- Microbe - mailman3.cels.anl.gov

Draft Agenda for All hands meeting
by Christopher Henry 25 Mar '13

25 Mar '13

Hello all, Here is the draft agenda for the all hands meeting. Day 1 (just PIs/leads/co-leads) Meghan: Recording secretary 8:30-9:00 Welcome and Goals of the Day (Adam) 9:00-9:30 Summary of what we are trying to accomplish and planning toward renewal; Summary of DOE Feedback (Adam and Rick) 9:30-10:00 Balancing production, functional campaigns, and building towards exciting cross-cutting science goals (Adam and Rick) 10:00-12:00 Deep Dive: What is necessary to move to a production platform for KBase (Rick setting framework/guiding discussion, Nomi: Summarizing actions) 12:00-1:00 Working Lunch: Open discussion of platform and infrastructure production development needs 2:00-4:00 Deep Dive: Managing development to solve the big problems (Adam setting framework/guiding discussion, Sergei: Summarizing actions) 4:00-5:30 Managing the process, building community, and outreach (Rick and Adam set framework and mediate discussion) Day 2 8:00-8:30 Welcome and Goals of the Day (Adam and Rick) 8:30-9:00 Balancing production, campaigns, and building towards cross-cutting science (Adam and Rick) 9:00-10:00 Building platform and infrastructure (Rick, Tom and Shane guided discussion) 10:00-10:30 Break 10:30-11:00 Big science questions: Genotype->Phenotype, Evolution, Ecology and Design (Leads each chalk talk 2-3 big questions to drive organization) 11:00-12:00 Solidifying the platform and first functional campaigns 1: Paramvir and Chris Guide Discussion (thinking across the science domains, advocating for microbes) 12:00-1:00 Working Lunch 1:00-2:00 Solidifying the platform and first functional campaigns 2: Doreen and David Guide Discussion (thinking across the science domains, advocating for plants) 2:00-3:00 Solidifying the platform and first functional campaigns 3: Folker and Dylan Guide Discussion (thinking across the science domains, advocating for communities) (FM: move me to an earlier time in the day please, I have a family thing and might have to leave early on day2) 3:00-3:30 Break 3:30-4:30 Publication, Collaboration, Outreach (Bob Guides) 4:30-5:00 Guided Summary (Adam and Rick) Day 3 Workshops: (Possibles) • Building a true knowledge modeling framework • Discovery and Design in the Plant Microbe Interface • Building a integrative model reconciliation platform: Metabolism, Regulation, Signalling, and Stress with applications to bacteria and algae. • Working across abstractions in KBase: molecules, networks, machine learning and dynamics. Chris

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Re: [Microbe] call today
by Christopher Henry 25 Mar '13

25 Mar '13

The usual number: 866-740-1260 4958182# Sorry, I was a little late. Chris On Mar 25, 2013, at 1:03 PM, "Steven E. Brenner" <brenner(a)compbio.berkeley.edu> wrote: > I'm getting the hold music at 866-740-1260 / 495-8182 > > On Mon, 25 Mar 2013, Matt DeJongh wrote: > >> What is the call number today? >> On Mon, Mar 25, 2013 at 11:57 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >> I'll hold a brief call in case anything has come up that needs discussion. >> Chris >> >> On Mar 25, 2013, at 10:52 AM, "Steven E. Brenner" <brenner(a)compbio.berkeley.edu> wrote: >> >> > Will there be a call today with someone else leading? >> > >> > (I will not be able to make the call next week, as I will be traveling making it 3am local time.) >> > >> > >> > >> > >> > On Mon, 25 Mar 2013, Paramvir Dehal wrote: >> > >> >> I won't be able to make the call today, I'll be at the JGI workshop. >> >> Paramvir >> >> >> > _______________________________________________ >> > Microbe mailing list >> > Microbe(a)lists.kbase.us >> > https://lists.kbase.us/mailman/listinfo/microbe >> >> _______________________________________________ >> 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 >> > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] call today
by Steven E. Brenner 25 Mar '13

25 Mar '13

I'm getting the hold music at 866-740-1260 / 495-8182 On Mon, 25 Mar 2013, Matt DeJongh wrote: > What is the call number today? > > > On Mon, Mar 25, 2013 at 11:57 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > I'll hold a brief call in case anything has come up that needs discussion. > Chris > > On Mar 25, 2013, at 10:52 AM, "Steven E. Brenner" <brenner(a)compbio.berkeley.edu> wrote: > > > Will there be a call today with someone else leading? > > > > (I will not be able to make the call next week, as I will be traveling making it 3am local time.) > > > > > > > > > > On Mon, 25 Mar 2013, Paramvir Dehal wrote: > > > >> I won't be able to make the call today, I'll be at the JGI workshop. > >> Paramvir > >> > > _______________________________________________ > > Microbe mailing list > > Microbe(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/microbe > > _______________________________________________ > 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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Re: [Microbe] call today
by Matt DeJongh 25 Mar '13

25 Mar '13

What is the call number today? On Mon, Mar 25, 2013 at 11:57 AM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > I'll hold a brief call in case anything has come up that needs discussion. > Chris > > On Mar 25, 2013, at 10:52 AM, "Steven E. Brenner" < > brenner(a)compbio.berkeley.edu> wrote: > > > Will there be a call today with someone else leading? > > > > (I will not be able to make the call next week, as I will be traveling > making it 3am local time.) > > > > > > > > > > On Mon, 25 Mar 2013, Paramvir Dehal wrote: > > > >> I won't be able to make the call today, I'll be at the JGI workshop. > >> Paramvir > >> > > _______________________________________________ > > Microbe mailing list > > Microbe(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/microbe > > _______________________________________________ > 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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Re: [Microbe] call today
by Christopher Henry 25 Mar '13

25 Mar '13

I'll hold a brief call in case anything has come up that needs discussion. Chris On Mar 25, 2013, at 10:52 AM, "Steven E. Brenner" <brenner(a)compbio.berkeley.edu> wrote: > Will there be a call today with someone else leading? > > (I will not be able to make the call next week, as I will be traveling making it 3am local time.) > > > > > On Mon, 25 Mar 2013, Paramvir Dehal wrote: > >> I won't be able to make the call today, I'll be at the JGI workshop. >> Paramvir >> > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] call today
by Steven E. Brenner 25 Mar '13

25 Mar '13

Will there be a call today with someone else leading? (I will not be able to make the call next week, as I will be traveling making it 3am local time.) On Mon, 25 Mar 2013, Paramvir Dehal wrote: > I won't be able to make the call today, I'll be at the JGI workshop. > Paramvir > >

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call today
by Paramvir Dehal 25 Mar '13

25 Mar '13

I won't be able to make the call today, I'll be at the JGI workshop. Paramvir

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Re: [Microbe] It's 5pm on Friday, and we just had a 3 hour meeting, so I give you this
by Adam Paul Arkin 23 Mar '13

23 Mar '13

I am pleased to see such a hero shares my lofty initials. 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 Mar 22, 2013, at 4:53 PM, Gavin A Price <gavinaprice(a)gmail.com> wrote: > http://www.youtube.com/watch?v=xDmv7b-NQEI > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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It's 5pm on Friday, and we just had a 3 hour meeting, so I give you this
by Gavin A Price 22 Mar '13

22 Mar '13

http://www.youtube.com/watch?v=xDmv7b-NQEI

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yet another toolbox for semi-automatic metabolic fba model reconstruction
by Michael Sneddon 22 Mar '13

22 Mar '13

This paper just came out. Looks like the toolbox runs in Matlab. Anyone know anything about this project? http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002980

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