- Microbe - mailman3.cels.anl.gov

Microbes Call Today
by Paramvir Dehal 23 Apr '12

23 Apr '12

Just a reminder that we are having a KBase Microbes call today - 11am Pacific/1pm Central/ 2pm Eastern 866-740-1260 Passcode 4952366# We are going to use readytalk, so please connect: http://www.readytalk.com passcode: 4952366 Agenda: 1) Microbial Quarterly Report Milestones 2) Bill presents GLAMM, using readytalk.com 3) Chris introduce document on Phenotype & FBA services Please let me know if there are other items you'd like to add to our agenda. Paramvir

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Re: [Microbe] Phenotype Exchange Data v0.1
by Christopher Henry 22 Apr '12

22 Apr '12

You've got to give me Model SEED compound and media IDs for now though. We can move to KBase IDs later once the prototype services are up (which will be very soon). Dont give me compound names. We will eventually have a separate service that returns compound IDs given input names. -----Original Message----- From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Ben Bowen Sent: Thursday, April 19, 2012 12:08 PM To: KBase Microbes List; Brettin, Thomas S.; Ross Overbeek; KBase developers at LBL/UCB; kbase-devel(a)lists.kbase.us Subject: Re: [Microbe] Phenotype Exchange Data v0.1 Hi All, Regarding the previous mail, thanks to those who have given feedback. Somethings that have come up are which gene & organism ids to use and how to specify the non-obvious waste & utilization reactions in the FBA growth condition description. Issues like requires chloride ions, must dispose of CO2, H2O, etc have been raised. Thoughts? Ben ----------------------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov On Wed, Apr 18, 2012 at 5:39 PM, Ben Bowen <bpbowen(a)lbl.gov> wrote: > Hi All, > > Attached is the following > 1) rationale for the minimum schema necessary to capture phenotype > data > 2) what we think example data would look like > 3) a file that helps to better understand the growth media > > Please advise us on what next steps should be. We are not clear on > the best organism IDs to use, gene ids, or how to supply the > description of growth media. In other words, we don't know if there > is a requirement for a given format or if it is okay to send whatever > we have. This table is a minimal derivation of how we were already > working with the data. > > Thanks, > > Ben > > ----------------------------- > Email: BPBowen(a)lbl.gov > Office: 510-486-5138 > MS 84RO171, Lawrence Berkeley Lab > Web: ms.lbl.gov

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Re: [Microbe] Phenotype Exchange Data v0.1
by Christopher Henry 21 Apr '12

21 Apr '12

In the planned FBA services, essential ions and compounds (e.g. water, chloride, etc) will be added to media by default. As for waste, we typically allow the models to excrete whatever they have a transported for, so there's no need to specify that. Chris -----Original Message----- From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Ben Bowen Sent: Thursday, April 19, 2012 12:08 PM To: KBase Microbes List; Brettin, Thomas S.; Ross Overbeek; KBase developers at LBL/UCB; kbase-devel(a)lists.kbase.us Subject: Re: [Microbe] Phenotype Exchange Data v0.1 Hi All, Regarding the previous mail, thanks to those who have given feedback. Somethings that have come up are which gene & organism ids to use and how to specify the non-obvious waste & utilization reactions in the FBA growth condition description. Issues like requires chloride ions, must dispose of CO2, H2O, etc have been raised. Thoughts? Ben ----------------------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov On Wed, Apr 18, 2012 at 5:39 PM, Ben Bowen <bpbowen(a)lbl.gov> wrote: > Hi All, > > Attached is the following > 1) rationale for the minimum schema necessary to capture phenotype > data > 2) what we think example data would look like > 3) a file that helps to better understand the growth media > > Please advise us on what next steps should be. We are not clear on > the best organism IDs to use, gene ids, or how to supply the > description of growth media. In other words, we don't know if there > is a requirement for a given format or if it is okay to send whatever > we have. This table is a minimal derivation of how we were already > working with the data. > > Thanks, > > Ben > > ----------------------------- > Email: BPBowen(a)lbl.gov > Office: 510-486-5138 > MS 84RO171, Lawrence Berkeley Lab > Web: ms.lbl.gov

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Re: [Microbe] Phenotype Exchange Data v0.1
by Ben Bowen 19 Apr '12

19 Apr '12

Hi All, Regarding the previous mail, thanks to those who have given feedback. Somethings that have come up are which gene & organism ids to use and how to specify the non-obvious waste & utilization reactions in the FBA growth condition description. Issues like requires chloride ions, must dispose of CO2, H2O, etc have been raised. Thoughts? Ben ----------------------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov On Wed, Apr 18, 2012 at 5:39 PM, Ben Bowen <bpbowen(a)lbl.gov> wrote: > Hi All, > > Attached is the following > 1) rationale for the minimum schema necessary to capture phenotype data > 2) what we think example data would look like > 3) a file that helps to better understand the growth media > > Please advise us on what next steps should be. We are not clear on > the best organism IDs to use, gene ids, or how to supply the > description of growth media. In other words, we don't know if there > is a requirement for a given format or if it is okay to send whatever > we have. This table is a minimal derivation of how we were already > working with the data. > > Thanks, > > Ben > > ----------------------------- > Email: BPBowen(a)lbl.gov > Office: 510-486-5138 > MS 84RO171, Lawrence Berkeley Lab > Web: ms.lbl.gov

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Phenotype Exchange Data v0.1
by Ben Bowen 18 Apr '12

18 Apr '12

Hi All, Attached is the following 1) rationale for the minimum schema necessary to capture phenotype data 2) what we think example data would look like 3) a file that helps to better understand the growth media Please advise us on what next steps should be. We are not clear on the best organism IDs to use, gene ids, or how to supply the description of growth media. In other words, we don't know if there is a requirement for a given format or if it is okay to send whatever we have. This table is a minimal derivation of how we were already working with the data. Thanks, Ben ----------------------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov

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4/9 Microbes meeting notes
by Paramvir Dehal 09 Apr '12

09 Apr '12

Attendees: Tom, Steven, Keith, John-Marc, Ross, Matt, Chris, Bill, Keith, Ben, Pavel Agenda: - Phenotype data - Quarterly Reports & milestones - May Science review Phenotype Data - Improve Phenotype Data design spec to link to ModelSEED API in an easier. - will need to move all IDs to KBase space - Work with Bob & Ross to get the IDs correct - Chris will consume data under the assumption the IDs are all KBase - These are for Genomes and Features (i.e. Genes), don’t have media IDs yet - ID Server should be straightforward to convert MicrobesOnline to KBase - KBase Service to translate continuous data to boolean growth, Gavin Price - Vanilla FBA and Phenotype simulation Service up by end of month - Gapfilling & Gap Generation Services will take longer - need to sort out how to maintain long running jobs - should bring this up at next developers call - Can be run on cluster using something like “qSub” - would like to have this completed in May - doc on FBA service in KBase to be written by Chris - internal use for now - brainstorming doc - Sending out Ben’s plan Experiments & Strains - Focus on this after completing Phenotype data necessary for Feb Demo - Meet with more users to define scope - Create use cases beyond, fitness, transcriptomics. Synthetic biology, etc Quarterly Reports - Create initial report for Bob by mid April - Will send out the Microbes Report to the group by this Thursday - Need to talk to Bob & Adam about the divergence of our current tasks and previous - Steven: maybe an external source to fund integrating function prediction Science Review - Present Science Goals to set context - it’s assumed goals are all solid and they will inform how software is designed - Technical Leads for each sub-projects - Implementation plans - 10-20% background, 90-80% nuts and bolts on software - Tom will send out templates used during infrastructure review - Sheryas’ presentation is a good template Next Meeting: - Bill to present on Metabolic Map visualization using GLAMM - Chris will discuss FBA services based off doc he is preparing

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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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