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

meeting notes 7/30
by Paramvir Dehal 30 Jul '12

30 Jul '12

*07/30/2012: Microbes CallAttendees: Mike, Jason, Gavin, Ben, Brian, Bill, Dylan, Matt, John-Marc, Aaron, Chris, Pavel, Aaron Meeting notes 1. Updates 1. Trees: Mike 1. ER finalized 2. Bruce is working on adding to CDM, no eta on completion, hopefully by build meeting 1. Fangfang has been talking to Bruce 2. Bruce was on a two week vacation, back now 3. Chris will email Ross & Bruce to find out what the eta is 1. Chris uses document store to hold data structures 2. Migrates to CDM when it’s ready 3. Allows more rapid development, avoids “I can’t do anything until my data is in the CDM problem” 3. Mike is working on data loaders and services 1. Number of services that just take input from the user and modify data - rerooting, trimming, basic tree tools as KBase services 4. Plants have cleared everything 2. Phenotype: Gavin 1. Pulling data and formating data for reconcilliation services 2. 99% of data has been collected from Adam Duestchbauer 1. remaining data delayed by arkin lab move 3. data quality and data checks being written. 1. Gavin has 3hrs to finish before Arkin servers go down 4. Chris: special phenotype call like get_entities call 5. Chris will write service against his document store method for the biochemistry 1. Chris, Scott, Paul 3. Biochemistry database 1. loaded into cdm, but out of date 2. getting rid of hash uuids replacing with kbase ids 3. expanded to plants, might not go in this week 4. Chris will send out schema 5. compound locations defined by model, not a property of the compound 6. FBA is done, gapfilling is done, 7. type “tutorial” in IRIS 8. need to consolidate hypothesis generation 2. August Build 1. Who’s coming 1. Not John-Marc, Bruce? 2. Paul and Scott 2. Manifest 3. Punch List 1. On “KBaseTeam/Microbes/Feb 2013” 2. 3. Future - the second 18months 4. Other Items 1. Tools for FBA, for BESC 1. Link for FBA Services tutorial? 2. Demo movies on dropbox *

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Re: [Microbe] meeting today!
by Steven E. Brenner 30 Jul '12

30 Jul '12

Sorry I cannot join as I am at an all-day NIH meeting in DC. This looks important -- Paramvir, can we coordinate a time for me to speak with you and get an update. I'm copying my lab manager to help find a time. On Mon, 30 Jul 2012, Paramvir Dehal wrote: > Hi Everyone, > > Just a reminder that we have the microbes call today 11am Pacific / 1pm > Central. Most of today's call will focus on the August Build. Let me know > if you have any additional agenda items. > > > 866-740-1260 Code: 4958182 > > Agenda > > 1) Updatesï¿½ ï¿½ ï¿½a) Trees > ï¿½ ï¿½ ï¿½b) Phenotype > > 2) Build Meeting > ï¿½ ï¿½ ï¿½a) Who's coming > ï¿½ ï¿½ ï¿½b) Manifest > ï¿½ ï¿½ ï¿½c) Must haves before build > > 3) Other Items? > > > > Paramvir > >

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Re: [Microbe] KBase FBA modeling
by Brettin, Thomas S. 30 Jul '12

30 Jul '12

Thanks. I probably can't make the call. Holed up in a workshop on next gen sequencing analysis HPC programming libraries. t From: Paramvir Dehal [mailto:[email protected]] Sent: Monday, July 30, 2012 12:31 PM To: Chris Cc: Brettin, Thomas S.; NomiHarris (nlharris(a)gmail.com) microbe(a)lists.kbase.us; Scott Devoid; Gavin A Price Subject: Re: [Microbe] KBase FBA modeling Hi Tom, We'll try and have it finished up today. Paramvir On Sun, Jul 29, 2012 at 10:01 AM, Chris <chrisshenry(a)gmail.com<mailto:[email protected]>> wrote: I integrated the phenotype stuff paramvir is doing, since that's a cross cut between our groups, but I believe there are other things he will be deploying. Sent from my iPad On Jul 29, 2012, at 9:49 AM, "Brettin, Thomas S." <brettints(a)ornl.gov<mailto:[email protected]>> wrote: > Was thinking the same thing. Would like to merge with the list paramvir has, unless Chris you did that already? > > t > > -----Original Message----- > From: Rick Stevens [mailto:[email protected]<mailto:[email protected]>] > Sent: Sunday, July 29, 2012 10:17 AM > To: Brettin, Thomas S. > Cc: Rick Stevens; 'Christopher Henry'; Scott Devoid; microbe(a)lists.kbase.us<mailto:[email protected]>; Nomi Harris (nlharris(a)gmail.com<mailto:[email protected]>); Gavin A Price > Subject: Re: [Microbe] KBase FBA modeling > > This is a great list../ plan > > Tom, > > we might want to encourage the other groups to be as succinct in their lists as well.. perhaps we should circulate a version > as an example of what we are looking for. > > --Rick > > On Jul 29, 2012, at 7:56 AM, Brettin, Thomas S. wrote: > >> Thanks Chris. This is great! >> >> Ideally, everything will be set up prior to the actual build meeting so all dependencies are in place. >> >> Let's work with Dan to make sure you have everything you need in the kbase image before the build, he's out on vacation this week, so next week. >> >> >> >> >> -----Original Message----- >> From: Christopher Henry [mailto:[email protected]<mailto:[email protected]>] >> Sent: Sunday, July 29, 2012 1:46 AM >> To: Brettin, Thomas S. >> Cc: Scott Devoid; Paramvir Dehal; Gavin A Price; William Riehl; Paul Frybarger; Matt DeJongh; microbe(a)lists.kbase.us<mailto:[email protected]> >> Subject: KBase FBA modeling >> >> Hi Tom, >> >> So I'm starting to think about our manifest for the upcoming build. >> It's looking like all FBA modeling in KBase is going to go in a single repository. I set this up in git hub here: >> https://github.com/ModelSEED/KBaseFBAModeling >> >> Right now, the equivalent repo in KBase is called "model_api", which I believe we've all decided is a bad name. I think a name like "KBaseFBAModeling", "FBAModeling" would be more appropriate. >> We're prepping three repositories for deployment on build week: >> >> 1.) MFAToolkit: a c++ code that does all our flux balance analysis processing on the backend >> -https://github.com/ModelSEED/MFAToolkit >> 2.) ModelSEED: a massively trimmed down repo with the new Model SEED, which is the environment where many of the KBase FBA algorithms will be written (it can be considered at its heart, a perl object oriented API for FBA modeling) >> -https://github.com/ModelSEED/ModelSEED >> 3.) KBaseFBAModeling: the repo for the web services and IRIS front ends for all KBase FBA modeling services >> -https://github.com/ModelSEED/KBaseFBAModeling >> >> These three repos hold all the code that currently support the modeling services in IRIS. Our goal is by the time of the build, these repos will hold all services for reconciling phenotype data with models. >> The services in these repos will soon be applied to build draft models of all genomes in KBase CDM (genome_to_FBAmodel command). Draft models will be loaded in the CDM. This will be done before the build. >> Biochemistry is being loaded this upcoming week, along with phenotype data hopefully. I believe this biochemistry will include plant biochemistry, with support for plant modeling. >> >> So services we're targeting for the build: >> 1.) Plant model reconstruction (end of next week) >> 2.) Microbial model reconstruction (already in IRIS) >> 3.) Metagenome model reconstruction (this week) >> 4.) Model flux balance analysis including (already in IRIS) >> -flux variability analysis >> -single gene knockout >> -minimal media prediction >> -metabolic production analysis for non growing models >> -flux minimization >> -phenotype simulation (not sure the IRIS script supports this, but the web service does) >> 5.) Gapfilling of models (already in IRIS) >> 6.) Phenotype simulation and reconciliation (end of next week) >> >> Data we are targeting for the build: >> 1.) Biochemistry CDM (including plant biochemistry) >> 2.) Model CDM >> 3.) Phenotype CDM >> 4.) Document store for models and biochemistry >> >> Documentation is in progress... obviously, it's a lot to document, and these services are somewhat complex. >> Questions/comments welcome. Particularly, I want to know if you see something you were expecting us to produce but appears to be missing. >> >> Chris >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us<mailto:[email protected]> >> https://lists.kbase.us/mailman/listinfo/microbe > _______________________________________________ Microbe mailing list Microbe(a)lists.kbase.us<mailto:[email protected]> https://lists.kbase.us/mailman/listinfo/microbe

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meeting today!
by Paramvir Dehal 30 Jul '12

30 Jul '12

Hi Everyone, Just a reminder that we have the microbes call today 11am Pacific / 1pm Central. Most of today's call will focus on the August Build. Let me know if you have any additional agenda items. *866-740-1260 Code: 4958182 * Agenda 1) Updates a) Trees b) Phenotype 2) Build Meeting a) Who's coming b) Manifest c) Must haves before build 3) Other Items? Paramvir

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Re: [Microbe] KBase FBA modeling
by Paramvir Dehal 30 Jul '12

30 Jul '12

Hi Tom, We'll try and have it finished up today. Paramvir On Sun, Jul 29, 2012 at 10:01 AM, Chris <chrisshenry(a)gmail.com> wrote: > I integrated the phenotype stuff paramvir is doing, since that's a cross > cut between our groups, but I believe there are other things he will be > deploying. > > Sent from my iPad > > On Jul 29, 2012, at 9:49 AM, "Brettin, Thomas S." <brettints(a)ornl.gov> > wrote: > > > Was thinking the same thing. Would like to merge with the list paramvir > has, unless Chris you did that already? > > > > t > > > > -----Original Message----- > > From: Rick Stevens [mailto:[email protected]] > > Sent: Sunday, July 29, 2012 10:17 AM > > To: Brettin, Thomas S. > > Cc: Rick Stevens; 'Christopher Henry'; Scott Devoid; > microbe(a)lists.kbase.us; Nomi Harris (nlharris(a)gmail.com) Gavin A Price > > Subject: Re: [Microbe] KBase FBA modeling > > > > This is a great list../ plan > > > > Tom, > > > > we might want to encourage the other groups to be as succinct in their > lists as well.. perhaps we should circulate a version > > as an example of what we are looking for. > > > > --Rick > > > > On Jul 29, 2012, at 7:56 AM, Brettin, Thomas S. wrote: > > > >> Thanks Chris. This is great! > >> > >> Ideally, everything will be set up prior to the actual build meeting so > all dependencies are in place. > >> > >> Let's work with Dan to make sure you have everything you need in the > kbase image before the build, he's out on vacation this week, so next week. > >> > >> > >> > >> > >> -----Original Message----- > >> From: Christopher Henry [mailto:[email protected]] > >> Sent: Sunday, July 29, 2012 1:46 AM > >> To: Brettin, Thomas S. > >> Cc: Scott Devoid; Paramvir Dehal; Gavin A Price; William Riehl; Paul > Frybarger; Matt DeJongh; microbe(a)lists.kbase.us > >> Subject: KBase FBA modeling > >> > >> Hi Tom, > >> > >> So I'm starting to think about our manifest for the upcoming build. > >> It's looking like all FBA modeling in KBase is going to go in a single > repository. I set this up in git hub here: > >> https://github.com/ModelSEED/KBaseFBAModeling > >> > >> Right now, the equivalent repo in KBase is called "model_api", which I > believe we've all decided is a bad name. I think a name like > "KBaseFBAModeling", "FBAModeling" would be more appropriate. > >> We're prepping three repositories for deployment on build week: > >> > >> 1.) MFAToolkit: a c++ code that does all our flux balance analysis > processing on the backend > >> -https://github.com/ModelSEED/MFAToolkit > >> 2.) ModelSEED: a massively trimmed down repo with the new Model SEED, > which is the environment where many of the KBase FBA algorithms will be > written (it can be considered at its heart, a perl object oriented API for > FBA modeling) > >> -https://github.com/ModelSEED/ModelSEED > >> 3.) KBaseFBAModeling: the repo for the web services and IRIS front ends > for all KBase FBA modeling services > >> -https://github.com/ModelSEED/KBaseFBAModeling > >> > >> These three repos hold all the code that currently support the modeling > services in IRIS. Our goal is by the time of the build, these repos will > hold all services for reconciling phenotype data with models. > >> The services in these repos will soon be applied to build draft models > of all genomes in KBase CDM (genome_to_FBAmodel command). Draft models will > be loaded in the CDM. This will be done before the build. > >> Biochemistry is being loaded this upcoming week, along with phenotype > data hopefully. I believe this biochemistry will include plant > biochemistry, with support for plant modeling. > >> > >> So services we're targeting for the build: > >> 1.) Plant model reconstruction (end of next week) > >> 2.) Microbial model reconstruction (already in IRIS) > >> 3.) Metagenome model reconstruction (this week) > >> 4.) Model flux balance analysis including (already in IRIS) > >> -flux variability analysis > >> -single gene knockout > >> -minimal media prediction > >> -metabolic production analysis for non growing models > >> -flux minimization > >> -phenotype simulation (not sure the IRIS script supports this, but > the web service does) > >> 5.) Gapfilling of models (already in IRIS) > >> 6.) Phenotype simulation and reconciliation (end of next week) > >> > >> Data we are targeting for the build: > >> 1.) Biochemistry CDM (including plant biochemistry) > >> 2.) Model CDM > >> 3.) Phenotype CDM > >> 4.) Document store for models and biochemistry > >> > >> Documentation is in progress... obviously, it's a lot to document, and > these services are somewhat complex. > >> Questions/comments welcome. Particularly, I want to know if you see > something you were expecting us to produce but appears to be missing. > >> > >> Chris > >> _______________________________________________ > >> 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] KBase FBA modeling
by Chris 29 Jul '12

29 Jul '12

I integrated the phenotype stuff paramvir is doing, since that's a cross cut between our groups, but I believe there are other things he will be deploying. Sent from my iPad On Jul 29, 2012, at 9:49 AM, "Brettin, Thomas S." <brettints(a)ornl.gov> wrote: > Was thinking the same thing. Would like to merge with the list paramvir has, unless Chris you did that already? > > t > > -----Original Message----- > From: Rick Stevens [mailto:[email protected]] > Sent: Sunday, July 29, 2012 10:17 AM > To: Brettin, Thomas S. > Cc: Rick Stevens; 'Christopher Henry'; Scott Devoid; microbe(a)lists.kbase.us; Nomi Harris (nlharris(a)gmail.com) Gavin A Price > Subject: Re: [Microbe] KBase FBA modeling > > This is a great list../ plan > > Tom, > > we might want to encourage the other groups to be as succinct in their lists as well.. perhaps we should circulate a version > as an example of what we are looking for. > > --Rick > > On Jul 29, 2012, at 7:56 AM, Brettin, Thomas S. wrote: > >> Thanks Chris. This is great! >> >> Ideally, everything will be set up prior to the actual build meeting so all dependencies are in place. >> >> Let's work with Dan to make sure you have everything you need in the kbase image before the build, he's out on vacation this week, so next week. >> >> >> >> >> -----Original Message----- >> From: Christopher Henry [mailto:[email protected]] >> Sent: Sunday, July 29, 2012 1:46 AM >> To: Brettin, Thomas S. >> Cc: Scott Devoid; Paramvir Dehal; Gavin A Price; William Riehl; Paul Frybarger; Matt DeJongh; microbe(a)lists.kbase.us >> Subject: KBase FBA modeling >> >> Hi Tom, >> >> So I'm starting to think about our manifest for the upcoming build. >> It's looking like all FBA modeling in KBase is going to go in a single repository. I set this up in git hub here: >> https://github.com/ModelSEED/KBaseFBAModeling >> >> Right now, the equivalent repo in KBase is called "model_api", which I believe we've all decided is a bad name. I think a name like "KBaseFBAModeling", "FBAModeling" would be more appropriate. >> We're prepping three repositories for deployment on build week: >> >> 1.) MFAToolkit: a c++ code that does all our flux balance analysis processing on the backend >> -https://github.com/ModelSEED/MFAToolkit >> 2.) ModelSEED: a massively trimmed down repo with the new Model SEED, which is the environment where many of the KBase FBA algorithms will be written (it can be considered at its heart, a perl object oriented API for FBA modeling) >> -https://github.com/ModelSEED/ModelSEED >> 3.) KBaseFBAModeling: the repo for the web services and IRIS front ends for all KBase FBA modeling services >> -https://github.com/ModelSEED/KBaseFBAModeling >> >> These three repos hold all the code that currently support the modeling services in IRIS. Our goal is by the time of the build, these repos will hold all services for reconciling phenotype data with models. >> The services in these repos will soon be applied to build draft models of all genomes in KBase CDM (genome_to_FBAmodel command). Draft models will be loaded in the CDM. This will be done before the build. >> Biochemistry is being loaded this upcoming week, along with phenotype data hopefully. I believe this biochemistry will include plant biochemistry, with support for plant modeling. >> >> So services we're targeting for the build: >> 1.) Plant model reconstruction (end of next week) >> 2.) Microbial model reconstruction (already in IRIS) >> 3.) Metagenome model reconstruction (this week) >> 4.) Model flux balance analysis including (already in IRIS) >> -flux variability analysis >> -single gene knockout >> -minimal media prediction >> -metabolic production analysis for non growing models >> -flux minimization >> -phenotype simulation (not sure the IRIS script supports this, but the web service does) >> 5.) Gapfilling of models (already in IRIS) >> 6.) Phenotype simulation and reconciliation (end of next week) >> >> Data we are targeting for the build: >> 1.) Biochemistry CDM (including plant biochemistry) >> 2.) Model CDM >> 3.) Phenotype CDM >> 4.) Document store for models and biochemistry >> >> Documentation is in progress... obviously, it's a lot to document, and these services are somewhat complex. >> Questions/comments welcome. Particularly, I want to know if you see something you were expecting us to produce but appears to be missing. >> >> Chris >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe >

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Re: [Microbe] KBase FBA modeling
by Brettin, Thomas S. 29 Jul '12

29 Jul '12

Was thinking the same thing. Would like to merge with the list paramvir has, unless Chris you did that already? t -----Original Message----- From: Rick Stevens [mailto:[email protected]] Sent: Sunday, July 29, 2012 10:17 AM To: Brettin, Thomas S. Cc: Rick Stevens; 'Christopher Henry'; Scott Devoid; microbe(a)lists.kbase.us; Nomi Harris (nlharris(a)gmail.com) Gavin A Price Subject: Re: [Microbe] KBase FBA modeling This is a great list../ plan Tom, we might want to encourage the other groups to be as succinct in their lists as well.. perhaps we should circulate a version as an example of what we are looking for. --Rick On Jul 29, 2012, at 7:56 AM, Brettin, Thomas S. wrote: > Thanks Chris. This is great! > > Ideally, everything will be set up prior to the actual build meeting so all dependencies are in place. > > Let's work with Dan to make sure you have everything you need in the kbase image before the build, he's out on vacation this week, so next week. > > > > > -----Original Message----- > From: Christopher Henry [mailto:[email protected]] > Sent: Sunday, July 29, 2012 1:46 AM > To: Brettin, Thomas S. > Cc: Scott Devoid; Paramvir Dehal; Gavin A Price; William Riehl; Paul Frybarger; Matt DeJongh; microbe(a)lists.kbase.us > Subject: KBase FBA modeling > > Hi Tom, > > So I'm starting to think about our manifest for the upcoming build. > It's looking like all FBA modeling in KBase is going to go in a single repository. I set this up in git hub here: > https://github.com/ModelSEED/KBaseFBAModeling > > Right now, the equivalent repo in KBase is called "model_api", which I believe we've all decided is a bad name. I think a name like "KBaseFBAModeling", "FBAModeling" would be more appropriate. > We're prepping three repositories for deployment on build week: > > 1.) MFAToolkit: a c++ code that does all our flux balance analysis processing on the backend > -https://github.com/ModelSEED/MFAToolkit > 2.) ModelSEED: a massively trimmed down repo with the new Model SEED, which is the environment where many of the KBase FBA algorithms will be written (it can be considered at its heart, a perl object oriented API for FBA modeling) > -https://github.com/ModelSEED/ModelSEED > 3.) KBaseFBAModeling: the repo for the web services and IRIS front ends for all KBase FBA modeling services > -https://github.com/ModelSEED/KBaseFBAModeling > > These three repos hold all the code that currently support the modeling services in IRIS. Our goal is by the time of the build, these repos will hold all services for reconciling phenotype data with models. > The services in these repos will soon be applied to build draft models of all genomes in KBase CDM (genome_to_FBAmodel command). Draft models will be loaded in the CDM. This will be done before the build. > Biochemistry is being loaded this upcoming week, along with phenotype data hopefully. I believe this biochemistry will include plant biochemistry, with support for plant modeling. > > So services we're targeting for the build: > 1.) Plant model reconstruction (end of next week) > 2.) Microbial model reconstruction (already in IRIS) > 3.) Metagenome model reconstruction (this week) > 4.) Model flux balance analysis including (already in IRIS) > -flux variability analysis > -single gene knockout > -minimal media prediction > -metabolic production analysis for non growing models > -flux minimization > -phenotype simulation (not sure the IRIS script supports this, but the web service does) > 5.) Gapfilling of models (already in IRIS) > 6.) Phenotype simulation and reconciliation (end of next week) > > Data we are targeting for the build: > 1.) Biochemistry CDM (including plant biochemistry) > 2.) Model CDM > 3.) Phenotype CDM > 4.) Document store for models and biochemistry > > Documentation is in progress... obviously, it's a lot to document, and these services are somewhat complex. > Questions/comments welcome. Particularly, I want to know if you see something you were expecting us to produce but appears to be missing. > > Chris > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] KBase FBA modeling
by Rick Stevens 29 Jul '12

29 Jul '12

This is a great list../ plan Tom, we might want to encourage the other groups to be as succinct in their lists as well.. perhaps we should circulate a version as an example of what we are looking for. --Rick On Jul 29, 2012, at 7:56 AM, Brettin, Thomas S. wrote: > Thanks Chris. This is great! > > Ideally, everything will be set up prior to the actual build meeting so all dependencies are in place. > > Let's work with Dan to make sure you have everything you need in the kbase image before the build, he's out on vacation this week, so next week. > > > > > -----Original Message----- > From: Christopher Henry [mailto:[email protected]] > Sent: Sunday, July 29, 2012 1:46 AM > To: Brettin, Thomas S. > Cc: Scott Devoid; Paramvir Dehal; Gavin A Price; William Riehl; Paul Frybarger; Matt DeJongh; microbe(a)lists.kbase.us > Subject: KBase FBA modeling > > Hi Tom, > > So I'm starting to think about our manifest for the upcoming build. > It's looking like all FBA modeling in KBase is going to go in a single repository. I set this up in git hub here: > https://github.com/ModelSEED/KBaseFBAModeling > > Right now, the equivalent repo in KBase is called "model_api", which I believe we've all decided is a bad name. I think a name like "KBaseFBAModeling", "FBAModeling" would be more appropriate. > We're prepping three repositories for deployment on build week: > > 1.) MFAToolkit: a c++ code that does all our flux balance analysis processing on the backend > -https://github.com/ModelSEED/MFAToolkit > 2.) ModelSEED: a massively trimmed down repo with the new Model SEED, which is the environment where many of the KBase FBA algorithms will be written (it can be considered at its heart, a perl object oriented API for FBA modeling) > -https://github.com/ModelSEED/ModelSEED > 3.) KBaseFBAModeling: the repo for the web services and IRIS front ends for all KBase FBA modeling services > -https://github.com/ModelSEED/KBaseFBAModeling > > These three repos hold all the code that currently support the modeling services in IRIS. Our goal is by the time of the build, these repos will hold all services for reconciling phenotype data with models. > The services in these repos will soon be applied to build draft models of all genomes in KBase CDM (genome_to_FBAmodel command). Draft models will be loaded in the CDM. This will be done before the build. > Biochemistry is being loaded this upcoming week, along with phenotype data hopefully. I believe this biochemistry will include plant biochemistry, with support for plant modeling. > > So services we're targeting for the build: > 1.) Plant model reconstruction (end of next week) > 2.) Microbial model reconstruction (already in IRIS) > 3.) Metagenome model reconstruction (this week) > 4.) Model flux balance analysis including (already in IRIS) > -flux variability analysis > -single gene knockout > -minimal media prediction > -metabolic production analysis for non growing models > -flux minimization > -phenotype simulation (not sure the IRIS script supports this, but the web service does) > 5.) Gapfilling of models (already in IRIS) > 6.) Phenotype simulation and reconciliation (end of next week) > > Data we are targeting for the build: > 1.) Biochemistry CDM (including plant biochemistry) > 2.) Model CDM > 3.) Phenotype CDM > 4.) Document store for models and biochemistry > > Documentation is in progress... obviously, it's a lot to document, and these services are somewhat complex. > Questions/comments welcome. Particularly, I want to know if you see something you were expecting us to produce but appears to be missing. > > Chris > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] KBase FBA modeling
by Brettin, Thomas S. 29 Jul '12

29 Jul '12

Thanks Chris. This is great! Ideally, everything will be set up prior to the actual build meeting so all dependencies are in place. Let's work with Dan to make sure you have everything you need in the kbase image before the build, he's out on vacation this week, so next week. -----Original Message----- From: Christopher Henry [mailto:[email protected]] Sent: Sunday, July 29, 2012 1:46 AM To: Brettin, Thomas S. Cc: Scott Devoid; Paramvir Dehal; Gavin A Price; William Riehl; Paul Frybarger; Matt DeJongh; microbe(a)lists.kbase.us Subject: KBase FBA modeling Hi Tom, So I'm starting to think about our manifest for the upcoming build. It's looking like all FBA modeling in KBase is going to go in a single repository. I set this up in git hub here: https://github.com/ModelSEED/KBaseFBAModeling Right now, the equivalent repo in KBase is called "model_api", which I believe we've all decided is a bad name. I think a name like "KBaseFBAModeling", "FBAModeling" would be more appropriate. We're prepping three repositories for deployment on build week: 1.) MFAToolkit: a c++ code that does all our flux balance analysis processing on the backend -https://github.com/ModelSEED/MFAToolkit 2.) ModelSEED: a massively trimmed down repo with the new Model SEED, which is the environment where many of the KBase FBA algorithms will be written (it can be considered at its heart, a perl object oriented API for FBA modeling) -https://github.com/ModelSEED/ModelSEED 3.) KBaseFBAModeling: the repo for the web services and IRIS front ends for all KBase FBA modeling services -https://github.com/ModelSEED/KBaseFBAModeling These three repos hold all the code that currently support the modeling services in IRIS. Our goal is by the time of the build, these repos will hold all services for reconciling phenotype data with models. The services in these repos will soon be applied to build draft models of all genomes in KBase CDM (genome_to_FBAmodel command). Draft models will be loaded in the CDM. This will be done before the build. Biochemistry is being loaded this upcoming week, along with phenotype data hopefully. I believe this biochemistry will include plant biochemistry, with support for plant modeling. So services we're targeting for the build: 1.) Plant model reconstruction (end of next week) 2.) Microbial model reconstruction (already in IRIS) 3.) Metagenome model reconstruction (this week) 4.) Model flux balance analysis including (already in IRIS) -flux variability analysis -single gene knockout -minimal media prediction -metabolic production analysis for non growing models -flux minimization -phenotype simulation (not sure the IRIS script supports this, but the web service does) 5.) Gapfilling of models (already in IRIS) 6.) Phenotype simulation and reconciliation (end of next week) Data we are targeting for the build: 1.) Biochemistry CDM (including plant biochemistry) 2.) Model CDM 3.) Phenotype CDM 4.) Document store for models and biochemistry Documentation is in progress... obviously, it's a lot to document, and these services are somewhat complex. Questions/comments welcome. Particularly, I want to know if you see something you were expecting us to produce but appears to be missing. Chris

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KBase FBA modeling
by Christopher Henry 29 Jul '12

29 Jul '12

Hi Tom, So I'm starting to think about our manifest for the upcoming build. It's looking like all FBA modeling in KBase is going to go in a single repository. I set this up in git hub here: https://github.com/ModelSEED/KBaseFBAModeling Right now, the equivalent repo in KBase is called "model_api", which I believe we've all decided is a bad name. I think a name like "KBaseFBAModeling", "FBAModeling" would be more appropriate. We're prepping three repositories for deployment on build week: 1.) MFAToolkit: a c++ code that does all our flux balance analysis processing on the backend -https://github.com/ModelSEED/MFAToolkit 2.) ModelSEED: a massively trimmed down repo with the new Model SEED, which is the environment where many of the KBase FBA algorithms will be written (it can be considered at its heart, a perl object oriented API for FBA modeling) -https://github.com/ModelSEED/ModelSEED 3.) KBaseFBAModeling: the repo for the web services and IRIS front ends for all KBase FBA modeling services -https://github.com/ModelSEED/KBaseFBAModeling These three repos hold all the code that currently support the modeling services in IRIS. Our goal is by the time of the build, these repos will hold all services for reconciling phenotype data with models. The services in these repos will soon be applied to build draft models of all genomes in KBase CDM (genome_to_FBAmodel command). Draft models will be loaded in the CDM. This will be done before the build. Biochemistry is being loaded this upcoming week, along with phenotype data hopefully. I believe this biochemistry will include plant biochemistry, with support for plant modeling. So services we're targeting for the build: 1.) Plant model reconstruction (end of next week) 2.) Microbial model reconstruction (already in IRIS) 3.) Metagenome model reconstruction (this week) 4.) Model flux balance analysis including (already in IRIS) -flux variability analysis -single gene knockout -minimal media prediction -metabolic production analysis for non growing models -flux minimization -phenotype simulation (not sure the IRIS script supports this, but the web service does) 5.) Gapfilling of models (already in IRIS) 6.) Phenotype simulation and reconciliation (end of next week) Data we are targeting for the build: 1.) Biochemistry CDM (including plant biochemistry) 2.) Model CDM 3.) Phenotype CDM 4.) Document store for models and biochemistry Documentation is in progress... obviously, it's a lot to document, and these services are somewhat complex. Questions/comments welcome. Particularly, I want to know if you see something you were expecting us to produce but appears to be missing. Chris

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