Hi all,
Just a reminder that we will have a meeting to discuss strategies for making IMP more efficient at 11AM Pacific tomorrow. For those in the office, we will be in MH 1405.
You can join virtually using the salilab Zoom link; https://ucsf.zoom.us/my/ salilab
*Agenda:*
1) Introduction. Scope of these meetings.
2) IMP efficiency projects. - Discuss status of and plans for completing: a) IncrementalScoringFunction (Issue 959 https://github.com/salilab/imp/issues/959) b) Parallelization of Replicas c) GPU accelleration
3) Additional projects to consider.
4) Schedule next/recurring meetings.
Cheers, -Daniel
On Sun, Jun 17, 2018 at 5:27 PM, Chemmama, Ilan Ilan.Chemmama@ucsf.edu wrote:
> Next Tuesday at 11AM PST works for me as well. > Best, > Ilan > > On Jun 15, 2018, at 10:16 AM, Ignacia Echeverria iecheverria@gmail.com > wrote: > > Next Tuesday works for me. > Best, > Ignacia > > On Thu, Jun 14, 2018 at 9:25 AM Daniel Saltzberg ds229@bu.edu wrote: > >> 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 >> wrote: >> >>> agree with Barak. morning is best >>> >>> On Jun 12, 2018 11:52 PM, "Barak Raveh" 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 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 >>>> >>>> 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 https://salilab.org/~ben/ >>>> "It is a capital mistake to theorize before one has data." >>>> - Sir Arthur Conan Doyle >>>> >>> >>> >>> >>> -- >>> Barak >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> 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) >> >> T: 415.514.4258 >> >> *Mailing Address:* >> UCSF MC 2552, >> Mission Bay, Byers Hall >> 1700 4th Street, Suite 503B >> https://maps.google.com/?q=1700+4th+Street,+Suite+503B+%0D%0ASan+Francisco,+CA+94158&entry=gmail&source=g >> San Francisco, CA 94158-2330 >> >> saltzberg@salilab.org >> ds229@bu.edu >> > > > -- > --------------------------------------- > Ignacia Echeverria > Postdoctoral Scholar > Department of Bioengineering and Therapeutic Sciences > University of California, San Francisco > http://salilab.org/~ignacia > ---------------------------------------- > > >