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

Microbial call today at 11AM Pacific/1PM central/2PM eastern
by Christopher Henry 19 Nov '12

19 Nov '12

Hi all, Microbial call today at 11AM Pacific/1PM central/2PM eastern. Number:866-740-1260 Code: 4958182 Chris

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Re: [Microbe] Microbes meeting today at 11P/1C/2E
by Ben Bowen 12 Nov '12

12 Nov '12

http://metaboliteatlas.lbl.gov/~bpb/Demo/scatter/matrix_vibriodata.html -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Nov 12, 2012 at 8:51 AM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > Hello all, > > Just a reminder, we have a microbes call today at the usual time: > 11P/1C/2E. > > Dial in information: 866-740-1260 > Code: 4958182# > > Best, > Chris > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

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Microbes meeting today at 11P/1C/2E
by Christopher Henry 12 Nov '12

12 Nov '12

Hello all, Just a reminder, we have a microbes call today at the usual time: 11P/1C/2E. Dial in information: 866-740-1260 Code: 4958182# Best, Chris

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Re: [Microbe] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Christopher Henry 09 Nov '12

09 Nov '12

This looks good Ben and Gavin. It's exactly what we need, and the JSON specs are something I can definitely produce from the models. Just make the specs for what you needs, and I'll make sure the modeling tools produce it. Chris On Nov 8, 2012, at 4:15 PM, Ben Bowen <ben.bowen(a)gmail.com> wrote: > Not that I've given up on moving the little circles around on the web-page, but Gavin and I came up with a different version of what the reconciliation explorer might look like (attached). I leave it to your imagination to envision little tooltips on mouseover that have lots of info for the different reconciliations and new-tabs that open up when you click on a compound or reaction. > > We have also begun to specify what the JSON object would look like. Next time I sit down to work on this, I'll make a toy JSON object and a web-page with the table and graphic. This probably won't be for several days; so if you want to add terms to the object or revise the "artists-rendering" please go crazy and put in whatever you want. It might be a good use of time to simultaneously, specify what the POST request will look like, where it will go, and what JSON object will be sent away from this page. > > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Mon, Nov 5, 2012 at 7:22 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Well, this gets more interesting when we lump in stats about how accuracy and model stats change when you select various solutions. > Accepting a model modification is a trade off in a variety of ways: > 1.) You may fix some errors but cause others > 2.) You may reduce the number of active reactions in the model > 3.) You may reduce the biomass reaction > 4.) You may lose annotations > > We need to report these stats in the interface so the user can see what they're trading off... > > On Nov 5, 2012, at 5:47 PM, Gavin Price wrote: > > > will the model changes be clustered or linked somehow? I'm not quite sure how this interface makes displaying the results clearer/easier to understand - it looks like the model changes are arbitrarily placed. > > > > -g > > > > On 11/5/2012 3:43 PM, Ben Bowen wrote: > >> I just put together the beginnings of what the user interface might look like. You can check progress here: > >> > >> http://metaboliteatlas.lbl.gov/~bpb/Demo/reconExplorer/reconciliationExplor… > >> > >> Some imagination is still required, but the majority of the mechanics are in place. > >> > >> Next, I'll import a toy json object that looks like what the gapfillGlobal will generate, and post a json object when your done selecting changes to the model. > >> > >> > >> ----------------------------- > >> Email: BPBowen(a)lbl.gov > >> Phone: (510) 214-6683 > >> MS 977-221, Lawrence Berkeley Lab > >> Web: ms.lbl.gov > >> > >> > >> On Sat, Nov 3, 2012 at 11:33 PM, Adam Paul Arkin <aparkin(a)lbl.gov> wrote: > >> That is really nice. > >> > >> Sent from my mobile device. Please excuse any seeming terseness or errors. > >> > >> Adam Paul Arkin > >> Dean A. Richard Newton Memorial Chair > >> ------------------------------------- > >> Director, Physical Biosciences Division > >> E.O. Lawrence Berkeley National Laboratory > >> > >> Professor, Department of Bioengineering > >> University of California > >> Berkeley, CA, 94720 > >> > >> PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov > >> Director of Bioinformatics, The Joint Bioenergy Institute, http://jbei.lbl.gov > >> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org > >> Head, Synthetic Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory > >> > >> > >> Office: 309B Hildebrand Hall (Berkeley Campus) > >> Mailing address: > >> E.O. Lawrence Berkeley National Laboratory > >> 1 Cyclotron Road, MS Stanley-922 > >> Berkeley, CA 94720 > >> > >> Contact: > >> W: http://genomics.lbl.gov > >> V: 510-495-2366 > >> C: 510-206-1389 > >> F: 510-486-6219 > >> > >> Assistant: > >> Gwyneth A. Terry > >> V: 510-495-2116 > >> E: GATerry(a)lbl.gov > >> ------------------------------------- > >> > >> On Nov 3, 2012, at 9:03 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > >> > >> > i love it!!!! We most definitely should do it. ASAP. > >> > Something like that could bring real shock and awe to the demo... > >> > > >> > On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: > >> > > >> >> If you go to this link and click "next" > >> >> http://elections.nytimes.com/2012/electoral-map > >> >> there is a nice d3 visualization. > >> >> > >> >> Instead of states: think media conditions (we have ~100) > >> >> Instead of electoral votes for radius: think how many discrepancies were resolved > >> >> Instead of dragging to explore voting outcomes: think which changes to the model you want to accept. > >> >> Instead of tooltips with electoral votes: have option to select 1, 2, or 3 best modification to the model. > >> >> > >> >> Add a button at the bottom for "commit" and get a nice, shiny new model to play with. > >> >> > >> >> ----------------------------- > >> >> Email: BPBowen(a)lbl.gov > >> >> Phone: (510) 214-6683 > >> >> MS 977-221, Lawrence Berkeley Lab > >> >> Web: ms.lbl.gov > >> >> _______________________________________________ > >> >> 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 > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > > <SpecificationsForReconciliationExplorer.pdf>

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Re: [Microbe] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Ben Bowen 08 Nov '12

08 Nov '12

Not that I've given up on moving the little circles around on the web-page, but Gavin and I came up with a different version of what the reconciliation explorer might look like (attached). I leave it to your imagination to envision little tooltips on mouseover that have lots of info for the different reconciliations and new-tabs that open up when you click on a compound or reaction. We have also begun to specify what the JSON object would look like. Next time I sit down to work on this, I'll make a toy JSON object and a web-page with the table and graphic. This probably won't be for several days; so if you want to add terms to the object or revise the "artists-rendering" please go crazy and put in whatever you want. It might be a good use of time to simultaneously, specify what the POST request will look like, where it will go, and what JSON object will be sent away from this page. -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Mon, Nov 5, 2012 at 7:22 PM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > Well, this gets more interesting when we lump in stats about how accuracy > and model stats change when you select various solutions. > Accepting a model modification is a trade off in a variety of ways: > 1.) You may fix some errors but cause others > 2.) You may reduce the number of active reactions in the model > 3.) You may reduce the biomass reaction > 4.) You may lose annotations > > We need to report these stats in the interface so the user can see what > they're trading off... > > On Nov 5, 2012, at 5:47 PM, Gavin Price wrote: > > > will the model changes be clustered or linked somehow? I'm not quite > sure how this interface makes displaying the results clearer/easier to > understand - it looks like the model changes are arbitrarily placed. > > > > -g > > > > On 11/5/2012 3:43 PM, Ben Bowen wrote: > >> I just put together the beginnings of what the user interface might > look like. You can check progress here: > >> > >> > http://metaboliteatlas.lbl.gov/~bpb/Demo/reconExplorer/reconciliationExplor… > >> > >> Some imagination is still required, but the majority of the mechanics > are in place. > >> > >> Next, I'll import a toy json object that looks like what the > gapfillGlobal will generate, and post a json object when your done > selecting changes to the model. > >> > >> > >> ----------------------------- > >> Email: BPBowen(a)lbl.gov > >> Phone: (510) 214-6683 > >> MS 977-221, Lawrence Berkeley Lab > >> Web: ms.lbl.gov > >> > >> > >> On Sat, Nov 3, 2012 at 11:33 PM, Adam Paul Arkin <aparkin(a)lbl.gov> > wrote: > >> That is really nice. > >> > >> Sent from my mobile device. Please excuse any seeming terseness or > errors. > >> > >> Adam Paul Arkin > >> Dean A. Richard Newton Memorial Chair > >> ------------------------------------- > >> Director, Physical Biosciences Division > >> E.O. Lawrence Berkeley National Laboratory > >> > >> Professor, Department of Bioengineering > >> University of California > >> Berkeley, CA, 94720 > >> > >> PI and Co-Director, Virtual Institute of Microbial Stress and Survival, > http://vimss.lbl.gov > >> Director of Bioinformatics, The Joint Bioenergy Institute, > http://jbei.lbl.gov > >> Investigator, Energy Biosciences Institute, > http://energybiosciencesinstitute.org > >> Head, Synthetic Biology, Physical Biosciences Division, Lawrence > Berkeley National Laboratory > >> > >> > >> Office: 309B Hildebrand Hall (Berkeley Campus) > >> Mailing address: > >> E.O. Lawrence Berkeley National Laboratory > >> 1 Cyclotron Road, MS Stanley-922 > >> Berkeley, CA 94720 > >> > >> Contact: > >> W: http://genomics.lbl.gov > >> V: 510-495-2366 > >> C: 510-206-1389 > >> F: 510-486-6219 > >> > >> Assistant: > >> Gwyneth A. Terry > >> V: 510-495-2116 > >> E: GATerry(a)lbl.gov > >> ------------------------------------- > >> > >> On Nov 3, 2012, at 9:03 PM, Christopher Henry <chrisshenry(a)gmail.com> > wrote: > >> > >> > i love it!!!! We most definitely should do it. ASAP. > >> > Something like that could bring real shock and awe to the demo... > >> > > >> > On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: > >> > > >> >> If you go to this link and click "next" > >> >> http://elections.nytimes.com/2012/electoral-map > >> >> there is a nice d3 visualization. > >> >> > >> >> Instead of states: think media conditions (we have ~100) > >> >> Instead of electoral votes for radius: think how many discrepancies > were resolved > >> >> Instead of dragging to explore voting outcomes: think which changes > to the model you want to accept. > >> >> Instead of tooltips with electoral votes: have option to select 1, > 2, or 3 best modification to the model. > >> >> > >> >> Add a button at the bottom for "commit" and get a nice, shiny new > model to play with. > >> >> > >> >> ----------------------------- > >> >> Email: BPBowen(a)lbl.gov > >> >> Phone: (510) 214-6683 > >> >> MS 977-221, Lawrence Berkeley Lab > >> >> Web: ms.lbl.gov > >> >> _______________________________________________ > >> >> 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 > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

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Re: [Microbe] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Christopher Henry 05 Nov '12

05 Nov '12

Well, this gets more interesting when we lump in stats about how accuracy and model stats change when you select various solutions. Accepting a model modification is a trade off in a variety of ways: 1.) You may fix some errors but cause others 2.) You may reduce the number of active reactions in the model 3.) You may reduce the biomass reaction 4.) You may lose annotations We need to report these stats in the interface so the user can see what they're trading off... On Nov 5, 2012, at 5:47 PM, Gavin Price wrote: > will the model changes be clustered or linked somehow? I'm not quite sure how this interface makes displaying the results clearer/easier to understand - it looks like the model changes are arbitrarily placed. > > -g > > On 11/5/2012 3:43 PM, Ben Bowen wrote: >> I just put together the beginnings of what the user interface might look like. You can check progress here: >> >> http://metaboliteatlas.lbl.gov/~bpb/Demo/reconExplorer/reconciliationExplor… >> >> Some imagination is still required, but the majority of the mechanics are in place. >> >> Next, I'll import a toy json object that looks like what the gapfillGlobal will generate, and post a json object when your done selecting changes to the model. >> >> >> ----------------------------- >> Email: BPBowen(a)lbl.gov >> Phone: (510) 214-6683 >> MS 977-221, Lawrence Berkeley Lab >> Web: ms.lbl.gov >> >> >> On Sat, Nov 3, 2012 at 11:33 PM, Adam Paul Arkin <aparkin(a)lbl.gov> wrote: >> That is really nice. >> >> Sent from my mobile device. Please excuse any seeming terseness or errors. >> >> Adam Paul Arkin >> Dean A. Richard Newton Memorial Chair >> ------------------------------------- >> Director, Physical Biosciences Division >> E.O. Lawrence Berkeley National Laboratory >> >> Professor, Department of Bioengineering >> University of California >> Berkeley, CA, 94720 >> >> PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov >> Director of Bioinformatics, The Joint Bioenergy Institute, http://jbei.lbl.gov >> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >> Head, Synthetic Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory >> >> >> Office: 309B Hildebrand Hall (Berkeley Campus) >> Mailing address: >> E.O. Lawrence Berkeley National Laboratory >> 1 Cyclotron Road, MS Stanley-922 >> Berkeley, CA 94720 >> >> Contact: >> W: http://genomics.lbl.gov >> V: 510-495-2366 >> C: 510-206-1389 >> F: 510-486-6219 >> >> Assistant: >> Gwyneth A. Terry >> V: 510-495-2116 >> E: GATerry(a)lbl.gov >> ------------------------------------- >> >> On Nov 3, 2012, at 9:03 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >> >> > i love it!!!! We most definitely should do it. ASAP. >> > Something like that could bring real shock and awe to the demo... >> > >> > On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: >> > >> >> If you go to this link and click "next" >> >> http://elections.nytimes.com/2012/electoral-map >> >> there is a nice d3 visualization. >> >> >> >> Instead of states: think media conditions (we have ~100) >> >> Instead of electoral votes for radius: think how many discrepancies were resolved >> >> Instead of dragging to explore voting outcomes: think which changes to the model you want to accept. >> >> Instead of tooltips with electoral votes: have option to select 1, 2, or 3 best modification to the model. >> >> >> >> Add a button at the bottom for "commit" and get a nice, shiny new model to play with. >> >> >> >> ----------------------------- >> >> Email: BPBowen(a)lbl.gov >> >> Phone: (510) 214-6683 >> >> MS 977-221, Lawrence Berkeley Lab >> >> Web: ms.lbl.gov >> >> _______________________________________________ >> >> 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] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Adam Paul Arkin 05 Nov '12

05 Nov '12

Cute! Please forgive any terseness. This is sent from my mobile device. Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 Director, The Synthetic Biology Institute, http://symbiotic.berkeley.edu CEO/CSO, The DOE Systems Biology Knowledgebase, http://kbase.us PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov Director of Bioinformatics, The Joint Bioenergy Institute, http://jbei.lbl.gov Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Office: 309B Hildebrand Hall (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS Stanley-922 Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov ------------------------------------- On Nov 5, 2012, at 3:43 PM, Ben Bowen <bpbowen(a)lbl.gov> wrote: > I just put together the beginnings of what the user interface might look like. You can check progress here: > > http://metaboliteatlas.lbl.gov/~bpb/Demo/reconExplorer/reconciliationExplor… > > Some imagination is still required, but the majority of the mechanics are in place. > > Next, I'll import a toy json object that looks like what the gapfillGlobal will generate, and post a json object when your done selecting changes to the model. > > > ----------------------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Sat, Nov 3, 2012 at 11:33 PM, Adam Paul Arkin <aparkin(a)lbl.gov> wrote: >> That is really nice. >> >> Sent from my mobile device. Please excuse any seeming terseness or errors. >> >> Adam Paul Arkin >> Dean A. Richard Newton Memorial Chair >> ------------------------------------- >> Director, Physical Biosciences Division >> E.O. Lawrence Berkeley National Laboratory >> >> Professor, Department of Bioengineering >> University of California >> Berkeley, CA, 94720 >> >> PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov >> Director of Bioinformatics, The Joint Bioenergy Institute, http://jbei.lbl.gov >> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >> Head, Synthetic Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory >> >> >> Office: 309B Hildebrand Hall (Berkeley Campus) >> Mailing address: >> E.O. Lawrence Berkeley National Laboratory >> 1 Cyclotron Road, MS Stanley-922 >> Berkeley, CA 94720 >> >> Contact: >> W: http://genomics.lbl.gov >> V: 510-495-2366 >> C: 510-206-1389 >> F: 510-486-6219 >> >> Assistant: >> Gwyneth A. Terry >> V: 510-495-2116 >> E: GATerry(a)lbl.gov >> ------------------------------------- >> >> On Nov 3, 2012, at 9:03 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: >> >> > i love it!!!! We most definitely should do it. ASAP. >> > Something like that could bring real shock and awe to the demo... >> > >> > On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: >> > >> >> If you go to this link and click "next" >> >> http://elections.nytimes.com/2012/electoral-map >> >> there is a nice d3 visualization. >> >> >> >> Instead of states: think media conditions (we have ~100) >> >> Instead of electoral votes for radius: think how many discrepancies were resolved >> >> Instead of dragging to explore voting outcomes: think which changes to the model you want to accept. >> >> Instead of tooltips with electoral votes: have option to select 1, 2, or 3 best modification to the model. >> >> >> >> Add a button at the bottom for "commit" and get a nice, shiny new model to play with. >> >> >> >> ----------------------------- >> >> Email: BPBowen(a)lbl.gov >> >> Phone: (510) 214-6683 >> >> MS 977-221, Lawrence Berkeley Lab >> >> Web: ms.lbl.gov >> >> _______________________________________________ >> >> 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] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Gavin Price 05 Nov '12

05 Nov '12

will the model changes be clustered or linked somehow? I'm not quite sure how this interface makes displaying the results clearer/easier to understand - it looks like the model changes are arbitrarily placed. -g On 11/5/2012 3:43 PM, Ben Bowen wrote: > I just put together the beginnings of what the user interface might > look like. You can check progress here: > > http://metaboliteatlas.lbl.gov/~bpb/Demo/reconExplorer/reconciliationExplor… > <http://metaboliteatlas.lbl.gov/%7Ebpb/Demo/reconExplorer/reconciliationExpl…> > > Some imagination is still required, but the majority of the mechanics > are in place. > > Next, I'll import a toy json object that looks like what the > gapfillGlobal will generate, and post a json object when your done > selecting changes to the model. > > > ----------------------------- > 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 Sat, Nov 3, 2012 at 11:33 PM, Adam Paul Arkin <aparkin(a)lbl.gov > <mailto:[email protected]>> wrote: > > That is really nice. > > Sent from my mobile device. Please excuse any seeming terseness or > errors. > > Adam Paul Arkin > Dean A. Richard Newton Memorial Chair > ------------------------------------- > Director, Physical Biosciences Division > E.O. Lawrence Berkeley National Laboratory > > Professor, Department of Bioengineering > University of California > Berkeley, CA, 94720 > > PI and Co-Director, Virtual Institute of Microbial Stress and > Survival, http://vimss.lbl.gov > Director of Bioinformatics, The Joint Bioenergy Institute, > http://jbei.lbl.gov > Investigator, Energy Biosciences Institute, > http://energybiosciencesinstitute.org > Head, Synthetic Biology, Physical Biosciences Division, Lawrence > Berkeley National Laboratory > > > Office: 309B Hildebrand Hall (Berkeley Campus) > Mailing address: > E.O. Lawrence Berkeley National Laboratory > 1 Cyclotron Road, MS Stanley-922 > Berkeley, CA 94720 > > Contact: > W: http://genomics.lbl.gov > V: 510-495-2366 <tel:510-495-2366> > C: 510-206-1389 <tel:510-206-1389> > F: 510-486-6219 <tel:510-486-6219> > > Assistant: > Gwyneth A. Terry > V: 510-495-2116 <tel:510-495-2116> > E: GATerry(a)lbl.gov <mailto:[email protected]> > ------------------------------------- > > On Nov 3, 2012, at 9:03 PM, Christopher Henry > <chrisshenry(a)gmail.com <mailto:[email protected]>> wrote: > > > i love it!!!! We most definitely should do it. ASAP. > > Something like that could bring real shock and awe to the demo... > > > > On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: > > > >> If you go to this link and click "next" > >> http://elections.nytimes.com/2012/electoral-map > >> there is a nice d3 visualization. > >> > >> Instead of states: think media conditions (we have ~100) > >> Instead of electoral votes for radius: think how many > discrepancies were resolved > >> Instead of dragging to explore voting outcomes: think which > changes to the model you want to accept. > >> Instead of tooltips with electoral votes: have option to select > 1, 2, or 3 best modification to the model. > >> > >> Add a button at the bottom for "commit" and get a nice, shiny > new model to play with. > >> > >> ----------------------------- > >> Email: BPBowen(a)lbl.gov <mailto:[email protected]> > >> Phone: (510) 214-6683 <tel:%28510%29%20214-6683> > >> MS 977-221, Lawrence Berkeley Lab > >> Web: ms.lbl.gov <http://ms.lbl.gov> > >> _______________________________________________ > >> 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 > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Ben Bowen 05 Nov '12

05 Nov '12

I just put together the beginnings of what the user interface might look like. You can check progress here: http://metaboliteatlas.lbl.gov/~bpb/Demo/reconExplorer/reconciliationExplor… Some imagination is still required, but the majority of the mechanics are in place. Next, I'll import a toy json object that looks like what the gapfillGlobal will generate, and post a json object when your done selecting changes to the model. ----------------------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Sat, Nov 3, 2012 at 11:33 PM, Adam Paul Arkin <aparkin(a)lbl.gov> wrote: > That is really nice. > > Sent from my mobile device. Please excuse any seeming terseness or errors. > > Adam Paul Arkin > Dean A. Richard Newton Memorial Chair > ------------------------------------- > Director, Physical Biosciences Division > E.O. Lawrence Berkeley National Laboratory > > Professor, Department of Bioengineering > University of California > Berkeley, CA, 94720 > > PI and Co-Director, Virtual Institute of Microbial Stress and Survival, > http://vimss.lbl.gov > Director of Bioinformatics, The Joint Bioenergy Institute, > http://jbei.lbl.gov > Investigator, Energy Biosciences Institute, > http://energybiosciencesinstitute.org > Head, Synthetic Biology, Physical Biosciences Division, Lawrence Berkeley > National Laboratory > > > Office: 309B Hildebrand Hall (Berkeley Campus) > Mailing address: > E.O. Lawrence Berkeley National Laboratory > 1 Cyclotron Road, MS Stanley-922 > Berkeley, CA 94720 > > Contact: > W: http://genomics.lbl.gov > V: 510-495-2366 > C: 510-206-1389 > F: 510-486-6219 > > Assistant: > Gwyneth A. Terry > V: 510-495-2116 > E: GATerry(a)lbl.gov > ------------------------------------- > > On Nov 3, 2012, at 9:03 PM, Christopher Henry <chrisshenry(a)gmail.com> > wrote: > > > i love it!!!! We most definitely should do it. ASAP. > > Something like that could bring real shock and awe to the demo... > > > > On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: > > > >> If you go to this link and click "next" > >> http://elections.nytimes.com/2012/electoral-map > >> there is a nice d3 visualization. > >> > >> Instead of states: think media conditions (we have ~100) > >> Instead of electoral votes for radius: think how many discrepancies > were resolved > >> Instead of dragging to explore voting outcomes: think which changes to > the model you want to accept. > >> Instead of tooltips with electoral votes: have option to select 1, 2, > or 3 best modification to the model. > >> > >> Add a button at the bottom for "commit" and get a nice, shiny new model > to play with. > >> > >> ----------------------------- > >> Email: BPBowen(a)lbl.gov > >> Phone: (510) 214-6683 > >> MS 977-221, Lawrence Berkeley Lab > >> Web: ms.lbl.gov > >> _______________________________________________ > >> 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] Sick
by Christopher Henry 05 Nov '12

05 Nov '12

Yup. Microbes call in 15 minutes. 866-740-1260 Code: 4958182 On Nov 5, 2012, at 12:41 PM, Gavin Price wrote: > BTW, I assume the call info is > > 866-740-1260 Code: 4958182 > > as usual > > On Mon, Nov 5, 2012 at 8:55 AM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Will do. Gavin, can you use your admin code to get the call started? > Chris > > On Nov 5, 2012, at 10:36 AM, Paramvir Dehal wrote: > > > Steven and Gavin managed to get me sick. I've got a fever of 103.2. Chris will run the microbes call. > > > > _______________________________________________ > > 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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