-------- Forwarded Message --------
Subject: Re: [IMP-dev] IMP Efficiency Comm
Date: Thu, 14 Jun 2018 09:24:54 -0700
From: Daniel Saltzberg <>
To: Dina Schneidman <>
CC: Barak Raveh <>, List for IMP development
<>, Ben Webb <>, SaliLab Mail
<>
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 <
<">mailto:>> wrote:
agree with Barak. morning is best
On Jun 12, 2018 11:52 PM, "Barak Raveh" <
<">mailto:>> 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 <
<">mailto:>> 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
-- <">mailto:>
https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle
-- Barak
_______________________________________________
IMP-dev mailing list
<">mailto:>
https://salilab.org/mailman/listinfo/imp-dev
<https://salilab.org/mailman/listinfo/imp-dev>
--
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,
Mission Bay, Byers Hall
1700 4th Street, Suite 503B
San Francisco, CA 94158-2330
<">mailto:>
<">mailto:>