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

Re: [Microbe] FBA and phenotype simulation tutorials
by Robert Olson 25 Apr '12

25 Apr '12

Would you like these added to the kbase.us tutorials pages? On Apr 25, 2012, at 11:16 PM, Christopher Henry wrote: > Hello all, > > Attached are two simple tutorials for the FBA and phenotype simulation services. > The module is checked in to the fbaServices module in the KBase git repository. > Note, I believe some more tweaking of the input and output datastructures will be needed, but this is pretty close. > > Chris > <runFBA tutorial.txt><simulatePhenotypes Tutorial.txt>_______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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FBA and phenotype simulation tutorials
by Christopher Henry 25 Apr '12

25 Apr '12

Hello all, Attached are two simple tutorials for the FBA and phenotype simulation services. The module is checked in to the fbaServices module in the KBase git repository. Note, I believe some more tweaking of the input and output datastructures will be needed, but this is pretty close. Chris

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Monday meeting notes
by Paramvir Dehal 23 Apr '12

23 Apr '12

*04/23/12: KBase Microbes MeetingAtendees: Paramvir, Bill, Michael, Steven, John-Marc, Chris, Paul, Scott, Matt, Tom Agenda: - Microbes Quarterly Report - KBase Science Review May 2-3rd - Phenotype and FBA services (Chris Henry) - Metabolic Visualizations (Bill Riehl) Quarterly Report & Milestones - Milestone: “Established initial organism pages, including data QC, metabolic, regulatory models for microbial sciences” - Establish web service for the above, preliminary UI elements - widgets, GLAMM - Reconciliation web services ~ May 2nd or so, prototype/initial service. Will be in May 14th build - What about our August Milestones? revise these too - Quarterly Report Google Doc (to be started by Paramvir) - everyone should take a look and contribute - leads of subprojects should take a look at report and make sure your progress is covered & take a look at detailed milestones KBase Science Review - technical review of our implementation - presenters will get a phone call from Paramvir or Chris to discuss - Algorithms and services - User experience component? - Adam and Rick added this, so who knows what they mean! - could be inputs & outputs - ontologies being used Chris will put his FBAServices slides in the KBase Microbes Dropbox folder* KBaseTeam\Microbes Bill will put his GLAMM presentation in the Microbes Dropbox and send an email with some narrative about. KBaseTeam\Microbes Paramvir

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Re: [Microbe] Microbes Call Today
by Paramvir Dehal 23 Apr '12

23 Apr '12

Sorry wrong passcode: *866-740-1260 Code: 4958182 * On Mon, Apr 23, 2012 at 8:17 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > 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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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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