September 2013 - Kbase-microcomm - mailman3.cels.anl.gov

no call today
by Dylan Chivian 26 Sep '13

26 Sep '13

I'm on travel. Next call will be Oct. 17th. Lets use email for any discussion and planning for the SAC. Thanks, - Dylan

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Re: [Kbase-MicroComm] call today?
by Dylan Chivian 19 Sep '13

19 Sep '13

OK. Hanging up. We REALLY have to talk about 1. SAC plans / demo / slides 2. Communities Typed Object design, including MetagenomeAnnotation. It's not enough for us to hear about it through the grapevine. We need to be involved in the design. Which members of your team are working on it? 3. Implications of the MG-RAST RESTful API change on the rest of KBase communities (as far as I can tell, they're the same API). The surprise change broke some of our code. We need warning before everything is replaced! We're talking with Andreas now about how to handle the loss of the abundanceprofile and sequences methods, but it's taking cycles we really don't have to spare right now. Perhaps as a stopgap you could restore those methods? Thanks, - Dylan On Thu, Sep 19, 2013 at 12:08 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > I'll give it 5 more minutes. > > Thanks, > - Dylan > > > > On Thu, Sep 19, 2013 at 12:01 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> I'm here. >> >> Thanks, >> - Dylan >> >> >> >> On Thu, Sep 19, 2013 at 11:45 AM, Dylan Chivian <dcchivian(a)lbl.gov>wrote: >> >>> ... also want to discuss MetagenomeAnnotation object and any other >>> objects you are thinking of adding to the workspace. Also, the new RESTful >>> API. >>> >>> Thanks, >>> - Dylan >>> >>> >>> >>> On Thu, Sep 19, 2013 at 11:44 AM, Dylan Chivian <dcchivian(a)lbl.gov>wrote: >>> >>>> Hi Folker and Andreas, >>>> >>>> are you still on travel? I'd like to discuss SAC plans / demos / slide >>>> decks now since I'll be out of town Sept 24-Oct 11. >>>> >>>> 866-740-1260, pc 4958182 >>>> >>>> Thanks, >>>> - Dylan >>>> >>>> >>> >> >

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Re: [Kbase-MicroComm] call today?
by Dylan Chivian 19 Sep '13

19 Sep '13

I'll give it 5 more minutes. Thanks, - Dylan On Thu, Sep 19, 2013 at 12:01 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > I'm here. > > Thanks, > - Dylan > > > > On Thu, Sep 19, 2013 at 11:45 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> ... also want to discuss MetagenomeAnnotation object and any other >> objects you are thinking of adding to the workspace. Also, the new RESTful >> API. >> >> Thanks, >> - Dylan >> >> >> >> On Thu, Sep 19, 2013 at 11:44 AM, Dylan Chivian <dcchivian(a)lbl.gov>wrote: >> >>> Hi Folker and Andreas, >>> >>> are you still on travel? I'd like to discuss SAC plans / demos / slide >>> decks now since I'll be out of town Sept 24-Oct 11. >>> >>> 866-740-1260, pc 4958182 >>> >>> Thanks, >>> - Dylan >>> >>> >> >

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Re: [Kbase-MicroComm] call today?
by Dylan Chivian 19 Sep '13

19 Sep '13

I'm here. Thanks, - Dylan On Thu, Sep 19, 2013 at 11:45 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > ... also want to discuss MetagenomeAnnotation object and any other objects > you are thinking of adding to the workspace. Also, the new RESTful API. > > Thanks, > - Dylan > > > > On Thu, Sep 19, 2013 at 11:44 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> Hi Folker and Andreas, >> >> are you still on travel? I'd like to discuss SAC plans / demos / slide >> decks now since I'll be out of town Sept 24-Oct 11. >> >> 866-740-1260, pc 4958182 >> >> Thanks, >> - Dylan >> >> >

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Re: [Kbase-MicroComm] call today?
by Dylan Chivian 19 Sep '13

19 Sep '13

... also want to discuss MetagenomeAnnotation object and any other objects you are thinking of adding to the workspace. Also, the new RESTful API. Thanks, - Dylan On Thu, Sep 19, 2013 at 11:44 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > Hi Folker and Andreas, > > are you still on travel? I'd like to discuss SAC plans / demos / slide > decks now since I'll be out of town Sept 24-Oct 11. > > 866-740-1260, pc 4958182 > > Thanks, > - Dylan > >

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call today?
by Dylan Chivian 19 Sep '13

19 Sep '13

Hi Folker and Andreas, are you still on travel? I'd like to discuss SAC plans / demos / slide decks now since I'll be out of town Sept 24-Oct 11. 866-740-1260, pc 4958182 Thanks, - Dylan

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Re: [Kbase-MicroComm] KBase MicroComm call today
by Folker Meyer 12 Sep '13

12 Sep '13

are you guys going to call in? On Sep 12, 2013, at 2:00 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > Here you go. Please be aware that these are still under discussion, so don't take them as final by any means! Also, not sure how the KBase hardening effort affects timetable. > > FY14 > * Metagenomics binning service (reads to pan-genome bins) > > * Pan-genome metabolic modeling (joint with microbes) > > * Prototype ecosystem modeling service based on pan-genome models > > * Comparative analysis services aimed at large-scale comparisons and time series datasets > > * Prototype community engineering services (based on pan-genome models) > > * Community engineering services (Do first step, community engineering hypothesis service) > > > Candidates for FY 15,16 > * Provide tools for microbial community guild discovery and functional dissection. > > * Integration of tools and data for fungal metagenomic analysisExpand microbial community > > * Metabolic modeling to link environmental metabolite profiling (e.g. via stable isotope probing). > > * Provide tools to link microbial community evolutionary to ecological dynamics (e.g. horizontal transfer, strain/haplotype sweeps). > > * Increase phylogenomic support for functional subsystem discovery from environmentally-derived genomes. > > * Metadata integration > > * Ability to use high quality metagenomic contigs from e.g. Moleculo or metagenomic assembly > > > Thanks, > - Dylan > > > > > On Thu, Sep 12, 2013 at 11:44 AM, Patrik D'haeseleer <patrikd(a)gmail.com> wrote: > Would you guys mind sending me a copy of your proposed FY14 milestones? > > Thanks! > > Patrik > > > On Thu, Sep 12, 2013 at 11:28 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > Hi Folker, > > we're on for the call today at 12pm Pacific, right? > > 866-740-1260, pc 4958182 > > I'd like to discuss the FY14 and FY15 milestones I proposed and hear any that you have. Have you had a chance to think about it some more since yesterday? > > Patrik, do you have one preferred email address? I never know which one to use for you ;) > > Thanks, > - Dylan > > >

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Re: [Kbase-MicroComm] KBase MicroComm call today
by Dylan Chivian 12 Sep '13

12 Sep '13

Here you go. Please be aware that these are still under discussion, so don't take them as final by any means! Also, not sure how the KBase hardening effort affects timetable. FY14 * Metagenomics binning service (reads to pan-genome bins) * Pan-genome metabolic modeling (joint with microbes) * Prototype ecosystem modeling service based on pan-genome models * Comparative analysis services aimed at large-scale comparisons and time series datasets * Prototype community engineering services (based on pan-genome models) * Community engineering services (Do first step, community engineering hypothesis service) Candidates for FY 15,16 * Provide tools for microbial community guild discovery and functional dissection. * Integration of tools and data for fungal metagenomic analysisExpand microbial community * Metabolic modeling to link environmental metabolite profiling (e.g. via stable isotope probing). * Provide tools to link microbial community evolutionary to ecological dynamics (e.g. horizontal transfer, strain/haplotype sweeps). * Increase phylogenomic support for functional subsystem discovery from environmentally-derived genomes. * Metadata integration * Ability to use high quality metagenomic contigs from e.g. Moleculo or metagenomic assembly Thanks, - Dylan On Thu, Sep 12, 2013 at 11:44 AM, Patrik D'haeseleer <patrikd(a)gmail.com>wrote: > Would you guys mind sending me a copy of your proposed FY14 milestones? > > Thanks! > > Patrik > > > On Thu, Sep 12, 2013 at 11:28 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > >> Hi Folker, >> >> we're on for the call today at 12pm Pacific, right? >> >> 866-740-1260, pc 4958182 >> >> I'd like to discuss the FY14 and FY15 milestones I proposed and hear any >> that you have. Have you had a chance to think about it some more since >> yesterday? >> >> Patrik, do you have one preferred email address? I never know which one >> to use for you ;) >> >> Thanks, >> - Dylan >> >> >

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Re: [Kbase-MicroComm] KBase MicroComm call today
by Adam Paul Arkin 12 Sep '13

12 Sep '13

We can still edit them. Pleasecwirk together to agree... Think Data milestones New data type New qa/qc services New integration services like enabling effective search New automated data pipelines Service milestones New analytical services New visualizations Resultant workflows enabled: Taxon binned metabolic modeling dirctly from partially asasembled shotgun With quality estimators on compartmentation and metabolic completeness... Etc Please excuse any terseness or errors. This is sent from my mobile. -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO DOE Systems Biology Knowledgebase, http://kbase.us Director, Berkeley Synthetic Biology Institute,http://synbio.berkeley.edu PI and Co-director, Virtual Institute of Microbial Stress and Survival,http://vimss.lbl.gov Investigator, Energy Biosciences Institute,http://energybiosciencesinstitute.org Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov ------------------------------------- On Sep 12, 2013, at 11:36 AM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > I haven't heard anything to that effect, but perhaps he's just talking about FY14? I think FY15 are just supposed to be rough ideas anyway, so should be mutable. Anyway, we can talk about it in a minute. > > Thanks, > - Dylan > > > On Thu, Sep 12, 2013 at 11:30 AM, Folker Meyer <folker(a)anl.gov> wrote: >> Hi Dylan, >> >> yes we are on for the 2pm call. (our time). >> >> I was told by Adam the milestones are final as of last night? Can we still edit them? >> >> >> >> best >> Folker >> On Sep 12, 2013, at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: >> >> > Hi Folker, >> > >> > we're on for the call today at 12pm Pacific, right? >> > >> > 866-740-1260, pc 4958182 >> > >> > I'd like to discuss the FY14 and FY15 milestones I proposed and hear any that you have. Have you had a chance to think about it some more since yesterday? >> > >> > Patrik, do you have one preferred email address? I never know which one to use for you ;) >> > >> > Thanks, >> > - Dylan >> > > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm

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Re: [Kbase-MicroComm] KBase MicroComm call today
by Paramvir Dehal 12 Sep '13

12 Sep '13

I'm still making changes to the Microbes milestones, minor changes, but I think we have until COB today. On Thu, Sep 12, 2013 at 2:30 PM, Folker Meyer <folker(a)anl.gov> wrote: > Hi Dylan, > > yes we are on for the 2pm call. (our time). > > I was told by Adam the milestones are final as of last night? Can we still > edit them? > > > > best > Folker > On Sep 12, 2013, at 1:28 PM, Dylan Chivian <dcchivian(a)lbl.gov> wrote: > > > Hi Folker, > > > > we're on for the call today at 12pm Pacific, right? > > > > 866-740-1260, pc 4958182 > > > > I'd like to discuss the FY14 and FY15 milestones I proposed and hear any > that you have. Have you had a chance to think about it some more since > yesterday? > > > > Patrik, do you have one preferred email address? I never know which one > to use for you ;) > > > > Thanks, > > - Dylan > > > > _______________________________________________ > Kbase-microcomm mailing list > Kbase-microcomm(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-microcomm >

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