- Microbe - mailman3.cels.anl.gov

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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Re: [Microbe] conference call 7 may
by Keith Keller 07 May '12

07 May '12

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

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Re: [Microbe] conference call 7 may
by Christopher Henry 07 May '12

07 May '12

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 -----Original Message----- From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Keith Keller Sent: Monday, May 07, 2012 9:39 AM To: KBase Microbes List Cc: Tom Brettin Subject: [Microbe] conference call 7 may Hello all, Neither Paramvir nor Chris are available for today's call, but Paramvir asked me to run a very quick call this morning. We have two agenda items: ==Everyone: 2-3 quick sentences on your plan for the build next week, including what days you'll be there ==Tom + anyone who went: a quick summary of the science review last week Usual call in number: 1-866-740-1260 Code: 4958182# (if I can find the admin code--I'm sure I have it somewhere!) --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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conference call 7 may
by Keith Keller 07 May '12

07 May '12

Hello all, Neither Paramvir nor Chris are available for today's call, but Paramvir asked me to run a very quick call this morning. We have two agenda items: ==Everyone: 2-3 quick sentences on your plan for the build next week, including what days you'll be there ==Tom + anyone who went: a quick summary of the science review last week Usual call in number: 1-866-740-1260 Code: 4958182# (if I can find the admin code--I'm sure I have it somewhere!) --keith -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab

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plant metabolite databases
by Ben Bowen 03 May '12

03 May '12

At the meeting today, the concept of plant metabolite data came up. I can't post on their list, but it is worth talking to specific groups at Riken (in Japan) about this. From what I've seen, they have extensively studied plant metabolites with mass spectrometry via a fairly large consortium. I use a service of their's (massbank) which is not specific to plants. While looking around on their site, I found this service that claims 50,000 plant metabolites http://kanaya.naist.jp/KNApSAcK/ I haven't used it though. ----------------------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 MS 84RO171, Lawrence Berkeley Lab Web: ms.lbl.gov

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Re: [Microbe] FBA and phenotype simulation tutorials
by Ben Bowen 02 May '12

02 May '12

It worked! Thanks! localhost:Running_ModelSEED bpb$ perl testRunModelSeed.pl Objective is:80.5696! Metabolite uptake and excretion: Metabolite Uptake cpd00041[e] 100 cpd00067[e] 100 cpd00161[e] 100 cpd00033[e] 100 cpd00249[e] 22.7267 cpd00051[e] 100 cpd00001[e] -100 cpd00009[e] 100 cpd00023[e] 100 cpd00011[e] -514.243 cpd00027[e] 100 cpd00013[e] -675.509 cpd00035[e] 100 cpd00060[e] 12.5816 cpd00182[e] 24.3472 cpd00322[e] 22.765 cpd00156[e] 33.1623 cpd00054[e] 100 cpd03279[e] -188.878 cpd00226[e] -100 cpd00254[e] 0.274645 cpd00007[e] 100 cpd00047[e] -819.516 cpd10516[e] 1.09858 -------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 Cell: 480-225-2341 MS 84RO171, Lawrence Berkeley Lab On Wed, May 2, 2012 at 2:03 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: > OK, the service is now visible at http://bio-data-1.mcs.anl.gov/services/fba > > BTW I tried checking out the code via > > git clone [email protected]:fbaServices.git > > but the module was empty; was that what you meant by the KBase git repo? > > On May 2, 2012, at 3:50 PM, Christopher Henry wrote: > >> I'm running on biologin-4.mcs.anl.gov:5000 >> >> -----Original Message----- >> From: Robert Olson [mailto:[email protected]] >> Sent: Wednesday, May 02, 2012 3:44 PM >> To: Christopher Henry >> Cc: 'Ben Bowen'; 'KBase Microbes List' >> Subject: Re: [Microbe] FBA and phenotype simulation tutorials >> >> I have a proxy server that I redirect to the local bio machine running the >> service; this makes it available to the world. so if you let me know where >> you're running the service I can set up the redirection. >> >> On May 2, 2012, at 3:36 PM, Christopher Henry wrote: >> >>> Well, initially, the service has to run on a computer in BIO >>> environment until we've succeeded in deploying this thing in the cloud >>> at the May integration meeting. >>> Bob, how did you run the plackup services in the BIO environment? >>> >>> -----Original Message----- >>> From: Robert Olson [mailto:[email protected]] >>> Sent: Wednesday, May 02, 2012 2:41 PM >>> To: Christopher Henry >>> Cc: 'Ben Bowen'; 'KBase Microbes List' >>> Subject: Re: [Microbe] FBA and phenotype simulation tutorials >>> >>> Should folks be using that biologin version or are you expecting them >>> to run the service themselves? If the former we'll need to put the >>> service behind the proxy since external access to that port will be >> blocked. >>> >>> On May 2, 2012, at 12:03 AM, Christopher Henry wrote: >>> >>>> Hi Ben, >>>> >>>> You should be able to run the service on any computer anywhere. I'll >>>> look into this tomorrow. >>>> >>>> Chris >>>> >>>> -----Original Message----- >>>> From: Ben Bowen [mailto:[email protected]] >>>> Sent: Tuesday, May 01, 2012 6:30 PM >>>> To: Robert Olson >>>> Cc: Christopher Henry; KBase Microbes List >>>> Subject: Re: [Microbe] FBA and phenotype simulation tutorials >>>> >>>> Is this a port blocking problem? or am I doing something wrong? >>>> Tutorial code attached, and error transcript below. >>>> >>>> localhost:Running_ModelSEED bpb$ perl testRunModelSeed.pl Error >>>> invoking >>>> runfba: 500 Can't connect to >>>> biologin-4.mcs.anl.gov:5000 (connect: Connection refused) at >>>> fbaServicesClient.pm line 57. >>>> >>>> I assume that I need to run this from my kbase login (not my computer >>>> at LBL), but I just wanted to check and make sure. >>>> >>>> Thanks, >>>> >>>> Ben >>>> >>>> -------------- >>>> Email: BPBowen(a)lbl.gov >>>> Office: 510-486-5138 >>>> Cell: 480-225-2341 >>>> MS 84RO171, Lawrence Berkeley Lab >>>> >>>> >>>> On Wed, Apr 25, 2012 at 9:29 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>>>> 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 >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Microbe mailing list >>>>> Microbe(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/microbe >>>>> >>>> >>> >>> >> >> >

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Re: [Microbe] FBA and phenotype simulation tutorials
by Robert Olson 02 May '12

02 May '12

OK, the service is now visible at http://bio-data-1.mcs.anl.gov/services/fba BTW I tried checking out the code via git clone [email protected]:fbaServices.git but the module was empty; was that what you meant by the KBase git repo? On May 2, 2012, at 3:50 PM, Christopher Henry wrote: > I'm running on biologin-4.mcs.anl.gov:5000 > > -----Original Message----- > From: Robert Olson [mailto:[email protected]] > Sent: Wednesday, May 02, 2012 3:44 PM > To: Christopher Henry > Cc: 'Ben Bowen'; 'KBase Microbes List' > Subject: Re: [Microbe] FBA and phenotype simulation tutorials > > I have a proxy server that I redirect to the local bio machine running the > service; this makes it available to the world. so if you let me know where > you're running the service I can set up the redirection. > > On May 2, 2012, at 3:36 PM, Christopher Henry wrote: > >> Well, initially, the service has to run on a computer in BIO >> environment until we've succeeded in deploying this thing in the cloud >> at the May integration meeting. >> Bob, how did you run the plackup services in the BIO environment? >> >> -----Original Message----- >> From: Robert Olson [mailto:[email protected]] >> Sent: Wednesday, May 02, 2012 2:41 PM >> To: Christopher Henry >> Cc: 'Ben Bowen'; 'KBase Microbes List' >> Subject: Re: [Microbe] FBA and phenotype simulation tutorials >> >> Should folks be using that biologin version or are you expecting them >> to run the service themselves? If the former we'll need to put the >> service behind the proxy since external access to that port will be > blocked. >> >> On May 2, 2012, at 12:03 AM, Christopher Henry wrote: >> >>> Hi Ben, >>> >>> You should be able to run the service on any computer anywhere. I'll >>> look into this tomorrow. >>> >>> Chris >>> >>> -----Original Message----- >>> From: Ben Bowen [mailto:[email protected]] >>> Sent: Tuesday, May 01, 2012 6:30 PM >>> To: Robert Olson >>> Cc: Christopher Henry; KBase Microbes List >>> Subject: Re: [Microbe] FBA and phenotype simulation tutorials >>> >>> Is this a port blocking problem? or am I doing something wrong? >>> Tutorial code attached, and error transcript below. >>> >>> localhost:Running_ModelSEED bpb$ perl testRunModelSeed.pl Error >>> invoking >>> runfba: 500 Can't connect to >>> biologin-4.mcs.anl.gov:5000 (connect: Connection refused) at >>> fbaServicesClient.pm line 57. >>> >>> I assume that I need to run this from my kbase login (not my computer >>> at LBL), but I just wanted to check and make sure. >>> >>> Thanks, >>> >>> Ben >>> >>> -------------- >>> Email: BPBowen(a)lbl.gov >>> Office: 510-486-5138 >>> Cell: 480-225-2341 >>> MS 84RO171, Lawrence Berkeley Lab >>> >>> >>> On Wed, Apr 25, 2012 at 9:29 PM, Robert Olson <olson(a)mcs.anl.gov> wrote: >>>> 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 >>>> >>>> >>>> >>>> _______________________________________________ >>>> Microbe mailing list >>>> Microbe(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/microbe >>>> >>> >> >> > >

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