New subject: Fwd: Re: IMP Efficiency Comm

14 Jun 2018


      -------- Forwarded Message --------
Subject: 	Re: [IMP-dev] IMP Efficiency Comm
Date: 	Thu, 14 Jun 2018 09:24:54 -0700
From: 	Daniel Saltzberg ds229@bu.edu
To: 	Dina Schneidman duhovka@gmail.com
CC: 	Barak Raveh barak.raveh@gmail.com, List for IMP development 
imp-dev@salilab.org, Ben Webb ben@salilab.org, SaliLab Mail 
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 <duhovka@gmail.com 
mailto:duhovka@gmail.com> wrote:
agree with Barak. morning is best
On Jun 12, 2018 11:52 PM, "Barak Raveh" <barak.raveh@gmail.com
     mailto: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 <ben@salilab.org
         mailto: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
             --             ben@salilab.org mailto: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)

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