May 2013 - Microbe - mailman3.cels.anl.gov

Re: [Microbe] what are the proper flags for gapfilling a model?
by Christopher Henry 23 May '13

23 May '13

Paramvir, I actually removed the "no submit" thing. I removed cluster services entirely from the FBA. Instead, a job is created and placed in the workspace, and a separate generic scheduler script runs that job. My thought is that the scheduler should handle submission to nersc when we're ready to do that. It shouldn't be done directly by the FBA service. This gives us maximum flexibility in handling the FBA jobs in KBase. Chris On May 23, 2013, at 2:18 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Matt, did anyone answer your questions? > > The --nosubmit is still necessary as far as I know. > > > On Tue, May 21, 2013 at 9:01 AM, Matt DeJongh <dejongh(a)hope.edu> wrote: > I remember that there is an undocuments --nosubmit or something like that ... is it still necessary? Anything else? Thanks, > > Matt > > -- > Matt DeJongh, Ph.D. > Computer Science Department > Hope College, Holland, MI 49423 > (616) 395-7429 > > _______________________________________________ > 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] what are the proper flags for gapfilling a model?
by Paramvir Dehal 23 May '13

23 May '13

Matt, did anyone answer your questions? The --nosubmit is still necessary as far as I know. On Tue, May 21, 2013 at 9:01 AM, Matt DeJongh <dejongh(a)hope.edu> wrote: > I remember that there is an undocuments --nosubmit or something like that > ... is it still necessary? Anything else? Thanks, > > Matt > > -- > Matt DeJongh, Ph.D. > Computer Science Department > Hope College, Holland, MI 49423 > (616) 395-7429 > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Re: [Microbe] workspace browser - choose workspace service?
by Neal Conrad 22 May '13

22 May '13

Hi Matt, Do you mean use a different workspace via something like "/browser.html/workspace/<workspace_name>"? If so, no, there's no url routing right now. I've been learning the ws browser code and working on some new features, so I'll append this to the list. Thanks, Neal On May 22, 2013, at 8:05 AM, Matt DeJongh wrote: > Is there a way to configure the workspace browser to use a different workspace service by specifying the URL? > > -- > Matt DeJongh, Ph.D. > Computer Science Department > Hope College, Holland, MI 49423 > (616) 395-7429 > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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workspace browser - choose workspace service?
by Matt DeJongh 22 May '13

22 May '13

Is there a way to configure the workspace browser to use a different workspace service by specifying the URL? -- Matt DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

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what are the proper flags for gapfilling a model?
by Matt DeJongh 21 May '13

21 May '13

I remember that there is an undocuments --nosubmit or something like that ... is it still necessary? Anything else? Thanks, Matt -- Matt DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

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3 month project objectives
by Paramvir Dehal 20 May '13

20 May '13

Hi guys, Let's try and do a group edit in the google doc: https://docs.google.com/a/lbl.gov/document/d/17IF8zbzk77mdRlvkdFEKESe9zQDqL… * Please indicate which lettered tasks you would like to lead by writing your name next to it in bold. Indicate which tasks you would like be a team member of by writing your name next to it. If you think a task is already done, a mistake, or should be removed from the list, add a comment with your reason why it should be removed. If you think something is critical/very high priority, indicate that in the comments as well. If there are tasks missing, add them to the end of the list. Do not mess up the numbering!!!!*

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3 month project wide objectives
by Paramvir Dehal 20 May '13

20 May '13

Hey guys, Adam and Rick have created a list of 3 month project objectives, it's a large list, but we have a lot of people on the project so we should assume that we'll get through most of it. I want everyone to go through the list, and for each Number.Lettered task mark the following: 1) Each of the Number.Letter tasks needs to have a single point person. If you'd like to lead that task, please let me know. 2) If something has already been done, let me know. 3) If you think something is a mistake, a bad idea, or doesn't have to be done immediately, let me know. 4) And anything that you guys feel is a very high priority and critical to our success, flag those ones as well. 5) If you feel like you could work on the team responsible for completing the task, let me know. Please consider all the tasks. Don't worry about putting your self down on too many tasks. I imagine that all of these tasks will be carried out by a 2-5 person team and Nomi will make sure that the time lines and resources are lined up right. The document is due to Rick and Adam on Wednesday, so please have this back to me and Chris by Tuesday. Chris and I will go over your input and give them a single doc from the Microbes team. Please note that these tasks are the only KBase related work authorized during those 3 months. Thanks, Paramvir

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call today!
by Paramvir Dehal 20 May '13

20 May '13

We'll have our weekly microbes call today at 11am P / 1pm C *866-740-1260 Code: 4958182* Here's the agenda so far: 1) Build Notes 2) Hackathon follow up 3) 3 month objectives Send me any agenda items you guys have. Paramvir

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call canceled today
by Paramvir Dehal 13 May '13

13 May '13

We should all be at the build, so no call today

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microbes call
by Paramvir Dehal 06 May '13

06 May '13

Let me know if you have any agenda items for our call. Not much has changed so the call will be very short. Agenda: Weekly release targets Next week's Hack-a-thon *866-740-1260 Code: 4958182 * * * *Paramvir*

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