Re: [IMP-dev] Fwd: Re: IMP Efficiency Comm

--
Andrej Sali, Ph.D.
Professor, Department of Bioengineering and Therapeutic Sciences

Associate Dean for Research, School of Pharmacy
Department of Pharmaceutical Chemistry
California Institute for Quantitative Biosciences

University of California, San Francisco
UCSF MC 2552
Byers Hall Room 503B
1700 4th Street
San Francisco, CA 94143, USA
Tel +1 (415) 514-4227; Fax +1 (415) 514-4231
Administrative Assistant: Steve Ha, " class="">assistant@salilab.org, Tel +1 (415) 514-4228, 502-8084
" class="">Email sali@salilab.org; Web http://salilab.org

On Jun 18, 2018, at 4:59 PM, Daniel Saltzberg <" class="">ds229@bu.edu> wrote:

Hi Riccardo,

Unfortunately, Tuesday is the only day I can do this week and then I am moving/out of town all of next week.

I'll make sure to write up a summary of what we talked about and pass it on so you can stay up to date.

Best,
-Daniel

On Sun, Jun 17, 2018 at 11:52 PM, Riccardo Pellarin <" target="_blank" class="">pellarin.riccardo@gmail.com> wrote:
Dear guys,

I’m abroad and could not read the mail. I would love to join, but cannot on this tuesday and wed. If you can postpone, it would be nice!

Also, I included Kai, he could be interested.

Cheers

Riccardo

Sent from my iPhone

> On Jun 14, 2018, at 6:34 PM, Ben Webb <" class="">ben@salilab.org> wrote:
>
>
>
>
> -------- Forwarded Message --------
> Subject: Re: [IMP-dev] IMP Efficiency Comm
> Date: Thu, 14 Jun 2018 09:24:54 -0700
> From: Daniel Saltzberg <" class="">ds229@bu.edu>
> To: Dina Schneidman <" class="">duhovka@gmail.com>
> CC: Barak Raveh <" class="">barak.raveh@gmail.com>, List for IMP development <" class="">imp-dev@salilab.org>, Ben Webb <" class="">ben@salilab.org>, SaliLab Mail <" class="">salilab@salilab.org>
>
>
>
> I like the idea of involving the entire IMP community, however, my initial goals for this meeting were not quite as large as Barak suggested! In that case, let's push the meeting off until next week so that we give people enough time to schedule and myself enough time to prepare a more focused agenda.
>
> I'll suggest next *Tuesday, June 19th at 11AM Pacific Time.* The meeting will go no longer than an hour and a half.
>
> For those new to this email thread, we are interested in identifying specific areas in IMP where efficiency and functionality can be significantly improved with a moderate amount of effort and task these projects to individuals or small groups. Some issues we discussed at the retreat are:
>
> * Scoring efficiency - Make IncrementalScoringFunction work with current restraints (EM, EV)
> * Parallelization of individual replicas
> * Parallelizing propagation of moves within coarse grained representation of rigid bodies.
> * Identification of GPU-friendly computations
>
> The purpose of this meeting and subsequent ones will be to discuss the root causes of these issues, discuss general strategies for solving them, document them/improve the documentation in github issues and assign people to work on them outside of the meeting.
>
> Cheers,
> -Daniel
>
> On Tue, Jun 12, 2018 at 11:33 PM, Dina Schneidman <" class="">duhovka@gmail.com <mailto:" class="">duhovka@gmail.com>> wrote:
>
> agree with Barak. morning is best
>
> On Jun 12, 2018 11:52 PM, "Barak Raveh" <" class="">barak.raveh@gmail.com
> <mailto:" class="">barak.raveh@gmail.com>> wrote:
>
> I think it's great if we can get all IMP developers including in
> Europe and Asia on board, at least for the first meeting. IMP
> development could benefit a lot from collaboration among the
> various IMP labs, and this could also support future
> collaboration among IMP labs.
>
> The timezone is an issue - my recollection is that we have
> developers in Spain (+8 hours), France (+9 hours), Israel (+10
> hours), possibly in Germany (+9 hours - Jan Kosinski at EMBL,
> Heidelberg may be interested). If I didn't forget anyone (Ben?)
> - a morning meeting here (say 10 or 11 am) could allow them to
> join in the European/ME evening.
>
>
> On Mon, Jun 11, 2018 at 10:36 AM, Ben Webb <" class="">ben@salilab.org

> <mailto:" class="">ben@salilab.org>> wrote:
>
> On 6/8/18 4:44 PM, Daniel Saltzberg wrote:
>
> We had a good discussion at the retreat about how
> improving the reliability and efficiency in IMP is
> critical for our current and future goals in structural
> modeling. To do this, we proposed a periodic meeting to
> discuss problems/inefficiencies in IMP, identify the
> root causes and collectively design the best ways to fix
> them.
>
>
> The best place for such discussion is the existing IMP
> developers' mailing list (cc'd):
> https://salilab.org/mailman/listinfo/imp-dev
> <https://salilab.org/mailman/listinfo/imp-dev>
>
> There are several people outside of the lab who are IMP
> developers and so may be interested in joining these
> meetings. They're not on the lab mailing list but are (or
> can be) on imp-dev.
>
> I suggest we have our first meeting next week...say
> Thursday 2PM? (or Ben, whatever day you plan to be in).
> We can decide on a recurring time then.
>
>
> If you want to have physical meetings as well, that's fine,
> although Fridays are better for me. 2pm's probably not a
> great time if anybody from Europe or Asia will be joining
> though.
>
> Ben

> -- " class="">ben@salilab.org <mailto:" class="">ben@salilab.org>
> https://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> - Sir Arthur Conan Doyle
>
>
>
>
> -- Barak
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>
>
> --
>
>
> Daniel Saltzberg
> Post-doctoral Scholar
> University of California at San Francisco
> Lab of Andrej Sali (www.salilab.org <http://www.salilab.org>)
>
> T: 415.514.4258
> _
> _
> _/Mailing Address:/_
> UCSF MC 2552,
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>
> " class="">saltzberg@salilab.org <mailto:" class="">saltzberg@salilab.org>
> " class="">ds229@bu.edu <mailto:" class="">ds229@bu.edu>

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Daniel Saltzberg
Post-doctoral Scholar
University of California at San Francisco
Lab of Andrej Sali (www.salilab.org)

T: 415.514.4258

Mailing Address:
UCSF MC 2552,
Mission Bay, Byers Hall
1700 4th Street, Suite 503B
San Francisco, CA 94158-2330

" target="_blank" class="">saltzberg@salilab.org
" target="_blank" class="">ds229@bu.edu

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