September 2012 - Microbe - mailman3.cels.anl.gov

Microbes call today 11am P/ 1pm C
by Paramvir Dehal 24 Sep '12

24 Sep '12

Hey guys, The call starts in about 1hr. Let me know if you guys have any agenda items. 866-740-1260 Code: 4958182 The Argonne team is visiting Berkeley this week and will be in transit during the call. Paramvir

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Google doc with proposed use scenarios for phenotype reconciliation
by Christopher Henry 15 Sep '12

15 Sep '12

Hello all, So the pieces are all falling into place on the phenotype simulation infrastructure. We are now facing the tasking of developing a mature design for the user-experience we are shooting for. I've prepped a google doc describing the IRIS and UI user experiences. https://docs.google.com/document/d/1h6yn1eQnR92Z6Orow-DmDcLCPjbQBMyzsHKHJuI… I honestly believe we can easily achieve both by the demo. I am expecting the IRIS pipeline to be complete in October, at which point I intend to switch gears to ensuring all UI elements will be in place. My team will be largely focused on the model UI initially, and I believe the berkley guys are already thinking about/working on the phenotype UI. One thing I want to caution people on. Most phenotype datasets that are out there right now... are not nearly as large or as comprehensive as the berkley data sets Adam D. is producing. I just want to be careful we're not building our entire user experience around handling a dataset that currently only one lab is producing. The vast majority of users will be uploading triple replicates of Biolog array results for a single strain. I'm not saying we don't need to handle Adam's data. Obviously, we do. Afterall, we want him to speak at the contractors meeting. I'm just saying we should be cautious about allowing that one dataset to drive the entire design.... Chris

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Re: [Microbe] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Ben Bowen 10 Sep '12

10 Sep '12

Hi Steven, We drafted tasks, timelines, and ownership for the demo. It was free-form brainstorming, and many good ideas were captured. You can see progress here: https://docs.google.com/spreadsheet/ccc?key=0Ai_DK9EJqbDEdHVudG9YX3h2NkJlZ0… Ben -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Sep 10, 2012 at 7:04 PM, Steven E. Brenner < brenner(a)compbio.berkeley.edu> wrote: > Sorry I could not make the call, as it was an untenable time in Shanghai. > > > On Mon, 10 Sep 2012, Gavin A Price wrote: > > The to-do list we started on in the meeting has been moved over to an >> excel style doc. Please use that one for >> further updates. It's in the collection KBase Project/Microbes like the >> first doc. >> >> -g >> >> On 9/10/2012 10:55 AM, Gavin Price wrote: >> Agenda: >> >> - Make list of items, owners, and dates for stuff that needs to be >> done for the microbes demo >> - Quick discussion of PNNL proteomics data and owners for use cases >> - Dealing with uneven sampling of genomes >> >> On 9/10/2012 10:20 AM, Ben Bowen wrote: >> Agenda Item: For the microbes-demo, list specific items we >> need to cross off and when they >> need to be done by. >> -------------- >> Email: BPBowen(a)lbl.gov >> Phone: (510) 214-6683 >> MS 977-221, Lawrence Berkeley Lab >> Web: ms.lbl.gov >> >> >> On Mon, Sep 10, 2012 at 10:07 AM, Michael Sneddon < >> mwsneddon(a)lbl.gov> wrote: >> One issue that came up last week is how we are going to >> deal with an uneven >> sampling of sequences in KBase in which certain >> sub-families will likely be >> vastly over/under represented. This came up in the >> context of >> visualizing/analyzing trees (where we would like to >> have some smart way to >> collapse internal nodes so that half the tree displayed >> to a user isn't just >> variants of e.coli). Talking briefly to Paramvir >> though, this seems to be a >> more general problem which will affect many aspects of >> data interpretation and >> visualization in kbase. >> >> This discussion will probably also be related to figuring out how to set >> up the "kbase" pipeline >> for processing new sequences and adding the new annotations, trees, etc >> to the CDS. I'm not sure >> how high on the priority list this is now, but if there is time it might >> be worth discussing. >> -michael >> >> >> >> On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov> wrote: >> Ready talk call in #: 1-866-740-1260 >> code 4958182 >> >> If Paramvir isn't calling in, I have the operator code and will >> start the conf. >> >> Please send any agenda items we need to discuss to me and I'll roll >> them up in an >> email slightly prior to the meeting. >> >> -g >> >> >> >> On 9/10/2012 9:19 AM, Paramvir Dehal wrote: >> We should still have one. Gavin, can you collect agenda items >> and send >> out the reminder email? >> >> Pavel, John-Marc and Bill are also at this conference. >> >> >> >> On Mon, Sep 10, 2012 at 7:46 AM, Gavin Price<gaprice(a)lbl.gov> >> wrote: >> Not sure if we're having one since paramvir is at a >> conference. >> >> -g >> >> >> ______________________________**_________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/**mailman/listinfo/microbe<https://lists.kbase.us/mailman/listinfo/microbe> >> >> ______________________________**_________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/**mailman/listinfo/microbe<https://lists.kbase.us/mailman/listinfo/microbe> >> >> >> >> ______________________________**_________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/**mailman/listinfo/microbe<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] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Steven E. Brenner 10 Sep '12

10 Sep '12

Sorry I could not make the call, as it was an untenable time in Shanghai. On Mon, 10 Sep 2012, Gavin A Price wrote: > The to-do list we started on in the meeting has been moved over to an excel style doc. Please use that one for > further updates. It's in the collection KBase Project/Microbes like the first doc. > > -g > > On 9/10/2012 10:55 AM, Gavin Price wrote: > Agenda: > > - Make list of items, owners, and dates for stuff that needs to be done for the microbes demo > - Quick discussion of PNNL proteomics data and owners for use cases > - Dealing with uneven sampling of genomes > > On 9/10/2012 10:20 AM, Ben Bowen wrote: > Agenda Item: For the microbes-demo, list specific items we need to cross off and when they > need to be done by. > -------------- > Email:ï¿½[email protected] > Phone:ï¿½(510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web:ï¿½ms.lbl.gov > > > On Mon, Sep 10, 2012 at 10:07 AM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > One issue that came up last week is how we are going to deal with an uneven > sampling of sequences in KBase in which certain sub-families will likely be > vastly over/under represented. ï¿½This came up in the context of > visualizing/analyzing trees (where we would like to have some smart way to > collapse internal nodes so that half the tree displayed to a user isn't just > variants of e.coli). ï¿½Talking briefly to Paramvir though, this seems to be a > more general problem which will affect many aspects of data interpretation and > visualization in kbase. > > This discussion will probably also be related to figuring out how to set up the "kbase" pipeline > for processing new sequences and adding the new annotations, trees, etc to the CDS. ï¿½I'm not sure > how high on the priority list this is now, but if there is time it might be worth discussing. > -michael > > > > On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov> wrote: > Ready talk call in #: 1-866-740-1260 > code 4958182 > > If Paramvir isn't calling in, I have the operator code and will start the conf. > > Please send any agenda items we need to discuss to me and I'll roll them up in an > email slightly prior to the meeting. > > -g > > > > On 9/10/2012 9:19 AM, Paramvir Dehal wrote: > We should still have one. Gavin, can you collect agenda items and send > out the reminder email? > > Pavel, John-Marc and Bill are also at this conference. > > > > On Mon, Sep 10, 2012 at 7:46 AM, Gavin Price<gaprice(a)lbl.gov> ï¿½wrote: > Not sure if we're having one since paramvir is at a > conference. > > -g > > > _______________________________________________ > 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] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Gavin A Price 10 Sep '12

10 Sep '12

The to-do list we started on in the meeting has been moved over to an excel style doc. Please use that one for further updates. It's in the collection KBase Project/Microbes like the first doc. -g On 9/10/2012 10:55 AM, Gavin Price wrote: > Agenda: > > - Make list of items, owners, and dates for stuff that needs to be > done for the microbes demo > - Quick discussion of PNNL proteomics data and owners for use cases > - Dealing with uneven sampling of genomes > > On 9/10/2012 10:20 AM, Ben Bowen wrote: >> Agenda Item: For the microbes-demo, list specific items we need to >> cross off and when they need to be done by. >> -------------- >> Email: BPBowen(a)lbl.gov <mailto:[email protected]> >> Phone: (510) 214-6683 >> MS 977-221, Lawrence Berkeley Lab >> Web: ms.lbl.gov <http://ms.lbl.gov> >> >> >> On Mon, Sep 10, 2012 at 10:07 AM, Michael Sneddon <mwsneddon(a)lbl.gov >> <mailto:[email protected]>> wrote: >> >> One issue that came up last week is how we are going to deal with >> an uneven sampling of sequences in KBase in which certain >> sub-families will likely be vastly over/under represented. This >> came up in the context of visualizing/analyzing trees (where we >> would like to have some smart way to collapse internal nodes so >> that half the tree displayed to a user isn't just variants of >> e.coli). Talking briefly to Paramvir though, this seems to be a >> more general problem which will affect many aspects of data >> interpretation and visualization in kbase. >> >> This discussion will probably also be related to figuring out how >> to set up the "kbase" pipeline for processing new sequences and >> adding the new annotations, trees, etc to the CDS. I'm not sure >> how high on the priority list this is now, but if there is time >> it might be worth discussing. >> >> -michael >> >> >> >> >> On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov >> <mailto:[email protected]>> wrote: >> >> Ready talk call in #: 1-866-740-1260 <tel:1-866-740-1260> >> code 4958182 >> >> If Paramvir isn't calling in, I have the operator code and >> will start the conf. >> >> Please send any agenda items we need to discuss to me and >> I'll roll them up in an email slightly prior to the meeting. >> >> -g >> >> >> >> On 9/10/2012 9:19 AM, Paramvir Dehal wrote: >> >> We should still have one. Gavin, can you collect agenda >> items and send >> out the reminder email? >> >> Pavel, John-Marc and Bill are also at this conference. >> >> >> >> On Mon, Sep 10, 2012 at 7:46 AM, Gavin >> Price<gaprice(a)lbl.gov <mailto:[email protected]>> wrote: >> >> Not sure if we're having one since paramvir is at a >> conference. >> >> -g >> >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us <mailto:[email protected]> >> https://lists.kbase.us/mailman/listinfo/microbe >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us <mailto:[email protected]> >> https://lists.kbase.us/mailman/listinfo/microbe >> >> >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us <mailto:[email protected]> >> https://lists.kbase.us/mailman/listinfo/microbe >> >>

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Re: [Microbe] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Ben Bowen 10 Sep '12

10 Sep '12

Here is another one: kind of slow to load http://metaboliteatlas.lbl.gov/~bpb/Demo/PhenotypePage/ViewKBaseCommands.ht… -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Sep 10, 2012 at 11:38 AM, Ben Bowen <ben.bowen(a)gmail.com> wrote: > > http://metaboliteatlas.lbl.gov/~bpb/Demo/PhenotypePage/ViewKBaseCommands2.h… > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Mon, Sep 10, 2012 at 10:55 AM, Gavin Price <gaprice(a)lbl.gov> wrote: > >> Agenda: >> >> - Make list of items, owners, and dates for stuff that needs to be done >> for the microbes demo >> - Quick discussion of PNNL proteomics data and owners for use cases >> - Dealing with uneven sampling of genomes >> >> >> On 9/10/2012 10:20 AM, Ben Bowen wrote: >> >> Agenda Item: For the microbes-demo, list specific items we need to cross >> off and when they need to be done by. >> -------------- >> Email: BPBowen(a)lbl.gov >> Phone: (510) 214-6683 >> MS 977-221, Lawrence Berkeley Lab >> Web: ms.lbl.gov >> >> >> On Mon, Sep 10, 2012 at 10:07 AM, Michael Sneddon <mwsneddon(a)lbl.gov>wrote: >> >>> One issue that came up last week is how we are going to deal with an >>> uneven sampling of sequences in KBase in which certain sub-families will >>> likely be vastly over/under represented. This came up in the context of >>> visualizing/analyzing trees (where we would like to have some smart way to >>> collapse internal nodes so that half the tree displayed to a user isn't >>> just variants of e.coli). Talking briefly to Paramvir though, this seems >>> to be a more general problem which will affect many aspects of data >>> interpretation and visualization in kbase. >>> >>> This discussion will probably also be related to figuring out how to >>> set up the "kbase" pipeline for processing new sequences and adding the new >>> annotations, trees, etc to the CDS. I'm not sure how high on the priority >>> list this is now, but if there is time it might be worth discussing. >>> >>> -michael >>> >>> >>> >>> >>> On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov> wrote: >>> >>>> Ready talk call in #: 1-866-740-1260 >>>> code 4958182 >>>> >>>> If Paramvir isn't calling in, I have the operator code and will start >>>> the conf. >>>> >>>> Please send any agenda items we need to discuss to me and I'll roll >>>> them up in an email slightly prior to the meeting. >>>> >>>> -g >>>> >>>> >>>> >>>> On 9/10/2012 9:19 AM, Paramvir Dehal wrote: >>>> >>>>> We should still have one. Gavin, can you collect agenda items and send >>>>> out the reminder email? >>>>> >>>>> Pavel, John-Marc and Bill are also at this conference. >>>>> >>>>> >>>>> >>>>> On Mon, Sep 10, 2012 at 7:46 AM, Gavin Price<gaprice(a)lbl.gov> wrote: >>>>> >>>>>> Not sure if we're having one since paramvir is at a conference. >>>>>> >>>>>> -g >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>> >>> >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe >> >> >

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Re: [Microbe] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Ben Bowen 10 Sep '12

10 Sep '12

http://metaboliteatlas.lbl.gov/~bpb/Demo/PhenotypePage/ViewKBaseCommands2.h… -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Sep 10, 2012 at 10:55 AM, Gavin Price <gaprice(a)lbl.gov> wrote: > Agenda: > > - Make list of items, owners, and dates for stuff that needs to be done > for the microbes demo > - Quick discussion of PNNL proteomics data and owners for use cases > - Dealing with uneven sampling of genomes > > > On 9/10/2012 10:20 AM, Ben Bowen wrote: > > Agenda Item: For the microbes-demo, list specific items we need to cross > off and when they need to be done by. > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Mon, Sep 10, 2012 at 10:07 AM, Michael Sneddon <mwsneddon(a)lbl.gov>wrote: > >> One issue that came up last week is how we are going to deal with an >> uneven sampling of sequences in KBase in which certain sub-families will >> likely be vastly over/under represented. This came up in the context of >> visualizing/analyzing trees (where we would like to have some smart way to >> collapse internal nodes so that half the tree displayed to a user isn't >> just variants of e.coli). Talking briefly to Paramvir though, this seems >> to be a more general problem which will affect many aspects of data >> interpretation and visualization in kbase. >> >> This discussion will probably also be related to figuring out how to set >> up the "kbase" pipeline for processing new sequences and adding the new >> annotations, trees, etc to the CDS. I'm not sure how high on the priority >> list this is now, but if there is time it might be worth discussing. >> >> -michael >> >> >> >> >> On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov> wrote: >> >>> Ready talk call in #: 1-866-740-1260 >>> code 4958182 >>> >>> If Paramvir isn't calling in, I have the operator code and will start >>> the conf. >>> >>> Please send any agenda items we need to discuss to me and I'll roll them >>> up in an email slightly prior to the meeting. >>> >>> -g >>> >>> >>> >>> On 9/10/2012 9:19 AM, Paramvir Dehal wrote: >>> >>>> We should still have one. Gavin, can you collect agenda items and send >>>> out the reminder email? >>>> >>>> Pavel, John-Marc and Bill are also at this conference. >>>> >>>> >>>> >>>> On Mon, Sep 10, 2012 at 7:46 AM, Gavin Price<gaprice(a)lbl.gov> wrote: >>>> >>>>> Not sure if we're having one since paramvir is at a conference. >>>>> >>>>> -g >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >> >> > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Re: [Microbe] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Gavin Price 10 Sep '12

10 Sep '12

Agenda: - Make list of items, owners, and dates for stuff that needs to be done for the microbes demo - Quick discussion of PNNL proteomics data and owners for use cases - Dealing with uneven sampling of genomes On 9/10/2012 10:20 AM, Ben Bowen wrote: > Agenda Item: For the microbes-demo, list specific items we need to > cross off and when they need to be done by. > -------------- > Email: BPBowen(a)lbl.gov <mailto:[email protected]> > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov <http://ms.lbl.gov> > > > On Mon, Sep 10, 2012 at 10:07 AM, Michael Sneddon <mwsneddon(a)lbl.gov > <mailto:[email protected]>> wrote: > > One issue that came up last week is how we are going to deal with > an uneven sampling of sequences in KBase in which certain > sub-families will likely be vastly over/under represented. This > came up in the context of visualizing/analyzing trees (where we > would like to have some smart way to collapse internal nodes so > that half the tree displayed to a user isn't just variants of > e.coli). Talking briefly to Paramvir though, this seems to be a > more general problem which will affect many aspects of data > interpretation and visualization in kbase. > > This discussion will probably also be related to figuring out how > to set up the "kbase" pipeline for processing new sequences and > adding the new annotations, trees, etc to the CDS. I'm not sure > how high on the priority list this is now, but if there is time it > might be worth discussing. > > -michael > > > > > On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov > <mailto:[email protected]>> wrote: > > Ready talk call in #: 1-866-740-1260 <tel:1-866-740-1260> > code 4958182 > > If Paramvir isn't calling in, I have the operator code and > will start the conf. > > Please send any agenda items we need to discuss to me and I'll > roll them up in an email slightly prior to the meeting. > > -g > > > > On 9/10/2012 9:19 AM, Paramvir Dehal wrote: > > We should still have one. Gavin, can you collect agenda > items and send > out the reminder email? > > Pavel, John-Marc and Bill are also at this conference. > > > > On Mon, Sep 10, 2012 at 7:46 AM, Gavin > Price<gaprice(a)lbl.gov <mailto:[email protected]>> wrote: > > Not sure if we're having one since paramvir is at a > conference. > > -g > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us <mailto:[email protected]> > https://lists.kbase.us/mailman/listinfo/microbe > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us <mailto:[email protected]> > https://lists.kbase.us/mailman/listinfo/microbe > > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us <mailto:[email protected]> > https://lists.kbase.us/mailman/listinfo/microbe > >

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Re: [Microbe] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Ben Bowen 10 Sep '12

10 Sep '12

Agenda Item: For the microbes-demo, list specific items we need to cross off and when they need to be done by. -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Sep 10, 2012 at 10:07 AM, Michael Sneddon <mwsneddon(a)lbl.gov> wrote: > One issue that came up last week is how we are going to deal with an > uneven sampling of sequences in KBase in which certain sub-families will > likely be vastly over/under represented. This came up in the context of > visualizing/analyzing trees (where we would like to have some smart way to > collapse internal nodes so that half the tree displayed to a user isn't > just variants of e.coli). Talking briefly to Paramvir though, this seems > to be a more general problem which will affect many aspects of data > interpretation and visualization in kbase. > > This discussion will probably also be related to figuring out how to set > up the "kbase" pipeline for processing new sequences and adding the new > annotations, trees, etc to the CDS. I'm not sure how high on the priority > list this is now, but if there is time it might be worth discussing. > > -michael > > > > > On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov> wrote: > >> Ready talk call in #: 1-866-740-1260 >> code 4958182 >> >> If Paramvir isn't calling in, I have the operator code and will start the >> conf. >> >> Please send any agenda items we need to discuss to me and I'll roll them >> up in an email slightly prior to the meeting. >> >> -g >> >> >> >> On 9/10/2012 9:19 AM, Paramvir Dehal wrote: >> >>> We should still have one. Gavin, can you collect agenda items and send >>> out the reminder email? >>> >>> Pavel, John-Marc and Bill are also at this conference. >>> >>> >>> >>> On Mon, Sep 10, 2012 at 7:46 AM, Gavin Price<gaprice(a)lbl.gov> wrote: >>> >>>> Not sure if we're having one since paramvir is at a conference. >>>> >>>> -g >>>> >>>> >>>> ______________________________**_________________ >>>> Microbe mailing list >>>> Microbe(a)lists.kbase.us >>>> https://lists.kbase.us/**mailman/listinfo/microbe<https://lists.kbase.us/mailman/listinfo/microbe> >>>> >>>> ______________________________**_________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/**mailman/listinfo/microbe<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] Microbes meeting today, 11am PST, 1pm CST [was: Re: Microbes mtg today?]
by Michael Sneddon 10 Sep '12

10 Sep '12

One issue that came up last week is how we are going to deal with an uneven sampling of sequences in KBase in which certain sub-families will likely be vastly over/under represented. This came up in the context of visualizing/analyzing trees (where we would like to have some smart way to collapse internal nodes so that half the tree displayed to a user isn't just variants of e.coli). Talking briefly to Paramvir though, this seems to be a more general problem which will affect many aspects of data interpretation and visualization in kbase. This discussion will probably also be related to figuring out how to set up the "kbase" pipeline for processing new sequences and adding the new annotations, trees, etc to the CDS. I'm not sure how high on the priority list this is now, but if there is time it might be worth discussing. -michael On Mon, Sep 10, 2012 at 9:25 AM, Gavin Price <gaprice(a)lbl.gov> wrote: > Ready talk call in #: 1-866-740-1260 > code 4958182 > > If Paramvir isn't calling in, I have the operator code and will start the > conf. > > Please send any agenda items we need to discuss to me and I'll roll them > up in an email slightly prior to the meeting. > > -g > > > > On 9/10/2012 9:19 AM, Paramvir Dehal wrote: > >> We should still have one. Gavin, can you collect agenda items and send >> out the reminder email? >> >> Pavel, John-Marc and Bill are also at this conference. >> >> >> >> On Mon, Sep 10, 2012 at 7:46 AM, Gavin Price<gaprice(a)lbl.gov> wrote: >> >>> Not sure if we're having one since paramvir is at a conference. >>> >>> -g >>> >>> >>> ______________________________**_________________ >>> Microbe mailing list >>> Microbe(a)lists.kbase.us >>> https://lists.kbase.us/**mailman/listinfo/microbe<https://lists.kbase.us/mailman/listinfo/microbe> >>> >>> ______________________________**_________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/**mailman/listinfo/microbe<https://lists.kbase.us/mailman/listinfo/microbe> >

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