Hey Jeff! I think qualifiers can help clear up the usage of the term "ensemble":
A* representative ensemble* could be a collection of models that are highly probable (according to the modeling process being used) and have been filtered from a larger set of models. This is probably what a depositor would submit to the PDB for archiving, but is ultimately somewhat arbitrary.
The usage of *statistical ensemble* and *thermodynamic ensemble* have clear meanings within the physics literature, so those should be safe.
In the case that an ensemble is meant to refer to a representation of a posterior distribution, like what MCMC produces, then I think the standard term *sample* should be preferred, since a sample can include improbable (low scoring) models, but is guaranteed to do so in proportion to the posterior density.
Thanks for looking into Slack! Here's a list of names/e-mails:
Aji Palar aji@salilab.org Arthur Zalevsky aozalevsky@gmail.com Andrew Latham aplatham@salilab.org Brinda Vallat brinda.vallat@rcsb.org Tracy Wang chenxi.wang@ucsf.edu Matthew Hancock matthewhancock97@gmail.com Neelesh Soni neeleshsoni03@gmail.com
If anyone prefers a different e-mail than what I have, I suppose they can reach out to you.
On Wed, Jun 28, 2023 at 3:06 PM Hoch,Jeffrey hoch@uchc.edu wrote:
> Thanks Jared. > > > > I think the terms so far should work – however we should make sure our > terms for ensembles align with thermodynamic ensembles (microcanonical, > canonical, grand canonical...others). > > > > Also we need terms to describe the scope of averaging for forward modeling > – which may or may not cover all of or align with an ensemble. > > > > We looked into a paid-up Slack license. A bit over $10pp/yr . I think I > can handle this. Can you assemble a list of names and email addresses of > those who should be included? I’ll have Jen Reeser set up the account. > > > > Yours, Jeff > > > > *From: *Jared Sagendorf jared.sagendorf@rcsb.org > *Date: *Friday, June 23, 2023 at 5:57 PM > *To: *"Hoch,Jeffrey" hoch@uchc.edu, "bayesian_validation@salilab.org" < > bayesian_validation@salilab.org> > *Cc: *"Pustovalova,Yulia" ypustovalova@uchc.edu, "Eghbalnia,Hamid R." < > heghbalnia@uchc.edu>, "Pozhidaeva,Alexandra" pozhidaeva@uchc.edu, > "Courtney,Joseph M." jcourtney@uchc.edu, "Gryk,Michael R." < > gryk@uchc.edu>, "Baskaran,Kumaran" baskaran@uchc.edu > *Subject: *Re: Next meeting agenda > > > > *** Attention: This is an external email. Use caution responding, opening > attachments or clicking on links. *** > > Hi all, thanks for the discussion today! Here's the slides I showed: > https://docs.google.com/presentation/d/1-70W4jeSS4FU8CQpYfRDng06PucfpKRW/edi... > https://urldefense.com/v3/__https:/docs.google.com/presentation/d/1-70W4jeSS4FU8CQpYfRDng06PucfpKRW/edit?usp=sharing&ouid=108826461676207075917&rtpof=true&sd=true__;!!Cn_UX_p3!kXCpANPzRWu_YB1HJbBxilFHKPcPyk6p2SjxCIuKsc5WDIemvgIApOaBDJ4VPkS8EHAkReXxj7Z18dUycGhUdZc$ > > Jeff will look into getting a Slack set up with a premium subscription and > we can continue refining the terminology as we go. > > I have a shared google drive set up through the RCSB google organization, > but unfortunately I can't seem to invite people with non-gmail e-mails - if > anyone knows a workaround let me know! > > - Jared > > > > > > > > On Wed, Jun 21, 2023 at 3:26 PM Jared Sagendorf jared.sagendorf@rcsb.org > wrote: > > Sure Jeff, pushing it forward two hours to 12:00 PST should work for most > of us. Hopefully that makes it easier for you! I'll update the calendar > event on our side. > > Congrats on the R24! > > See you Friday, > > > > - Jared > > > > On Wed, Jun 21, 2023 at 12:20 PM Hoch,Jeffrey hoch@uchc.edu wrote: > > Hi Jared – met too! I added a term to the dictionary . Yulia, Michael > and I will be driving back from a Gordon Conference in Vermont Friday > morning, and it might be tight for us to make the schedule time. I know > there are many schedules to check, but would it be possible to bump the > time back a couple of hours to take some of the stress out? -Jeff > > > > PS – good news is that we heard BMRB will be funded via an R24 mechanism. > Don’t know the budget yet, though. > > > > *From: *Jared Sagendorf jared.sagendorf@rcsb.org > *Date: *Wednesday, June 21, 2023 at 2:08 PM > *To: *"Hoch,Jeffrey" hoch@uchc.edu > *Subject: *Next meeting agenda > > > > *** Attention: This is an external email. Use caution responding, opening > attachments or clicking on links. *** > > Hi Jeff, looking forward to the next meeting! > > For the agenda this week, I was thinking we could start with having a look > at some of the terminology, now that we have a dictionary in place. I'll > put together a few slides that I hope will explain the way the Sali group > speaks about modeling, and we can identify if there's any inconsistencies > between the two groups. > > Aside from that, I thought it would be good to begin a discussion on what > the current hurdles are to actually implementing a fully Bayesian > validation pipeline for the PDB. What are the unsolved problems or > unimplemented steps that are missing to actually push this forward, and > could we work together to start solving those issues? > > Also happy to send out any items you would like to bring up! > > > > - Jared > >