- Microbe - mailman3.cels.anl.gov

Re: [Microbe] FBA and phenotype simulation tutorials
by Christopher Henry 02 May '12

02 May '12

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 >>> >> > >

1 0

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

02 May '12

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 >>> >> > >

1 0

Re: [Microbe] FBA and phenotype simulation tutorials
by Christopher Henry 02 May '12

02 May '12

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 >> >

1 0

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

02 May '12

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 >> >

1 0

Re: [Microbe] FBA and phenotype simulation tutorials
by Christopher Henry 02 May '12

02 May '12

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 >

1 0

Re: [Microbe] FBA and phenotype simulation tutorials
by Ben Bowen 01 May '12

01 May '12

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 >

1 0

Re: [Microbe] FBA and phenotype simulation tutorials
by Robert Olson 25 Apr '12

25 Apr '12

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

1 0

FBA and phenotype simulation tutorials
by Christopher Henry 25 Apr '12

25 Apr '12

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

1 0

Monday meeting notes
by Paramvir Dehal 23 Apr '12

23 Apr '12

*04/23/12: KBase Microbes MeetingAtendees: Paramvir, Bill, Michael, Steven, John-Marc, Chris, Paul, Scott, Matt, Tom Agenda: - Microbes Quarterly Report - KBase Science Review May 2-3rd - Phenotype and FBA services (Chris Henry) - Metabolic Visualizations (Bill Riehl) Quarterly Report & Milestones - Milestone: “Established initial organism pages, including data QC, metabolic, regulatory models for microbial sciences” - Establish web service for the above, preliminary UI elements - widgets, GLAMM - Reconciliation web services ~ May 2nd or so, prototype/initial service. Will be in May 14th build - What about our August Milestones? revise these too - Quarterly Report Google Doc (to be started by Paramvir) - everyone should take a look and contribute - leads of subprojects should take a look at report and make sure your progress is covered & take a look at detailed milestones KBase Science Review - technical review of our implementation - presenters will get a phone call from Paramvir or Chris to discuss - Algorithms and services - User experience component? - Adam and Rick added this, so who knows what they mean! - could be inputs & outputs - ontologies being used Chris will put his FBAServices slides in the KBase Microbes Dropbox folder* KBaseTeam\Microbes Bill will put his GLAMM presentation in the Microbes Dropbox and send an email with some narrative about. KBaseTeam\Microbes Paramvir

1 0

Re: [Microbe] Microbes Call Today
by Paramvir Dehal 23 Apr '12

23 Apr '12

Sorry wrong passcode: *866-740-1260 Code: 4958182 * On Mon, Apr 23, 2012 at 8:17 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Just a reminder that we are having a KBase Microbes call today - 11am > Pacific/1pm Central/ 2pm Eastern > > 866-740-1260 Passcode 4952366# > > We are going to use readytalk, so please connect: > > http://www.readytalk.com > passcode: 4952366 > > Agenda: > > 1) Microbial Quarterly Report Milestones > 2) Bill presents GLAMM, using readytalk.com > 3) Chris introduce document on Phenotype & FBA services > > Please let me know if there are other items you'd like to add to our > agenda. > > Paramvir >

1 0