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/reconciliationExplore...

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: [email protected] 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 <[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 C: 510-206-1389 F: 510-486-6219

Assistant: Gwyneth A. Terry V: 510-495-2116 E: [email protected] -------------------------------------

On Nov 3, 2012, at 9:03 PM, Christopher Henry <[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.

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