- Microbe - mailman3.cels.anl.gov

Re: [Microbe] call today?
by Steven E. Brenner 22 Oct '12

22 Oct '12

Sorry I missed -- I just got back from Asia and a power outage at home during this time meant I didn't get the messages (and couldn't call). On Mon, 22 Oct 2012, Christopher Henry wrote: > Yes. I will run the call. > The agenda is just an update on all currently active projects and progress towards end-of-November build. > > Chris > > On Oct 22, 2012, at 11:49 AM, John-Marc Chandonia wrote: > >> Are we on for the 11 am KBase Microbes call today? I think Paramvir >> is in transit. >> >> 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] call today?
by Christopher Henry 22 Oct '12

22 Oct '12

Yes. I will run the call. The agenda is just an update on all currently active projects and progress towards end-of-November build. Chris On Oct 22, 2012, at 11:49 AM, John-Marc Chandonia wrote: > Are we on for the 11 am KBase Microbes call today? I think Paramvir > is in transit. > > 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] call today?
by Gavin Price 22 Oct '12

22 Oct '12

Paramvir said we're having a call - I presume he's going to send out call info soon. -g On 10/22/2012 9:49 AM, John-Marc Chandonia wrote: > Are we on for the 11 am KBase Microbes call today? I think Paramvir > is in transit. > > JMC > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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call today?
by John-Marc Chandonia 22 Oct '12

22 Oct '12

Are we on for the 11 am KBase Microbes call today? I think Paramvir is in transit. 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] Fwd: Phenotype reconciliation workflow
by Adam Paul Arkin 10 Oct '12

10 Oct '12

Nice! Please forgive any terseness. This is sent from my mobile device. 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 Director, The Synthetic Biology Institute, http://symbiotic.berkeley.edu CEO/CSO, The DOE Systems Biology Knowledgebase, http://kbase.us PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov Director of Bioinformatics, The Joint Bioenergy Institute, http://jbei.lbl.gov Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Office: 309B Hildebrand Hall (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS Stanley-922 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 Oct 10, 2012, at 12:25 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Hello all, > > I sent this to Paramvir and Ben, but I realize it may be of general interest. It's just an enhanced detailed workflow of the phenotype reconciliation process I think we need to really handle Adam D.'s data. > > Chris > <PhenotypeReconciliationWorkflow.pptx> > > Begin forwarded message: > >> From: Christopher Henry <chrisshenry(a)gmail.com> >> Date: October 10, 2012 12:43:03 AM CDT >> To: Ben Bowen <ben.bowen(a)gmail.com> >> Cc: Paramvir Dehal <psdehal(a)lbl.gov>, Ross Overbeek <rossoverbeek(a)gmail.com> >> Subject: Phenotype reconciliation workflow >> >> So I've been thinking this over. I don't think the problem is so difficult or underdetermined as we originally thought. Check out the attached workflow (start at purple box... red and green boxes are endpoints). This is what we need to implement to handle Adam D.'s data, and while it looks complex, I actually don't think it's that bad... each individual step is pretty straightforward, and many steps don't involve incredibly complex modeling (I particularly like the idea of seeking reaction essentiality patterns that match gene essentiality patterns...). I think our mistake was to think we should try and handle all phenotypes the same way... We have three distinct classes of phenotypes that should be handled differently: >> >> 1.) Wildtype growth condition phenotypes - the Biolog scenario (pretty easy to handle) >> 2.) Gene essentiality phenotypes (harder to handle, but offers chance to make new annotations) >> 3.) Multi-gene KO phenotypes (very tough to handle... almost certainly must be handled one-by-one manually... at least until we have good pipelines for (1) and (2) >> >> So we just handle things in the right order: >> >> 1.) Wildtype phenotypes >> 2.) Single gene KO phenotypes >> -Genes with confident annotations >> -Genes with unconfident or no annotations >> 3.) Multigene KO phenotypes >> >> On Oct 9, 2012, at 8:48 AM, Ben Bowen wrote: >> >>> Agreed. Just a little bit of book-keeping will be of huge service >>> -------------- >>> Email: BPBowen(a)lbl.gov >>> Phone: (510) 214-6683 >>> MS 977-221, Lawrence Berkeley Lab >>> Web: ms.lbl.gov >>> >>> >>> On Mon, Oct 8, 2012 at 10:47 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>> I agree the mapping of genes based on phenotypes is a concern. I think it should be possible, but we'll need to combine the modeling with some heuristics based on pre-analysis of the data. >>> Chris >>> >>> On Oct 8, 2012, at 5:26 PM, Ben Bowen wrote: >>> >>>> I'm tingling with anticipation. FYI: I gapfilled to grown on alanine as C and N source and it added alanine ABC transporter. seems reasonable. >>>> >>>> There is a layer that we need to put something together for. Given a list of gap-filled reactions, go back to the gene-fitness data and identify candidate genes that are responsible for the function. If you look at the matrix of fitness data and some added reactions, can you really pick out which gene is responsible? In the alanine example above, there are 100s of essential genes, and many won't have known function. I've been trying to sort out the mechanics of this. Hopefully, on Wednesday, I'll have some kind of rational approach sorted out. >>>> >>>> >>>> -------------- >>>> Email: BPBowen(a)lbl.gov >>>> Phone: (510) 214-6683 >>>> MS 977-221, Lawrence Berkeley Lab >>>> Web: ms.lbl.gov >>>> >>>> >>>> On Mon, Oct 8, 2012 at 2:58 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>>> Sorry I missed this call today. I've had an extremely busy couple of weeks. I've been working alot on the gapfilling commands, with some big improvements that you should appreciate Ben. >>>> I'm working on writing detailed tutorials of the new process, but essentially gapfilling is now split over two steps: (i) gapfill which identifies one or more solutions to resolve a false negative, and (ii) managesol which shows all current gapfilling solutions for a model and allows you to delete solutions or specify solutions for integration in the model. See the example output below. >>>> >>>> Now you can begin to imagine the next step in implementing our reconciliation pipeline: batch gapfilling creates solutions for all false negative conditions, and managesol allows you to see and select solutions for implementation. I'll also add an ability to simulate all gapfilling solutions against phenotype data so they can be assessed based on their ability to replicate experiments. The final step will be to automate the selection of an ideal cross section of solutions to fit phenotype data. >>>> >>>> >>>> 1.) model gapfill testmodel --media Media2 >>>> ********************************************* >>>> Gapfilling formulation: GF9 >>>> Media: Media2 >>>> --------------------------------------------- >>>> 1 gapfilling solution(s) found. >>>> --------------------------------------------- >>>> New gapfilling solution: GF9.0 >>>> Solution cost:2 >>>> Gapfilled reactions 2{ >>>> ID Direction Equation >>>> rxn8[c] < (1) A name[c] <=> (1) D name[c] >>>> rxn4[c] > (1) D name[e] <=> (1) D name[c] >>>> } >>>> --------------------------------------------- >>>> >>>> --Note: the solution is saved in the model automatically, but not yet integrated.... you view and integrate solutions using the "managesol" command: >>>> >>>> 2.) model managesol testmodel >>>> ********************************************* >>>> No unintegrated gap generation studies! >>>> ********************************************* >>>> ********************************************* >>>> 10 unintegrated gapfilling studies! >>>> ********************************************* >>>> Gapfilling formulation: GF0 >>>> Media: Complete >>>> --------------------------------------------- >>>> 1 gapfilling solution(s) found. >>>> --------------------------------------------- >>>> New gapfilling solution: GF0.0 >>>> Solution cost:2 >>>> Gapfilled reactions 2{ >>>> ID Direction Equation >>>> rxn2[c] > (1) B name[e] <=> (1) B name[c] >>>> rxn8[c] > (1) A name[c] <=> (1) D name[c] >>>> } >>>> --------------------------------------------- >>>> ********************************************* >>>> Gapfilling formulation: GF1 >>>> Media: Media2 >>>> --------------------------------------------- >>>> 1 gapfilling solution(s) found. >>>> --------------------------------------------- >>>> New gapfilling solution: GF1.0 >>>> Solution cost:2 >>>> Gapfilled reactions 2{ >>>> ID Direction Equation >>>> rxn8[c] < (1) A name[c] <=> (1) D name[c] >>>> rxn4[c] > (1) D name[e] <=> (1) D name[c] >>>> } >>>> --------------------------------------------- >>>> >>>> On Oct 8, 2012, at 12:58 PM, Ben Bowen wrote: >>>> >>>>> I would be happy to give a brief update on the phenotype simulations >>>>> -------------- >>>>> Email: BPBowen(a)lbl.gov >>>>> Phone: (510) 214-6683 >>>>> MS 977-221, Lawrence Berkeley Lab >>>>> Web: ms.lbl.gov >>>>> >>>>> >>>>> On Mon, Oct 8, 2012 at 10:53 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: >>>>> Hey guys, >>>>> >>>>> Sorry for the short notice, we have a microbes call in 10min. The only >>>>> thing I have for the agenda is to talk about keeping track of our >>>>> needs and making sure we get help from Tom, Nomi and others. Let me >>>>> know if you have additional agenda items. >>>>> >>>>> 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 > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] Fwd: Phenotype reconciliation workflow
by Rick Stevens 10 Oct '12

10 Oct '12

thanks Chris. On Oct 10, 2012, at 2:25 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Hello all, > > I sent this to Paramvir and Ben, but I realize it may be of general interest. It's just an enhanced detailed workflow of the phenotype reconciliation process I think we need to really handle Adam D.'s data. > > Chris > <PhenotypeReconciliationWorkflow.pptx> > Begin forwarded message: > >> From: Christopher Henry <chrisshenry(a)gmail.com> >> Date: October 10, 2012 12:43:03 AM CDT >> To: Ben Bowen <ben.bowen(a)gmail.com> >> Cc: Paramvir Dehal <psdehal(a)lbl.gov>, Ross Overbeek <rossoverbeek(a)gmail.com> >> Subject: Phenotype reconciliation workflow >> >> So I've been thinking this over. I don't think the problem is so difficult or underdetermined as we originally thought. Check out the attached workflow (start at purple box... red and green boxes are endpoints). This is what we need to implement to handle Adam D.'s data, and while it looks complex, I actually don't think it's that bad... each individual step is pretty straightforward, and many steps don't involve incredibly complex modeling (I particularly like the idea of seeking reaction essentiality patterns that match gene essentiality patterns...). I think our mistake was to think we should try and handle all phenotypes the same way... We have three distinct classes of phenotypes that should be handled differently: >> >> 1.) Wildtype growth condition phenotypes - the Biolog scenario (pretty easy to handle) >> 2.) Gene essentiality phenotypes (harder to handle, but offers chance to make new annotations) >> 3.) Multi-gene KO phenotypes (very tough to handle... almost certainly must be handled one-by-one manually... at least until we have good pipelines for (1) and (2) >> >> So we just handle things in the right order: >> >> 1.) Wildtype phenotypes >> 2.) Single gene KO phenotypes >> -Genes with confident annotations >> -Genes with unconfident or no annotations >> 3.) Multigene KO phenotypes >> >> On Oct 9, 2012, at 8:48 AM, Ben Bowen wrote: >> >>> Agreed. Just a little bit of book-keeping will be of huge service >>> -------------- >>> Email: BPBowen(a)lbl.gov >>> Phone: (510) 214-6683 >>> MS 977-221, Lawrence Berkeley Lab >>> Web: ms.lbl.gov >>> >>> >>> On Mon, Oct 8, 2012 at 10:47 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>> I agree the mapping of genes based on phenotypes is a concern. I think it should be possible, but we'll need to combine the modeling with some heuristics based on pre-analysis of the data. >>> Chris >>> >>> On Oct 8, 2012, at 5:26 PM, Ben Bowen wrote: >>> >>>> I'm tingling with anticipation. FYI: I gapfilled to grown on alanine as C and N source and it added alanine ABC transporter. seems reasonable. >>>> >>>> There is a layer that we need to put something together for. Given a list of gap-filled reactions, go back to the gene-fitness data and identify candidate genes that are responsible for the function. If you look at the matrix of fitness data and some added reactions, can you really pick out which gene is responsible? In the alanine example above, there are 100s of essential genes, and many won't have known function. I've been trying to sort out the mechanics of this. Hopefully, on Wednesday, I'll have some kind of rational approach sorted out. >>>> >>>> >>>> -------------- >>>> Email: BPBowen(a)lbl.gov >>>> Phone: (510) 214-6683 >>>> MS 977-221, Lawrence Berkeley Lab >>>> Web: ms.lbl.gov >>>> >>>> >>>> On Mon, Oct 8, 2012 at 2:58 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>>> Sorry I missed this call today. I've had an extremely busy couple of weeks. I've been working alot on the gapfilling commands, with some big improvements that you should appreciate Ben. >>>> I'm working on writing detailed tutorials of the new process, but essentially gapfilling is now split over two steps: (i) gapfill which identifies one or more solutions to resolve a false negative, and (ii) managesol which shows all current gapfilling solutions for a model and allows you to delete solutions or specify solutions for integration in the model. See the example output below. >>>> >>>> Now you can begin to imagine the next step in implementing our reconciliation pipeline: batch gapfilling creates solutions for all false negative conditions, and managesol allows you to see and select solutions for implementation. I'll also add an ability to simulate all gapfilling solutions against phenotype data so they can be assessed based on their ability to replicate experiments. The final step will be to automate the selection of an ideal cross section of solutions to fit phenotype data. >>>> >>>> >>>> 1.) model gapfill testmodel --media Media2 >>>> ********************************************* >>>> Gapfilling formulation: GF9 >>>> Media: Media2 >>>> --------------------------------------------- >>>> 1 gapfilling solution(s) found. >>>> --------------------------------------------- >>>> New gapfilling solution: GF9.0 >>>> Solution cost:2 >>>> Gapfilled reactions 2{ >>>> ID Direction Equation >>>> rxn8[c] < (1) A name[c] <=> (1) D name[c] >>>> rxn4[c] > (1) D name[e] <=> (1) D name[c] >>>> } >>>> --------------------------------------------- >>>> >>>> --Note: the solution is saved in the model automatically, but not yet integrated.... you view and integrate solutions using the "managesol" command: >>>> >>>> 2.) model managesol testmodel >>>> ********************************************* >>>> No unintegrated gap generation studies! >>>> ********************************************* >>>> ********************************************* >>>> 10 unintegrated gapfilling studies! >>>> ********************************************* >>>> Gapfilling formulation: GF0 >>>> Media: Complete >>>> --------------------------------------------- >>>> 1 gapfilling solution(s) found. >>>> --------------------------------------------- >>>> New gapfilling solution: GF0.0 >>>> Solution cost:2 >>>> Gapfilled reactions 2{ >>>> ID Direction Equation >>>> rxn2[c] > (1) B name[e] <=> (1) B name[c] >>>> rxn8[c] > (1) A name[c] <=> (1) D name[c] >>>> } >>>> --------------------------------------------- >>>> ********************************************* >>>> Gapfilling formulation: GF1 >>>> Media: Media2 >>>> --------------------------------------------- >>>> 1 gapfilling solution(s) found. >>>> --------------------------------------------- >>>> New gapfilling solution: GF1.0 >>>> Solution cost:2 >>>> Gapfilled reactions 2{ >>>> ID Direction Equation >>>> rxn8[c] < (1) A name[c] <=> (1) D name[c] >>>> rxn4[c] > (1) D name[e] <=> (1) D name[c] >>>> } >>>> --------------------------------------------- >>>> >>>> On Oct 8, 2012, at 12:58 PM, Ben Bowen wrote: >>>> >>>>> I would be happy to give a brief update on the phenotype simulations >>>>> -------------- >>>>> Email: BPBowen(a)lbl.gov >>>>> Phone: (510) 214-6683 >>>>> MS 977-221, Lawrence Berkeley Lab >>>>> Web: ms.lbl.gov >>>>> >>>>> >>>>> On Mon, Oct 8, 2012 at 10:53 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: >>>>> Hey guys, >>>>> >>>>> Sorry for the short notice, we have a microbes call in 10min. The only >>>>> thing I have for the agenda is to talk about keeping track of our >>>>> needs and making sure we get help from Tom, Nomi and others. Let me >>>>> know if you have additional agenda items. >>>>> >>>>> 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 >>>> >>>> >>> >>> >> > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Fwd: Phenotype reconciliation workflow
by Christopher Henry 10 Oct '12

10 Oct '12

Hello all, I sent this to Paramvir and Ben, but I realize it may be of general interest. It's just an enhanced detailed workflow of the phenotype reconciliation process I think we need to really handle Adam D.'s data. Chris Begin forwarded message: > From: Christopher Henry <chrisshenry(a)gmail.com> > Date: October 10, 2012 12:43:03 AM CDT > To: Ben Bowen <ben.bowen(a)gmail.com> > Cc: Paramvir Dehal <psdehal(a)lbl.gov>, Ross Overbeek <rossoverbeek(a)gmail.com> > Subject: Phenotype reconciliation workflow > > So I've been thinking this over. I don't think the problem is so difficult or underdetermined as we originally thought. Check out the attached workflow (start at purple box... red and green boxes are endpoints). This is what we need to implement to handle Adam D.'s data, and while it looks complex, I actually don't think it's that bad... each individual step is pretty straightforward, and many steps don't involve incredibly complex modeling (I particularly like the idea of seeking reaction essentiality patterns that match gene essentiality patterns...). I think our mistake was to think we should try and handle all phenotypes the same way... We have three distinct classes of phenotypes that should be handled differently: > > 1.) Wildtype growth condition phenotypes - the Biolog scenario (pretty easy to handle) > 2.) Gene essentiality phenotypes (harder to handle, but offers chance to make new annotations) > 3.) Multi-gene KO phenotypes (very tough to handle... almost certainly must be handled one-by-one manually... at least until we have good pipelines for (1) and (2) > > So we just handle things in the right order: > > 1.) Wildtype phenotypes > 2.) Single gene KO phenotypes > -Genes with confident annotations > -Genes with unconfident or no annotations > 3.) Multigene KO phenotypes > > On Oct 9, 2012, at 8:48 AM, Ben Bowen wrote: > >> Agreed. Just a little bit of book-keeping will be of huge service >> -------------- >> Email: BPBowen(a)lbl.gov >> Phone: (510) 214-6683 >> MS 977-221, Lawrence Berkeley Lab >> Web: ms.lbl.gov >> >> >> On Mon, Oct 8, 2012 at 10:47 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >> I agree the mapping of genes based on phenotypes is a concern. I think it should be possible, but we'll need to combine the modeling with some heuristics based on pre-analysis of the data. >> Chris >> >> On Oct 8, 2012, at 5:26 PM, Ben Bowen wrote: >> >>> I'm tingling with anticipation. FYI: I gapfilled to grown on alanine as C and N source and it added alanine ABC transporter. seems reasonable. >>> >>> There is a layer that we need to put something together for. Given a list of gap-filled reactions, go back to the gene-fitness data and identify candidate genes that are responsible for the function. If you look at the matrix of fitness data and some added reactions, can you really pick out which gene is responsible? In the alanine example above, there are 100s of essential genes, and many won't have known function. I've been trying to sort out the mechanics of this. Hopefully, on Wednesday, I'll have some kind of rational approach sorted out. >>> >>> >>> -------------- >>> Email: BPBowen(a)lbl.gov >>> Phone: (510) 214-6683 >>> MS 977-221, Lawrence Berkeley Lab >>> Web: ms.lbl.gov >>> >>> >>> On Mon, Oct 8, 2012 at 2:58 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >>> Sorry I missed this call today. I've had an extremely busy couple of weeks. I've been working alot on the gapfilling commands, with some big improvements that you should appreciate Ben. >>> I'm working on writing detailed tutorials of the new process, but essentially gapfilling is now split over two steps: (i) gapfill which identifies one or more solutions to resolve a false negative, and (ii) managesol which shows all current gapfilling solutions for a model and allows you to delete solutions or specify solutions for integration in the model. See the example output below. >>> >>> Now you can begin to imagine the next step in implementing our reconciliation pipeline: batch gapfilling creates solutions for all false negative conditions, and managesol allows you to see and select solutions for implementation. I'll also add an ability to simulate all gapfilling solutions against phenotype data so they can be assessed based on their ability to replicate experiments. The final step will be to automate the selection of an ideal cross section of solutions to fit phenotype data. >>> >>> >>> 1.) model gapfill testmodel --media Media2 >>> ********************************************* >>> Gapfilling formulation: GF9 >>> Media: Media2 >>> --------------------------------------------- >>> 1 gapfilling solution(s) found. >>> --------------------------------------------- >>> New gapfilling solution: GF9.0 >>> Solution cost:2 >>> Gapfilled reactions 2{ >>> ID Direction Equation >>> rxn8[c] < (1) A name[c] <=> (1) D name[c] >>> rxn4[c] > (1) D name[e] <=> (1) D name[c] >>> } >>> --------------------------------------------- >>> >>> --Note: the solution is saved in the model automatically, but not yet integrated.... you view and integrate solutions using the "managesol" command: >>> >>> 2.) model managesol testmodel >>> ********************************************* >>> No unintegrated gap generation studies! >>> ********************************************* >>> ********************************************* >>> 10 unintegrated gapfilling studies! >>> ********************************************* >>> Gapfilling formulation: GF0 >>> Media: Complete >>> --------------------------------------------- >>> 1 gapfilling solution(s) found. >>> --------------------------------------------- >>> New gapfilling solution: GF0.0 >>> Solution cost:2 >>> Gapfilled reactions 2{ >>> ID Direction Equation >>> rxn2[c] > (1) B name[e] <=> (1) B name[c] >>> rxn8[c] > (1) A name[c] <=> (1) D name[c] >>> } >>> --------------------------------------------- >>> ********************************************* >>> Gapfilling formulation: GF1 >>> Media: Media2 >>> --------------------------------------------- >>> 1 gapfilling solution(s) found. >>> --------------------------------------------- >>> New gapfilling solution: GF1.0 >>> Solution cost:2 >>> Gapfilled reactions 2{ >>> ID Direction Equation >>> rxn8[c] < (1) A name[c] <=> (1) D name[c] >>> rxn4[c] > (1) D name[e] <=> (1) D name[c] >>> } >>> --------------------------------------------- >>> >>> On Oct 8, 2012, at 12:58 PM, Ben Bowen wrote: >>> >>>> I would be happy to give a brief update on the phenotype simulations >>>> -------------- >>>> Email: BPBowen(a)lbl.gov >>>> Phone: (510) 214-6683 >>>> MS 977-221, Lawrence Berkeley Lab >>>> Web: ms.lbl.gov >>>> >>>> >>>> On Mon, Oct 8, 2012 at 10:53 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: >>>> Hey guys, >>>> >>>> Sorry for the short notice, we have a microbes call in 10min. The only >>>> thing I have for the agenda is to talk about keeping track of our >>>> needs and making sure we get help from Tom, Nomi and others. Let me >>>> know if you have additional agenda items. >>>> >>>> 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 >>> >>> >> >> >

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Re: [Microbe] call in 10min
by Ben Bowen 08 Oct '12

08 Oct '12

I would be happy to give a brief update on the phenotype simulations -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Oct 8, 2012 at 10:53 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Hey guys, > > Sorry for the short notice, we have a microbes call in 10min. The only > thing I have for the agenda is to talk about keeping track of our > needs and making sure we get help from Tom, Nomi and others. Let me > know if you have additional agenda items. > > Paramvir > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

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call in 10min
by Paramvir Dehal 08 Oct '12

08 Oct '12

Hey guys, Sorry for the short notice, we have a microbes call in 10min. The only thing I have for the agenda is to talk about keeping track of our needs and making sure we get help from Tom, Nomi and others. Let me know if you have additional agenda items. Paramvir

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Microbes call today 11am P/ 1pm C
by Paramvir Dehal 24 Sep '12

24 Sep '12

Hey guys, The call starts in about 1hr. Let me know if you guys have any agenda items. 866-740-1260 Code: 4958182 The Argonne team is visiting Berkeley this week and will be in transit during the call. Paramvir

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