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Microbes Telecon 10/17 11am P / 1pm C
by Paramvir Dehal 12 Oct '11

12 Oct '11

This a reminder that we have a Microbes Telecon next monday at 11am P / 1pm C. Are there any agenda items people would like to bring up? 1-866-740-1260 Code: 4958182# Paramvir

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Re: [Microbe] Microbe group telecon
by Paramvir Dehal 03 Oct '11

03 Oct '11

Sorry everyone, I'm stuck in a meeting up on the hill that should have ended along time ago. We'll have to reschedule. Sorry again, Paramvir On Mon, Oct 3, 2011 at 10:17 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Unfortunately, I don't have the chairperson password, so I couldn't get > things started myself. I'll try and get that for the next call so Paramvir > has backup. > > Let's try again another time. Sorry all. > > Chris > > -----Original Message----- > From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] > On Behalf Of Ben Bowen > Sent: Monday, October 03, 2011 12:14 PM > To: John-Marc Chandonia > Cc: KBase Microbes List > Subject: Re: [Microbe] Microbe group telecon > > I just disconnected too > -------------- > Email: BPBowen(a)lbl.gov > Office: 510-486-5138 > Cell: 480-225-2341 > MS 84RO171, Lawrence Berkeley Lab > > > > On Mon, Oct 3, 2011 at 10:10 AM, John-Marc Chandonia <JMChandonia(a)lbl.gov> > wrote: >> On Thu, Sep 29, 2011 at 02:53:47PM -0700, Paramvir Dehal wrote: >>> 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# >> >> I waited 10 minutes then gave up--is this the right number? >> >> JMC >> -- >> John-Marc Chandonia (JMChandonia(a)lbl.gov) We're > everywhere... >> Physical Biosciences Division, Berkeley National Lab for your > convenience. >> http://www.strgen.org/~jmc/ -- Psi >> Corps <*> >> >> _______________________________________________ >> 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 > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

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Re: [Microbe] Microbe group telecon
by Christopher Henry 03 Oct '11

03 Oct '11

Unfortunately, I don't have the chairperson password, so I couldn't get things started myself. I'll try and get that for the next call so Paramvir has backup. Let's try again another time. Sorry all. Chris -----Original Message----- From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Ben Bowen Sent: Monday, October 03, 2011 12:14 PM To: John-Marc Chandonia Cc: KBase Microbes List Subject: Re: [Microbe] Microbe group telecon I just disconnected too -------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 Cell: 480-225-2341 MS 84RO171, Lawrence Berkeley Lab On Mon, Oct 3, 2011 at 10:10 AM, John-Marc Chandonia <JMChandonia(a)lbl.gov> wrote: > On Thu, Sep 29, 2011 at 02:53:47PM -0700, Paramvir Dehal wrote: >> 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# > > I waited 10 minutes then gave up--is this the right number? > > JMC > -- > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... > Physical Biosciences Division, Berkeley National Lab for your convenience. > http://www.strgen.org/~jmc/ -- Psi > Corps <*> > > _______________________________________________ > 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] Microbe group telecon
by Ben Bowen 03 Oct '11

03 Oct '11

I just disconnected too -------------- Email: BPBowen(a)lbl.gov Office: 510-486-5138 Cell: 480-225-2341 MS 84RO171, Lawrence Berkeley Lab On Mon, Oct 3, 2011 at 10:10 AM, John-Marc Chandonia <JMChandonia(a)lbl.gov> wrote: > On Thu, Sep 29, 2011 at 02:53:47PM -0700, Paramvir Dehal wrote: >> 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# > > I waited 10 minutes then gave up--is this the right number? > > JMC > -- > John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... > Physical Biosciences Division, Berkeley National Lab for your convenience. > http://www.strgen.org/~jmc/ -- Psi Corps <*> > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Re: [Microbe] Microbe group telecon
by John-Marc Chandonia 03 Oct '11

03 Oct '11

On Thu, Sep 29, 2011 at 02:53:47PM -0700, Paramvir Dehal wrote: > 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# I waited 10 minutes then gave up--is this the right number? JMC -- John-Marc Chandonia (JMChandonia(a)lbl.gov) We're everywhere... Physical Biosciences Division, Berkeley National Lab for your convenience. http://www.strgen.org/~jmc/ -- Psi Corps <*>

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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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