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

yet another toolbox for semi-automatic metabolic fba model reconstruction
by Michael Sneddon 22 Mar '13

22 Mar '13

This paper just came out. Looks like the toolbox runs in Matlab. Anyone know anything about this project? http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002980

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KBase Metabolic Modeling Bootcamp on Friday March 22, 1-3 PM
by Christopher Henry 20 Mar '13

20 Mar '13

Hello everyone, Here is the info for the modeling bootcamp this week. Please don't join until 1:10 if possible. We only have 25 slots on Webex, and I want to make sure our external customers get in first. We will be holding a KBase Modeling Bootcamp on Friday, March 22 from 1-3PM central time. We will hold the bootcamp on webex. The meeting connection information is: Where: https://meetings.webex.com/ Meeting number: 196 566 331 Password: This meeting does not require a password. For audio, the conference call number will be: US/CAN Toll Free: 1-888-850-4523 Participant Passcode: 913601 Don't use the webex number. Please be aware, I am RECORDING these bootcamps (audio and screen cast) for posting online. In this boot camp, we will use IRIS: http://prototypesite.net/iris/ We will use the workspace browser: http://140.221.92.49/ We will probably explore a number of other KBase labs: http://www.kbase.us/labs/ And I'll be using this google doc to store commands to make it easier to follow along: https://docs.google.com/document/d/1zwlrCMpMqGWjigjxFwihzcpsx_F69Uk8s9FxWtm… So load up your phenotype data… warm up your Globus KBase account… pick out your favorite genome, and get ready to have some modeling fun!!! And bring a notebook and sharpened pencils… because I definitely want feedback. Sorry for the late notice. If you can't make it to this one, not to fear. There will be many many more. Also, we post videos online: http://205.208.105.217/KBaseBootCamp01.html Best regards, Chris

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call today 11am P / 1pm C
by Paramvir Dehal 18 Mar '13

18 Mar '13

* * *866-740-1260 Code: 4958182* * * Let me know if you've got anything you'd like to add to the agenda. Agenda: Discuss Review

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Bootcamp Canceled today
by Christopher Henry 15 Mar '13

15 Mar '13

Hello everyone, The boot camp is canceled today. I'm at home with a sick baby, and I'm sick myself. We'll hold it next week, March 22, 1-3PM. Chris On Feb 21, 2013, at 10:00 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Hello everyone, > > We will be holding a KBase Modeling Bootcamp tomorrow (Friday) from Noon-2PM central time. As we have done previously, we will hold the bootcamp on webex. The meeting connection information is: > Where: https://meetings.webex.com/ > Meeting number: 195 363 936 > Password: This meeting does not require a password. > > Also, as previously, I would like to offer a conference call number for people to use for audio. The conference call number will be: > US/CAN Toll Free: 1-888-850-4523 > Participant Passcode: 913601 > > Don't use the webex number. Please be aware, I am RECORDING these bootcamps (audio and screen cast) for posting online. > > In this boot camp, we will use IRIS: > http://prototypesite.net/iris/ > > We will use the workspace browser: > http://140.221.92.49/ > > We will probably explore a number of KBase labs: > http://www.kbase.us/labs/ > > And I'll be using this google doc to store commands to make it easier to follow along: > https://docs.google.com/document/d/1zwlrCMpMqGWjigjxFwihzcpsx_F69Uk8s9FxWtm… > > So load up your phenotype data… warm up your Globus KBase account… pick out your favorite genome, and get ready to have some modeling fun!!! > And bring a notebook and sharpened pencils… because I definitely want feedback. > > Sorry for the late notice. If you can't make it to this one, not to fear. There will be many many more. Also, we post videos online: > http://205.208.105.217/KBaseBootCamp01.html > > I'm going to go ahead and officially schedule the FIRST post demo Modeling Bootcamp: > Friday, March 15, 1-3 PM central time > > Best regards, > > Chris

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Re: [Microbe] FBA model runner UI prototype
by Ben Bowen 14 Mar '13

14 Mar '13

I'm using the tool now on Chris's phenotypeDemo workspace, and it is totally awesome! Really nice work! See attached Attached are around 15 different medias for a few of the models Chris built. We need to add about 100 more medias and we'll run out of rows. To save space and make the columns skinny you could - remove the word "complete" from the cells; - remove the "model name" from all the cells (its in the row label); - vertically orient the text in the column headings ; and - limit the precision of the numbers to something like about ~3 decimal places. Ben -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Thu, Mar 14, 2013 at 11:25 AM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > Mostly as an excuse to learn some javascript, I have started piecing > together a simple interface for running FBA models. > > http://140.221.84.246/microbes_model_runner/fba_model_runner.html > > The interface allows you to create a table of runFBA parameters, with > different media conditions for each column and model formulations for each > row. Calls to runfba are automatically generated, and the table is filled > in with growth results as the runfba jobs are completed. See the attached > screenshot for an example. > > Since this minimal interface may already be useful for some of you, I > thought I'd send it around now for testing and to see what everyone thinks. > > I can only take partial credit for what you see - the nicer looking bits > were mostly stolen from Matt and Bill's model builder, and Paramvir came up > with the original idea :) . > > -michael > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

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FBA model runner UI prototype
by Michael Sneddon 14 Mar '13

14 Mar '13

Mostly as an excuse to learn some javascript, I have started piecing together a simple interface for running FBA models. http://140.221.84.246/microbes_model_runner/fba_model_runner.html The interface allows you to create a table of runFBA parameters, with different media conditions for each column and model formulations for each row. Calls to runfba are automatically generated, and the table is filled in with growth results as the runfba jobs are completed. See the attached screenshot for an example. Since this minimal interface may already be useful for some of you, I thought I'd send it around now for testing and to see what everyone thinks. I can only take partial credit for what you see - the nicer looking bits were mostly stolen from Matt and Bill's model builder, and Paramvir came up with the original idea :) . -michael

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Re: [Microbe] microbes internal self review
by Keith Keller 13 Mar '13

13 Mar '13

On Tue, Mar 12, 2013 at 9:07 PM, Keith Keller <kkeller(a)lbl.gov> wrote: > > We did Gavin's review this afternoon We reviewed my services today, which means we're done first. You know what that makes us, of course: ARCHITECTURE REVIEW CHAMPIONS! --keith -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab

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Re: [Microbe] microbes internal self review
by Keith Keller 12 Mar '13

12 Mar '13

Hey all, > https://docs.google.com/a/lbl.gov/document/d/1ebc6jWxnudsOtZWo3RNoWDhFFDFG3… We did Gavin's review this afternoon, and afterwards Gavin very kindly organized the review into bullet points (below Paramvir's original writeup). It might help other people to use that, or it might be better with a looser format. (We're going to use the bullets for my arch review.) --keith -- Keith Keller kkeller(a)lbl.gov Physical Biosciences Division, Lawrence Berkeley National Lab

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Re: [Microbe] microbes internal self review
by Pavel Novichkov 12 Mar '13

12 Mar '13

Great idea! P. On Mar 12, 2013, at 2:49 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Hey Everyone, > > Okay, before we kick off more projects, we're going to take a bit of time to look at what we've done, how we've done it, what we've learned, and how we'd like to improve. To do that, we need review what we've done. This will be more of an informal architecture & process review than a code review. > > Here's how it will work. Everyone will pair up and describe verbally what they've done using the guidelines in our google doc: > > https://docs.google.com/a/lbl.gov/document/d/1ebc6jWxnudsOtZWo3RNoWDhFFDFG3… > > The listener should ask questions and will be responsible for taking notes and reporting back to me. And then they should switch roles. What I'd like to get out of this are things that we think need to be refactored and a more subjective set of guidelines for improving our process. I'll collate the notes and we can have a discussion at our next Microbes call on 3/18. > > I've paired people, let me know if I've left anyone out. > > Chris & Mike > Paul & Neal > Matt D. & Bill > Pavel & Steve > Keith & Gavin > John-Marc & Marcin > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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microbes internal self review
by Paramvir Dehal 12 Mar '13

12 Mar '13

Hey Everyone, Okay, before we kick off more projects, we're going to take a bit of time to look at what we've done, how we've done it, what we've learned, and how we'd like to improve. To do that, we need review what we've done. This will be more of an informal architecture & process review than a code review. Here's how it will work. Everyone will pair up and describe verbally what they've done using the guidelines in our google doc: https://docs.google.com/a/lbl.gov/document/d/1ebc6jWxnudsOtZWo3RNoWDhFFDFG3… The listener should ask questions and will be responsible for taking notes and reporting back to me. And then they should switch roles. What I'd like to get out of this are things that we think need to be refactored and a more subjective set of guidelines for improving our process. I'll collate the notes and we can have a discussion at our next Microbes call on 3/18. I've paired people, let me know if I've left anyone out. Chris & Mike Paul & Neal Matt D. & Bill Pavel & Steve Keith & Gavin John-Marc & Marcin

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