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Re: [Microbe] Microbes Call now
by Keith Keller 27 Aug '12

27 Aug '12

On Mon, Aug 27, 2012 at 11:11 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Paramvir is on vacation this week, and I don't have the admin key on the conference call number. > I'm thinking we need to switch to a system with no admin key, so we can have meetings without Paramvir. I think Paramvir sent both of us the access code, but I can't find it at the moment. If I do find it I'll send it to you. > But it's too late to start with that this week. I propose we have a call one week from today to get back on track, sense we haven't has a call in a while. That sounds like a good plan. --keith -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab

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Re: [Microbe] Microbes Call now
by Christopher Henry 27 Aug '12

27 Aug '12

Paramvir is on vacation this week, and I don't have the admin key on the conference call number. I'm thinking we need to switch to a system with no admin key, so we can have meetings without Paramvir. I'm thinking of having my admin set up weekly calls using Argonne's system. But it's too late to start with that this week. I propose we have a call one week from today to get back on track, sense we haven't has a call in a while. On Aug 27, 2012, at 1:00 PM, John-Marc Chandonia wrote: > On Mon, Jul 16, 2012 at 11:07:31AM -0700, Paramvir Dehal wrote: >> Sorry for not emailing earlier: >> >> 866-740-1260 Code: 4958182 > > Are we on for today? I'm dialed in but it hasn't started yet. > > 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] Microbes Call now
by Michael Sneddon 27 Aug '12

27 Aug '12

I believe Paramvir is on vacation, so probably not unless we hear something differently... On Mon, Aug 27, 2012 at 11:00 AM, John-Marc Chandonia <JMChandonia(a)lbl.gov>wrote: > On Mon, Jul 16, 2012 at 11:07:31AM -0700, Paramvir Dehal wrote: > > Sorry for not emailing earlier: > > > > 866-740-1260 Code: 4958182 > > Are we on for today? I'm dialed in but it hasn't started yet. > > 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] Microbes Call now
by Ben Bowen 27 Aug '12

27 Aug '12

I'm called in too. -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Aug 27, 2012 at 11:00 AM, John-Marc Chandonia <JMChandonia(a)lbl.gov>wrote: > On Mon, Jul 16, 2012 at 11:07:31AM -0700, Paramvir Dehal wrote: > > Sorry for not emailing earlier: > > > > 866-740-1260 Code: 4958182 > > Are we on for today? I'm dialed in but it hasn't started yet. > > 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] Microbes Call now
by John-Marc Chandonia 27 Aug '12

27 Aug '12

On Mon, Jul 16, 2012 at 11:07:31AM -0700, Paramvir Dehal wrote: > Sorry for not emailing earlier: > > 866-740-1260 Code: 4958182 Are we on for today? I'm dialed in but it hasn't started yet. 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] Growmatch for KBase
by gaprice＠lbl.gov 17 Aug '12

17 Aug '12

> 1.) get_phenotype_data -genome shewnella -experiment "Adam D. data" > > PhenotypeData.tbl > -Still needs to be implemented, but this just dumps the > appropriate data in the appropriate format from the CDM... we can do > this in 1 day (Gavin, can you do this??) Sure, but there are several things that need to happen before I can do this: - the Shew pheno data needs to be loaded - requires load of the new biochem data incl the new compounds identified during the Shew load - Bruce is out of town until Monday - the CMDI API needs to be built, no idea what the status here is, but shouldn't take long - ideally, the functions built based on the use cases are done, again, not sure what the status is, this might take more time - can use the E/R API only, but will be duplicating effort with the use case coding and will be far less efficient and a much bigger, uglier, and stupider piece of code - should probably talk about what options we want wrt the query - e.g. exclude non-defined media, list of compounds upon which to exclude environments (actually, now I think about it - if a non-defined compound like yeast extract or casamino acids is in the environment, do we want a defined = False flag? Otherwise the users will have to specify all the non-defined compounds to exclude. Another option would be to have the defined flag in the compounds table) - I'm guessing a basic query would be for all experiments with a) aggregate strains based on genome X b) defined environments within specific temp and pH ranges and c) a normal fitness phenotype (not any of the special cases like time series or motility or anything like that) - will also need a threshold of some kind for mapping fitness data -> binary growth calls. Please excuse the brusque response, I really need to get to sleep. -g On 8/16/2012 2:24 PM, Chris Henry wrote: > Okay... it's been requested that I explain the growmatch > implementation in KBase. I will attempt to do so here. > > So growmatch is a system for correcting false positive and false > negative predictions by models. > > False positives: predictions of growth in conditions and with > mutations where growth is not observed experimentally > > The "Gapgen" command is designed to fix a single false positive > prediction by automatically generating one or more hypotheses on how > the model can be modified to fix the false positive. Hypotheses gapgen > will propose include: > 1.) removal of a reaction entirely from the model > 2.) adjustment of the GPR for a reaction (e.g. removal of an isozyme) > 3.) addition of a new biomass component > 4.) removal of a media component > > The gapgen command is "in", although we're still in the process of > fixing it, but it will be "in" by Sunday. The command is there, it's > in IRIS. You can run it, and it will give you predictions. The way it > works now is it comes up with a prediction and automatically modifies > the model accordingly (unless you tell it not to). Of course, thorough > documentation is still needed. This will be there by Sunday as well. > > False negatives: the model predicts that no growth will occur in a > condition where growth is observed > > The "Gapfill" command is designed to fix a single false negative > prediction by automatically generating one or more hypotheses of how > the model must be modified to enable growth in the specified > environment and with the specified mutations. Hypotheses considered > include: > 1.) Addition of new reactions to model > 2.) Adjustment of reaction GPR (addition of an isozyme) > 3.) Removal of a biomass component > 4.) Addition of a media component > > The "gapfill" command is most certainly "in" and can definitely be run > right now. Again, thorough documentation is still needed. This will be > there by Sunday as well. > > Now, we get to "simphenotypes". This command is "in" although we're > testing it now, but it will definitely be in by Sunday (with > documentaiton). This command accepts a table of phenotypes as input, > such as: > > Base Media;KO;Media Additions;Observed growth > Carbon-D-Glucose;peg.1;folate;1 > Carbon-Glycine;peg.2;folate;0 > > This command adds three new columns to the table: > Base media;KO;Media:Additions;Observed growth;Simulated > growth;Simulated growth fraction;Class > Carbon-D-Glucose;peg.1;folate;1;0;0;False negative > > OK. So that's where we stand now, or more correctly, where we will > stand on Sunday (if all goes well with the build). How is all this > going to fit together??? > > This is the full growmatch pipeline I am proposing: > 1.) get_phenotype_data -genome shewnella -experiment "Adam D. data" > > PhenotypeData.tbl > -Still needs to be implemented, but this just dumps the > appropriate data in the appropriate format from the CDM... we can do > this in 1 day (Gavin, can you do this??) > > 2.) simphenotypes < PhenotypeData.tbl > SimulatedPhenotypes.tbl > -Now done. > > 3.) generatehypotheses < SimulatedPhenotypes.tbl > PhenotypeHypotheses.tbl > -Not yet implemented, but this command just loads the phenotype > data, identifies all false positives and false negatives, uses cluster > services to run gapfill and gapgen commands on each false positive and > false negative, gathers results, and adds the resulting hypotheses as > a new column in our phenotype table WITHOUT modifying the model > > 4.) testhypotheses < PhenotypeHypotheses.tbl > > PhenotypeHypothesisSensitivity.tbl > -Not yet implemented in KBase, but this command runs all > phenotypes on each individual hypothesis to determine the impact of > each hypothesis on EVERY phenotype (not just the specific phenotype > the hypothesis was generated for) > > 5.) integratehypotheses < PhenotypeHypothesisSensitivity.tbl > > HypothesisList.txt > -Not yet implemented, but this command merges all hypotheses > together to identify the combination of hypotheses that maximizes the > fit with experimental data. Note, it will produce multiple "combined > hypotheses", and it's up to the user to select the right one out of > maybe 10-15 possibilities. > > 6.) implementhypothesis < HypothesisList.txt -index 5 > OptimizedFBAModel > -Not yet implemented, but this command just implements the selected > hypothesis combination (combination "5" in this case) into the model > > So there you have it. Of course, one could merge all these into a > single command. I'm not doing this, because I feel it will be useful > to have them in more modular form. Now, commands 1 and 3-6 are not > implemented yet. Many of these are simple and should be done this > month (gapfill and gapgen are the real meat here), but I note, these > commands are all frosting. You can run growthmatch right now using the > simphenotypes, gapfill, and gapgen commands alone, and this is in fact > what Costas Maranas calls "growmatch". What I am aiming to give you > with the pipeline described above is an entirely automated process. > > Is this clearer? > > On Thu, Aug 16, 2012 at 4:35 PM, Scott Devoid <devoid(a)ci.uchicago.edu > <mailto:[email protected]>> wrote: > > So I just talked with Bill & Ben Bowen. They wanted to know when and > in what form growmatch would get added to KBase... Do the gapgen & > gapfill functions essentially form the "inner loop" of growmatch? > > ~ Scott > > > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] Growmatch for KBase
by Rick stevens 16 Aug '12

16 Aug '12

Great description. Send from my iPad On Aug 16, 2012, at 4:24 PM, Chris Henry <chrisshenry(a)gmail.com> wrote: > Okay... it's been requested that I explain the growmatch implementation in KBase. I will attempt to do so here. > > So growmatch is a system for correcting false positive and false negative predictions by models. > > False positives: predictions of growth in conditions and with mutations where growth is not observed experimentally > > The "Gapgen" command is designed to fix a single false positive prediction by automatically generating one or more hypotheses on how the model can be modified to fix the false positive. Hypotheses gapgen will propose include: > 1.) removal of a reaction entirely from the model > 2.) adjustment of the GPR for a reaction (e.g. removal of an isozyme) > 3.) addition of a new biomass component > 4.) removal of a media component > > The gapgen command is "in", although we're still in the process of fixing it, but it will be "in" by Sunday. The command is there, it's in IRIS. You can run it, and it will give you predictions. The way it works now is it comes up with a prediction and automatically modifies the model accordingly (unless you tell it not to). Of course, thorough documentation is still needed. This will be there by Sunday as well. > > False negatives: the model predicts that no growth will occur in a condition where growth is observed > > The "Gapfill" command is designed to fix a single false negative prediction by automatically generating one or more hypotheses of how the model must be modified to enable growth in the specified environment and with the specified mutations. Hypotheses considered include: > 1.) Addition of new reactions to model > 2.) Adjustment of reaction GPR (addition of an isozyme) > 3.) Removal of a biomass component > 4.) Addition of a media component > > The "gapfill" command is most certainly "in" and can definitely be run right now. Again, thorough documentation is still needed. This will be there by Sunday as well. > > Now, we get to "simphenotypes". This command is "in" although we're testing it now, but it will definitely be in by Sunday (with documentaiton). This command accepts a table of phenotypes as input, such as: > > Base Media;KO;Media Additions;Observed growth > Carbon-D-Glucose;peg.1;folate;1 > Carbon-Glycine;peg.2;folate;0 > > This command adds three new columns to the table: > Base media;KO;Media:Additions;Observed growth;Simulated growth;Simulated growth fraction;Class > Carbon-D-Glucose;peg.1;folate;1;0;0;False negative > > OK. So that's where we stand now, or more correctly, where we will stand on Sunday (if all goes well with the build). How is all this going to fit together??? > > This is the full growmatch pipeline I am proposing: > 1.) get_phenotype_data -genome shewnella -experiment "Adam D. data" > PhenotypeData.tbl > -Still needs to be implemented, but this just dumps the appropriate data in the appropriate format from the CDM... we can do this in 1 day (Gavin, can you do this??) > > 2.) simphenotypes < PhenotypeData.tbl > SimulatedPhenotypes.tbl > -Now done. > > 3.) generatehypotheses < SimulatedPhenotypes.tbl > PhenotypeHypotheses.tbl > -Not yet implemented, but this command just loads the phenotype data, identifies all false positives and false negatives, uses cluster services to run gapfill and gapgen commands on each false positive and false negative, gathers results, and adds the resulting hypotheses as a new column in our phenotype table WITHOUT modifying the model > > 4.) testhypotheses < PhenotypeHypotheses.tbl > PhenotypeHypothesisSensitivity.tbl > -Not yet implemented in KBase, but this command runs all phenotypes on each individual hypothesis to determine the impact of each hypothesis on EVERY phenotype (not just the specific phenotype the hypothesis was generated for) > > 5.) integratehypotheses < PhenotypeHypothesisSensitivity.tbl > HypothesisList.txt > -Not yet implemented, but this command merges all hypotheses together to identify the combination of hypotheses that maximizes the fit with experimental data. Note, it will produce multiple "combined hypotheses", and it's up to the user to select the right one out of maybe 10-15 possibilities. > > 6.) implementhypothesis < HypothesisList.txt -index 5 > OptimizedFBAModel > -Not yet implemented, but this command just implements the selected hypothesis combination (combination "5" in this case) into the model > > So there you have it. Of course, one could merge all these into a single command. I'm not doing this, because I feel it will be useful to have them in more modular form. Now, commands 1 and 3-6 are not implemented yet. Many of these are simple and should be done this month (gapfill and gapgen are the real meat here), but I note, these commands are all frosting. You can run growthmatch right now using the simphenotypes, gapfill, and gapgen commands alone, and this is in fact what Costas Maranas calls "growmatch". What I am aiming to give you with the pipeline described above is an entirely automated process. > > Is this clearer? > > On Thu, Aug 16, 2012 at 4:35 PM, Scott Devoid <devoid(a)ci.uchicago.edu> wrote: > So I just talked with Bill & Ben Bowen. They wanted to know when and > in what form growmatch would get added to KBase... Do the gapgen & > gapfill functions essentially form the "inner loop" of growmatch? > > ~ Scott > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Growmatch for KBase
by Chris Henry 16 Aug '12

16 Aug '12

Okay... it's been requested that I explain the growmatch implementation in KBase. I will attempt to do so here. So growmatch is a system for correcting false positive and false negative predictions by models. False positives: predictions of growth in conditions and with mutations where growth is not observed experimentally The "Gapgen" command is designed to fix a single false positive prediction by automatically generating one or more hypotheses on how the model can be modified to fix the false positive. Hypotheses gapgen will propose include: 1.) removal of a reaction entirely from the model 2.) adjustment of the GPR for a reaction (e.g. removal of an isozyme) 3.) addition of a new biomass component 4.) removal of a media component The gapgen command is "in", although we're still in the process of fixing it, but it will be "in" by Sunday. The command is there, it's in IRIS. You can run it, and it will give you predictions. The way it works now is it comes up with a prediction and automatically modifies the model accordingly (unless you tell it not to). Of course, thorough documentation is still needed. This will be there by Sunday as well. False negatives: the model predicts that no growth will occur in a condition where growth is observed The "Gapfill" command is designed to fix a single false negative prediction by automatically generating one or more hypotheses of how the model must be modified to enable growth in the specified environment and with the specified mutations. Hypotheses considered include: 1.) Addition of new reactions to model 2.) Adjustment of reaction GPR (addition of an isozyme) 3.) Removal of a biomass component 4.) Addition of a media component The "gapfill" command is most certainly "in" and can definitely be run right now. Again, thorough documentation is still needed. This will be there by Sunday as well. Now, we get to "simphenotypes". This command is "in" although we're testing it now, but it will definitely be in by Sunday (with documentaiton). This command accepts a table of phenotypes as input, such as: Base Media;KO;Media Additions;Observed growth Carbon-D-Glucose;peg.1;folate;1 Carbon-Glycine;peg.2;folate;0 This command adds three new columns to the table: Base media;KO;Media:Additions;Observed growth;Simulated growth;Simulated growth fraction;Class Carbon-D-Glucose;peg.1;folate;1;0;0;False negative OK. So that's where we stand now, or more correctly, where we will stand on Sunday (if all goes well with the build). How is all this going to fit together??? This is the full growmatch pipeline I am proposing: 1.) get_phenotype_data -genome shewnella -experiment "Adam D. data" > PhenotypeData.tbl -Still needs to be implemented, but this just dumps the appropriate data in the appropriate format from the CDM... we can do this in 1 day (Gavin, can you do this??) 2.) simphenotypes < PhenotypeData.tbl > SimulatedPhenotypes.tbl -Now done. 3.) generatehypotheses < SimulatedPhenotypes.tbl > PhenotypeHypotheses.tbl -Not yet implemented, but this command just loads the phenotype data, identifies all false positives and false negatives, uses cluster services to run gapfill and gapgen commands on each false positive and false negative, gathers results, and adds the resulting hypotheses as a new column in our phenotype table WITHOUT modifying the model 4.) testhypotheses < PhenotypeHypotheses.tbl > PhenotypeHypothesisSensitivity.tbl -Not yet implemented in KBase, but this command runs all phenotypes on each individual hypothesis to determine the impact of each hypothesis on EVERY phenotype (not just the specific phenotype the hypothesis was generated for) 5.) integratehypotheses < PhenotypeHypothesisSensitivity.tbl > HypothesisList.txt -Not yet implemented, but this command merges all hypotheses together to identify the combination of hypotheses that maximizes the fit with experimental data. Note, it will produce multiple "combined hypotheses", and it's up to the user to select the right one out of maybe 10-15 possibilities. 6.) implementhypothesis < HypothesisList.txt -index 5 > OptimizedFBAModel -Not yet implemented, but this command just implements the selected hypothesis combination (combination "5" in this case) into the model So there you have it. Of course, one could merge all these into a single command. I'm not doing this, because I feel it will be useful to have them in more modular form. Now, commands 1 and 3-6 are not implemented yet. Many of these are simple and should be done this month (gapfill and gapgen are the real meat here), but I note, these commands are all frosting. You can run growthmatch right now using the simphenotypes, gapfill, and gapgen commands alone, and this is in fact what Costas Maranas calls "growmatch". What I am aiming to give you with the pipeline described above is an entirely automated process. Is this clearer? On Thu, Aug 16, 2012 at 4:35 PM, Scott Devoid <devoid(a)ci.uchicago.edu>wrote: > So I just talked with Bill & Ben Bowen. They wanted to know when and > in what form growmatch would get added to KBase... Do the gapgen & > gapfill functions essentially form the "inner loop" of growmatch? > > ~ Scott >

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Re: [Microbe] Microbes telecon today!
by Paramvir Dehal 13 Aug '12

13 Aug '12

Nevermind. Dylan just reminded me that everyone will be in transit. No meeting today. Paramvir On Mon, Aug 13, 2012 at 9:32 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > We've got a call today at 11am Pacific / 1pm Central > > 866-740-1260 Code: 4958182 > > We'll keep it short and quick because the build meeting starts at > noon. The only agenda item I have is the 36 month goals. > > Paramvir

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Microbes telecon today!
by Paramvir Dehal 13 Aug '12

13 Aug '12

We've got a call today at 11am Pacific / 1pm Central 866-740-1260 Code: 4958182 We'll keep it short and quick because the build meeting starts at noon. The only agenda item I have is the 36 month goals. Paramvir

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