Fwd: Re: IMP Efficiency Comm
-------- 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 _______________________________________________ IMP-dev mailing list IMP-dev@salilab.org mailto:IMP-dev@salilab.org https://salilab.org/mailman/listinfo/imp-dev https://salilab.org/mailman/listinfo/imp-dev
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 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 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 > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org mailto:IMP-dev@salilab.org > 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 > > saltzberg@salilab.org mailto:saltzberg@salilab.org > ds229@bu.edu mailto:ds229@bu.edu > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
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 < 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 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 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 > > _______________________________________________ > > IMP-dev mailing list > > IMP-dev@salilab.org mailto:IMP-dev@salilab.org > > 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 > > > > saltzberg@salilab.org mailto:saltzberg@salilab.org > > ds229@bu.edu mailto:ds229@bu.edu > > _______________________________________________ > > IMP-dev mailing list > > IMP-dev@salilab.org > > https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >
riccardo, there will be many more such meetings :)
-- 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, assistant@salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali@salilab.org; Web http://salilab.org
> On Jun 18, 2018, at 4:59 PM, Daniel Saltzberg 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 <pellarin.riccardo@gmail.com mailto: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 <ben@salilab.org mailto: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 <ds229@bu.edu mailto:ds229@bu.edu> > > To: Dina Schneidman <duhovka@gmail.com mailto:duhovka@gmail.com> > > CC: Barak Raveh <barak.raveh@gmail.com mailto:barak.raveh@gmail.com>, List for IMP development <imp-dev@salilab.org mailto:imp-dev@salilab.org>, Ben Webb <ben@salilab.org mailto:ben@salilab.org>, SaliLab Mail <salilab@salilab.org mailto: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 <mailto: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 > > <mailto: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 > > <mailto: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 > > <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 <mailto:ben@salilab.org mailto:ben@salilab.org> > > https://salilab.org/~ben/ 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 mailto:IMP-dev@salilab.org <mailto:IMP-dev@salilab.org mailto:IMP-dev@salilab.org> > > https://salilab.org/mailman/listinfo/imp-dev https://salilab.org/mailman/listinfo/imp-dev > > <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/ <http://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 > > > > saltzberg@salilab.org mailto:saltzberg@salilab.org <mailto:saltzberg@salilab.org mailto:saltzberg@salilab.org> > > ds229@bu.edu mailto:ds229@bu.edu <mailto:ds229@bu.edu mailto:ds229@bu.edu> > > _______________________________________________ > > IMP-dev mailing list > > IMP-dev@salilab.org mailto:IMP-dev@salilab.org > > https://salilab.org/mailman/listinfo/imp-dev https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org mailto:IMP-dev@salilab.org > 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 > > saltzberg@salilab.org mailto:saltzberg@salilab.org > ds229@bu.edu mailto:ds229@bu.edu > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
OK no problem! Let me know next event. Daniel, where are you heading to?
cheers!
Riccardo
Riccardo Pellarin, PhD =================== Institut Pasteur CNRS UMR 3528 25, rue du Docteur Roux 75724 Paris Cedex 15, France riccardo.pellarin@pasteur.fr +33 (0)1 44 38 93 63
On Mon, Jun 18, 2018 at 7:51 PM, Andrej Sali sali@salilab.org wrote:
> riccardo, there will be many more such meetings :) > > -- > 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, assistant@salilab.org, Tel +1 (415) > 514-4228, 502-8084 > Email sali@salilab.org sali@salilab.org; Web http://salilab.org > > On Jun 18, 2018, at 4:59 PM, Daniel Saltzberg 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 < > 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 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 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 >> > _______________________________________________ >> > IMP-dev mailing list >> > IMP-dev@salilab.org mailto:IMP-dev@salilab.org >> > 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 >> > >> > saltzberg@salilab.org mailto:saltzberg@salilab.org >> > ds229@bu.edu mailto:ds229@bu.edu >> > _______________________________________________ >> > IMP-dev mailing list >> > IMP-dev@salilab.org >> > https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> 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 > San Francisco, CA 94158-2330 > > saltzberg@salilab.org > ds229@bu.edu > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >
participants (4)
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Andrej Sali -
Ben Webb -
Daniel Saltzberg -
Riccardo Pellarin