henry; 'KBase Microbes List' Subject: Re: [Kbase-devel] Phenotype data format proposal 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 <chrisshenry(a)gmail.com> Date: Wed, 4 Apr 2012 16:49:37 -0500 To: 'KBase Microbes List' <Microbe(a)lists.kbase.us>, <kbase-devel(a)lists.kbase.us> 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, it's been decided that we will also introduce a data format for "growth phenotypes", which Ben is in charge of formulating. "Growth Phenotypes" will be highly derived datasets (basically knockouts/fitness pairs). "Growth Phenotypes" will ultimately be computed from the experimental data-structure described in the attached file, and "Growth phenotypes" will be used as direct inputs into FBA and Growmatch algorithms. Chris _______________________________________________ Kbase-devel mailing list Kbase-devel(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Microbe] [Kbase-devel] Phenotype data format proposal
by Adam Paul Arkin 04 Apr '12

04 Apr '12

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 <chrisshenry(a)gmail.com> Date: Wed, 4 Apr 2012 16:49:37 -0500 To: 'KBase Microbes List' <Microbe(a)lists.kbase.us>, <kbase-devel(a)lists.kbase.us> 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 > Kbase-devel(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/kbase-devel

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Phenotype data format proposal
by Christopher Henry 04 Apr '12

04 Apr '12

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, it's been decided that we will also introduce a data format for "growth phenotypes", which Ben is in charge of formulating. "Growth Phenotypes" will be highly derived datasets (basically knockouts/fitness pairs). "Growth Phenotypes" will ultimately be computed from the experimental data-structure described in the attached file, and "Growth phenotypes" will be used as direct inputs into FBA and Growmatch algorithms. Chris

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