September 2011 - Microbe - mailman3.cels.anl.gov

Microbe group telecon
by Paramvir Dehal 29 Sep '11

29 Sep '11

Hi Guys, We're going to have a telecon on Monday 10am Pacific, let me know if you can make it. We haven't settled on a final time for a recurring meeting yet, so don't worry if you can't make this one. 866-740-1260 Code: 4958182# Paramvir

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Re: [Microbe] Complete Microbes Demo Workflow
by Paramvir Dehal 22 Sep '11

22 Sep '11

Hi Steven, this is only for the 18month demo. SIFTER isn't being used for the first pass annotation because we are using the MicrobesOnline decorated trees as input to SIFTER. Our work flow is to get structural and functional annotations from RAST, make trees in MicrobesOnline and then refine annotations with SIFTER. Paramvir On Thu, Sep 22, 2011 at 9:23 AM, Steven E. Brenner <brenner(a)compbio.berkeley.edu> wrote: > Hi, > > I'm not sure why SIFTER isn't being used for the first-pass annotation. My > understanding was that RAST would be used for metagenomics due to speed > issues with SIFTER. > > Steven > > On Thu, 22 Sep 2011, Paramvir Dehal wrote: > >> I added a bit about projecting our other omics data onto the models. I >> accidentally a word in that last email. We should have a color code >> for development verses new functionality. >> >> On Thu, Sep 22, 2011 at 8:52 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: >>> >>> I'll make my changes to this. We have a color code for development >>> verses existing functionality. It's not clear that the new development >>> is in the kbase layer as opposed to within the cores. >>> >>> On Thu, Sep 22, 2011 at 8:35 AM, Christopher Henry >>> <chrisshenry(a)gmail.com> wrote: >>>> >>>> Okay. I realize I never explained the meaning of the colors. I added a >>>> key >>>> for this, and I deleted the first slide. >>>> Chris >>>> >>>> -----Original Message----- >>>> From: Paramvir Dehal [mailto:[email protected]] >>>> Sent: Thursday, September 22, 2011 10:32 AM >>>> To: Christopher Henry >>>> Cc: KBase Microbes List >>>> Subject: Re: [Microbe] Complete Microbes Demo Workflow >>>> >>>> Hi all, >>>> >>>> I added a couple boxes and SIFTER. I'll try and add a bit more stuff, >>>> but I >>>> might be constrained by space. >>>> >>>> Paramvir >>>> >>>> On Thu, Sep 22, 2011 at 8:03 AM, Christopher Henry >>>> <chrisshenry(a)gmail.com> >>>> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> >>>>> >>>>> Complete microbes demo workflow is attached. Look at slide 2, not slide >>>>> 1. >>>>> Please modify if you think things are missing and need to be added. >>>>> For example, sifter isn't on there. >>>>> >>>>> >>>>> >>>>> Chris >>>>> >>>>> _______________________________________________ >>>>> Microbe mailing list >>>>> Microbe(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/microbe >>>>> >>>>> >>>> >>> >> >

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Re: [Microbe] Complete Microbes Demo Workflow
by Steven E. Brenner 22 Sep '11

22 Sep '11

Hi, I'm not sure why SIFTER isn't being used for the first-pass annotation. My understanding was that RAST would be used for metagenomics due to speed issues with SIFTER. Steven On Thu, 22 Sep 2011, Paramvir Dehal wrote: > I added a bit about projecting our other omics data onto the models. I > accidentally a word in that last email. We should have a color code > for development verses new functionality. > > On Thu, Sep 22, 2011 at 8:52 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: >> I'll make my changes to this. We have a color code for development >> verses existing functionality. It's not clear that the new development >> is in the kbase layer as opposed to within the cores. >> >> On Thu, Sep 22, 2011 at 8:35 AM, Christopher Henry >> <chrisshenry(a)gmail.com> wrote: >>> Okay. I realize I never explained the meaning of the colors. I added a key >>> for this, and I deleted the first slide. >>> Chris >>> >>> -----Original Message----- >>> From: Paramvir Dehal [mailto:[email protected]] >>> Sent: Thursday, September 22, 2011 10:32 AM >>> To: Christopher Henry >>> Cc: KBase Microbes List >>> Subject: Re: [Microbe] Complete Microbes Demo Workflow >>> >>> Hi all, >>> >>> I added a couple boxes and SIFTER. I'll try and add a bit more stuff, but I >>> might be constrained by space. >>> >>> Paramvir >>> >>> On Thu, Sep 22, 2011 at 8:03 AM, Christopher Henry <chrisshenry(a)gmail.com> >>> wrote: >>>> Hi all, >>>> >>>> >>>> >>>> Complete microbes demo workflow is attached. Look at slide 2, not slide 1. >>>> Please modify if you think things are missing and need to be added. >>>> For example, sifter isn't on there. >>>> >>>> >>>> >>>> Chris >>>> >>>> _______________________________________________ >>>> Microbe mailing list >>>> Microbe(a)lists.kbase.us >>>> https://lists.kbase.us/mailman/listinfo/microbe >>>> >>>> >>> >> >

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Re: [Microbe] Complete Microbes Demo Workflow
by Paramvir Dehal 22 Sep '11

22 Sep '11

I added a bit about projecting our other omics data onto the models. I accidentally a word in that last email. We should have a color code for development verses new functionality. On Thu, Sep 22, 2011 at 8:52 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > I'll make my changes to this. We have a color code for development > verses existing functionality. It's not clear that the new development > is in the kbase layer as opposed to within the cores. > > On Thu, Sep 22, 2011 at 8:35 AM, Christopher Henry > <chrisshenry(a)gmail.com> wrote: >> Okay. I realize I never explained the meaning of the colors. I added a key >> for this, and I deleted the first slide. >> Chris >> >> -----Original Message----- >> From: Paramvir Dehal [mailto:[email protected]] >> Sent: Thursday, September 22, 2011 10:32 AM >> To: Christopher Henry >> Cc: KBase Microbes List >> Subject: Re: [Microbe] Complete Microbes Demo Workflow >> >> Hi all, >> >> I added a couple boxes and SIFTER. I'll try and add a bit more stuff, but I >> might be constrained by space. >> >> Paramvir >> >> On Thu, Sep 22, 2011 at 8:03 AM, Christopher Henry <chrisshenry(a)gmail.com> >> wrote: >>> Hi all, >>> >>> >>> >>> Complete microbes demo workflow is attached. Look at slide 2, not slide 1. >>> Please modify if you think things are missing and need to be added. >>> For example, sifter isn't on there. >>> >>> >>> >>> Chris >>> >>> _______________________________________________ >>> Microbe mailing list >>> Microbe(a)lists.kbase.us >>> https://lists.kbase.us/mailman/listinfo/microbe >>> >>> >> >

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Re: [Microbe] Complete Microbes Demo Workflow
by Paramvir Dehal 22 Sep '11

22 Sep '11

I'll make my changes to this. We have a color code for development verses existing functionality. It's not clear that the new development is in the kbase layer as opposed to within the cores. On Thu, Sep 22, 2011 at 8:35 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Okay. I realize I never explained the meaning of the colors. I added a key > for this, and I deleted the first slide. > Chris > > -----Original Message----- > From: Paramvir Dehal [mailto:[email protected]] > Sent: Thursday, September 22, 2011 10:32 AM > To: Christopher Henry > Cc: KBase Microbes List > Subject: Re: [Microbe] Complete Microbes Demo Workflow > > Hi all, > > I added a couple boxes and SIFTER. I'll try and add a bit more stuff, but I > might be constrained by space. > > Paramvir > > On Thu, Sep 22, 2011 at 8:03 AM, Christopher Henry <chrisshenry(a)gmail.com> > wrote: >> Hi all, >> >> >> >> Complete microbes demo workflow is attached. Look at slide 2, not slide 1. >> Please modify if you think things are missing and need to be added. >> For example, sifter isn't on there. >> >> >> >> Chris >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe >> >> >

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Re: [Microbe] Complete Microbes Demo Workflow
by Christopher Henry 22 Sep '11

22 Sep '11

Okay. I realize I never explained the meaning of the colors. I added a key for this, and I deleted the first slide. Chris -----Original Message----- From: Paramvir Dehal [mailto:[email protected]] Sent: Thursday, September 22, 2011 10:32 AM To: Christopher Henry Cc: KBase Microbes List Subject: Re: [Microbe] Complete Microbes Demo Workflow Hi all, I added a couple boxes and SIFTER. I'll try and add a bit more stuff, but I might be constrained by space. Paramvir On Thu, Sep 22, 2011 at 8:03 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Hi all, > > > > Complete microbes demo workflow is attached. Look at slide 2, not slide 1. > Please modify if you think things are missing and need to be added. > For example, sifter isn't on there. > > > > Chris > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Re: [Microbe] Complete Microbes Demo Workflow
by Paramvir Dehal 22 Sep '11

22 Sep '11

Hi all, I added a couple boxes and SIFTER. I'll try and add a bit more stuff, but I might be constrained by space. Paramvir On Thu, Sep 22, 2011 at 8:03 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Hi all, > > > > Complete microbes demo workflow is attached. Look at slide 2, not slide 1. > Please modify if you think things are missing and need to be added. For > example, sifter isn’t on there. > > > > Chris > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Complete Microbes Demo Workflow
by Christopher Henry 22 Sep '11

22 Sep '11

Hi all, Complete microbes demo workflow is attached. Look at slide 2, not slide 1. Please modify if you think things are missing and need to be added. For example, sifter isn't on there. Chris

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Partial workflow
by Christopher Henry 20 Sep '11

20 Sep '11

Example workflow -> highlighting transactions between KBase and Cores

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Registering KBase accounts
by Christopher Henry 20 Sep '11

20 Sep '11

Hi all, Everyone who needs to get a KBase account for the meeting this Thursday and Friday should register at this website: https://trac.kbase.us/projects/kbase/register Also, send Terry Disz (disz(a)mcs.anl.gov) an email with your name, preferred username, and email so we can forward on to the KBase systems guys. Chris

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