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

Re: [Microbe] unable to call in for today's call
by Adam Paul Arkin 21 May '12

21 May '12

yup= sorry there was an enigma microbes call at 10. A From: <gaprice(a)lbl.gov> Date: Mon, 21 May 2012 15:02:30 -0700 To: <microbe(a)lists.kbase.us> Subject: Re: [Microbe] unable to call in for today's call > > Maybe Adam is referring to a different conference call? The Microbes call is > always at 11. > > -g > > On 5/21/2012 2:45 PM, Steven E. Brenner wrote: >> At 10? >> >> I caught the eclipse at the Lawrence Hall of Science with my daughter. Crazy >> crowded. >> >> On Mon, 21 May 2012, Adam Paul Arkin wrote: >> >> >>> Yes at 10! >>> A >>> >>> From: Pavel Novichkov <psnovichkov(a)lbl.gov> <mailto:[email protected]> >>> Date: Mon, 21 May 2012 11:12:49 -0700 >>> To: John-Marc Chandonia <JMChandonia(a)lbl.gov> <mailto:[email protected]> >>> Cc: Ben Bowen <bpbowen(a)lbl.gov> <mailto:[email protected]> , KBase Microbes >>> List <Microbe(a)lists.kbase.us> <mailto:[email protected]> >>> Subject: Re: [Microbe] unable to call in for today's call >>> >>> Paramvir, Chris, >>> >>> I am online too... >>> Do we have con call today? >>> P. >>> >>> On Monday, May 21, 2012, John-Marc Chandonia <JMChandonia(a)lbl.gov> >>> <mailto:[email protected]> wrote: >>>> > On Mon, May 21, 2012 at 09:01:19AM -0700, Ben Bowen wrote: >>>>> >> I'm at a conference most of this week, and will miss today's >>>>> call. Did >>>>> >> anyone see the eclipse yesterday? Vancouver was smothered in >>>>> heavy fog, >>>>> >> and I think it only darkened by a bit during the eclipse. >>>> > >>>> > I'm online, waiting for a chairperson to start the call. >>>> > >>>> > Yesterday, I drove up to Chico to catch the eclipse--it was fun to >>>> > watch with a crowd of astronomy nerds. >>>> > >>>> > JMC >>>> > -- >>>> > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're >>>> everywhere... >>>> > Physical Biosciences Division, Berkeley National Lab for your >>>> convenience. >>>> > http://www.strgen.org/~jmc/ -- Psi >>>> Corps <*> >>>> > _______________________________________________ Microbe mailing >>>> list Microbe(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/microbe >>> >>> >>> >>> >> >> >> >> _______________________________________________ >> Microbe mailing list >> [email protected]://lists.kbase.us/mailman/listinfo/microbe >> > > _______________________________________________ Microbe mailing list > Microbe(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] unable to call in for today's call
by gaprice＠lbl.gov 21 May '12

21 May '12

Maybe Adam is referring to a different conference call? The Microbes call is always at 11. -g On 5/21/2012 2:45 PM, Steven E. Brenner wrote: > At 10? > > I caught the eclipse at the Lawrence Hall of Science with my daughter. > Crazy crowded. > > On Mon, 21 May 2012, Adam Paul Arkin wrote: > >> Yes--- at 10! >> A >> >> From: Pavel Novichkov <psnovichkov(a)lbl.gov> >> Date: Mon, 21 May 2012 11:12:49 -0700 >> To: John-Marc Chandonia <JMChandonia(a)lbl.gov> >> Cc: Ben Bowen <bpbowen(a)lbl.gov>, KBase Microbes List >> <Microbe(a)lists.kbase.us> >> Subject: Re: [Microbe] unable to call in for today's call >> >> Paramvir, Chris, >> >> I am online too... >> Do we have con call today? >> P. >> >> On Monday, May 21, 2012, John-Marc Chandonia >> <JMChandonia(a)lbl.gov> wrote: >> > On Mon, May 21, 2012 at 09:01:19AM -0700, Ben Bowen wrote: >> >> I'm at a conference most of this week, and will miss today's call. >> Did >> >> anyone see the eclipse yesterday? Vancouver was smothered in >> heavy fog, >> >> and I think it only darkened by a bit during the eclipse. >> > >> > I'm online, waiting for a chairperson to start the call. >> > >> > Yesterday, I drove up to Chico to catch the eclipse--it was fun to >> > watch with a crowd of astronomy nerds. >> > >> > JMC >> > -- >> > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're >> everywhere... >> > Physical Biosciences Division, Berkeley National Lab for your >> convenience. >> > http://www.strgen.org/~jmc/ -- Psi >> Corps <*> >> > _______________________________________________ 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

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Re: [Microbe] unable to call in for today's call
by Steven E. Brenner 21 May '12

21 May '12

At 10? I caught the eclipse at the Lawrence Hall of Science with my daughter. Crazy crowded. On Mon, 21 May 2012, Adam Paul Arkin wrote: > Yes— at 10! > A > > From: Pavel Novichkov <psnovichkov(a)lbl.gov> > Date: Mon, 21 May 2012 11:12:49 -0700 > To: John-Marc Chandonia <JMChandonia(a)lbl.gov> > Cc: Ben Bowen <bpbowen(a)lbl.gov>, KBase Microbes List <Microbe(a)lists.kbase.us> > Subject: Re: [Microbe] unable to call in for today's call > > Paramvir, Chris, > > I am online too... > Do we have con call today? > P. > > On Monday, May 21, 2012, John-Marc Chandonia <JMChandonia(a)lbl.gov> wrote: > > On Mon, May 21, 2012 at 09:01:19AM -0700, Ben Bowen wrote: > >> I'm at a conference most of this week, and will miss today's call. Did > >> anyone see the eclipse yesterday? Vancouver was smothered in heavy fog, > >> and I think it only darkened by a bit during the eclipse. > > > > I'm online, waiting for a chairperson to start the call. > > > > Yesterday, I drove up to Chico to catch the eclipse--it was fun to > > watch with a crowd of astronomy nerds. > > > > JMC > > -- > > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... > > Physical Biosciences Division, Berkeley National Lab for your convenience. > > http://www.strgen.org/~jmc/ -- Psi Corps <*> > > _______________________________________________ Microbe mailing list Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > > >

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Re: [Microbe] unable to call in for today's call
by Adam Paul Arkin 21 May '12

21 May '12

Yes at 10! A From: Pavel Novichkov <psnovichkov(a)lbl.gov> Date: Mon, 21 May 2012 11:12:49 -0700 To: John-Marc Chandonia <JMChandonia(a)lbl.gov> Cc: Ben Bowen <bpbowen(a)lbl.gov>, KBase Microbes List <Microbe(a)lists.kbase.us> Subject: Re: [Microbe] unable to call in for today's call > Paramvir, Chris, > > I am online too... > Do we have con call today? > P. > > On Monday, May 21, 2012, John-Marc Chandonia <JMChandonia(a)lbl.gov> wrote: >> > On Mon, May 21, 2012 at 09:01:19AM -0700, Ben Bowen wrote: >>> >> I'm at a conference most of this week, and will miss today's call. Did >>> >> anyone see the eclipse yesterday? Vancouver was smothered in heavy fog, >>> >> and I think it only darkened by a bit during the eclipse. >> > >> > I'm online, waiting for a chairperson to start the call. >> > >> > Yesterday, I drove up to Chico to catch the eclipse--it was fun to >> > watch with a crowd of astronomy nerds. >> > >> > JMC >> > -- >> > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... >> > Physical Biosciences Division, Berkeley National Lab for your >> convenience. >> > http://www.strgen.org/~jmc/ -- Psi Corps >> <*> >> > _______________________________________________ Microbe mailing list >> Microbe(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] unable to call in for today's call
by Paramvir Dehal 21 May '12

21 May '12

Sorry guys, I'm out of town and forgot to ask someone to take it over. On May 21, 2012 2:12 PM, "Pavel Novichkov" <psnovichkov(a)lbl.gov> wrote: > Paramvir, Chris, > > I am online too... > Do we have con call today? > P. > > On Monday, May 21, 2012, John-Marc Chandonia <JMChandonia(a)lbl.gov> wrote: > > On Mon, May 21, 2012 at 09:01:19AM -0700, Ben Bowen wrote: > >> I'm at a conference most of this week, and will miss today's call. Did > >> anyone see the eclipse yesterday? Vancouver was smothered in heavy fog, > >> and I think it only darkened by a bit during the eclipse. > > > > I'm online, waiting for a chairperson to start the call. > > > > Yesterday, I drove up to Chico to catch the eclipse--it was fun to > > watch with a crowd of astronomy nerds. > > > > JMC > > -- > > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're > everywhere... > > Physical Biosciences Division, Berkeley National Lab for your > convenience. > > http://www.strgen.org/~jmc/ -- Psi > Corps <*> > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Re: [Microbe] unable to call in for today's call
by Pavel Novichkov 21 May '12

21 May '12

Paramvir, Chris, I am online too... Do we have con call today? P. On Monday, May 21, 2012, John-Marc Chandonia <JMChandonia(a)lbl.gov> wrote: > On Mon, May 21, 2012 at 09:01:19AM -0700, Ben Bowen wrote: >> I'm at a conference most of this week, and will miss today's call. Did >> anyone see the eclipse yesterday? Vancouver was smothered in heavy fog, >> and I think it only darkened by a bit during the eclipse. > > I'm online, waiting for a chairperson to start the call. > > Yesterday, I drove up to Chico to catch the eclipse--it was fun to > watch with a crowd of astronomy nerds. > > JMC > -- > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... > Physical Biosciences Division, Berkeley National Lab for your convenience. > http://www.strgen.org/~jmc/ -- Psi Corps <*> >

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Re: [Microbe] unable to call in for today's call
by John-Marc Chandonia 21 May '12

21 May '12

On Mon, May 21, 2012 at 09:01:19AM -0700, Ben Bowen wrote: > I'm at a conference most of this week, and will miss today's call. Did > anyone see the eclipse yesterday? Vancouver was smothered in heavy fog, > and I think it only darkened by a bit during the eclipse. I'm online, waiting for a chairperson to start the call. Yesterday, I drove up to Chico to catch the eclipse--it was fun to watch with a crowd of astronomy nerds. JMC -- John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... Physical Biosciences Division, Berkeley National Lab for your convenience. http://www.strgen.org/~jmc/ -- Psi Corps <*>

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unable to call in for today's call
by Ben Bowen 21 May '12

21 May '12

I'm at a conference most of this week, and will miss today's call. Did anyone see the eclipse yesterday? Vancouver was smothered in heavy fog, and I think it only darkened by a bit during the eclipse. My only Kbase-announcement would be the testing of Chris's FBA services for a significant number of measured growth-phenotypes for mutants and wild-type. It all worked well, and my only hang-up was that some of our medias haven't been defined in the media-database at this point and that it was somewhat challenging recognizing our list of media-definitions with the requirements for the FBA-services. Ben ----------------------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov

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boolean growth server running
by Gavin A Price 20 May '12

20 May '12

Hi all, I have a basic version of the boolean growth service running on Magellan. I'm hoping to get some feedback on the direction I'm going and the features I have, as well as what I'm planning. First rule: Do not share this link outside KBase. The server is running on the Django test server which is not production worthy. Also, the server makes parts of the Microbes Online fitness database visible to the world, and that data is private. That being said, Keith has blessed me running the server as is, so I take no responsibility whatsoever for the disaster that will undoubtedly happen (hi Keith!). Some rudimentary documentation is here: http://140.221.92.10:8000/booleangrowth/api/v1/docs I recommend you read it and the Tastypie link before you interact with the server. There are also some development notes linked that include my to do list and some musings on how to make the service better. Finally, there's a link to the entry point of the server. Any feedback regarding bugs, requested features, the direction I'm planning, etc. are welcomed and, indeed, strongly encouraged. I don't want to to write a bunch of code and then find out no one wants to use it. Thanks, Gavin

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Re: [Microbe] conference call 7 may
by Paramvir Dehal 08 May '12

08 May '12

Thanks Keith! I'll be going for the beginning of the week, Monday to Wednesday. On May 7, 2012 8:43 AM, "Keith Keller" <kkeller(a)lbl.gov> wrote: > Hi all, > > Nice quick call today. Thank you for letting me be Paramvir for an hour. > :) > > Here are my notes, including Chris' build targets for next week. > Please correct me if I miss anything; I was actually writing notes on > physical paper. Old school! Feel free to add on if you weren't on > the call. > > On Mon, May 7, 2012 at 8:03 AM, Christopher Henry <chrisshenry(a)gmail.com> > wrote: > > Sorry I won't be on the call today. Next week, we'll be building: > > 1.) Model reconstruction > > 2.) Model autocompletion > > 3.) Model FBA > > 4.) Model phenotype simulation > > Pavel: not going, working on regulatory reconstruction > Stephen: not going, will have his SIFTER staff contact Keith/Paramvir > Gavin: going, undecided build target > John-Marc: not going, working on interacting with CDM/CS > Bill: going Mon-Thu, working on GLAMM > Michael: going Mon-Thu, undecided build target > Ben: not going, working on interaction data > Keith: going Tue-Thu, working on deploying a subset of MO into Magellan > > Outreach: Brian wants us to think about people and schedule for a 1-2 > day alpha tutorial for close collaborators, probably tentatively > June-ish. Ben has a collaborator in mind; Paramvir and Chris have > people in mind too. We don't want too many people this time around > since we're still new > > Brian also reminded us to work on our workshop reports from the JGI > users meeting. > > Ben gave a quick summary of the review meeting. Chris got FBA and > phenotype comparison services online! Bob also demonstrated a cool > scripting terminal. We talked about the timelines for future builds; > we want to have most of the low level stuff complete by the August > build so that future builds can focus on polishing up and integration. > > That's it! See you Wednesday and/or next week. > > --keith > > -- > Keith Keller > kkeller(a)lbl.gov > Physical Biosciences Division, Lawrence Berkeley National Lab > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

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