[3dem] 3dem Digest, Vol 216, Issue 9

Tue Aug 12 08:22:57 PDT 2025

Hi Paul,

When we got our Arctica at Montana State University, we wound up in a similar position. We partnered with our campus research-specific IT ("Research Cyber Infrastructure) to develop a managed CryoSPARC instance for academic users, that worked with our HPC/SLURM cluster. Research groups purchased the compute time yearly (i.e. 50% access to n GPUs per year). The cryo-EM facility also has a number of dedicated GPUs for live processing and other projects, built into the yearly budget. 

This was quite a bit of setup initially, but is now pretty mindless. Users collect data, log into Globus where they can see the microscope drive and also their networked storage at RCI, move the data with one click, log into the campus CryoSPARC installation, and process there. Or if they are more advanced, they can log into the command line and use RELION or EMAN2. I'm not longer there, but have pushed them to get managed Doppio running as well for a nicer RELION GUI. 

I would not recommend processing for academic users unless they truly are one-off type projects. We had a once-yearly 3 credit structural biology class where users were introduced to processing and HPC, having it as a core component of the class and graded project. Additionally, good written documentation to cover the basics is invaluable. 

For one off academic projects, typically I would do the processing myself unless it was out of the ordinary. That got me on a couple of publications. I did not charge for that because of the complications of charging federal grants. As mentioned, the facility always purchased some GPU time regardless and typically didn't use all of it. 

Best,
Colin Gauvin

On Tue, Aug 12, 2025, at 8:12 AM, 3dem-request at ncmir.ucsd.edu wrote:
> Send 3dem mailing list submissions to
> 3dem at ncmir.ucsd.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem 
> or, via email, send a message with subject or body 'help' to
> 3dem-request at ncmir.ucsd.edu
> 
> You can reach the person managing the list at
> 3dem-owner at ncmir.ucsd.edu
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of 3dem digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Very Vague Question (Ludtke, Steven J.)
>    2. Re: Very Vague Question (Ayil Perrott)
>    3. Re: Very Vague Question (Marcus FISLAGE)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 12 Aug 2025 14:08:26 +0000
> From: "Ludtke, Steven J." <sludtke at bcm.edu>
> To: "Chipman,Paul" <pchipman at ufl.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Very Vague Question
> Message-ID: <C24304C6-C9D2-4B99-AC79-BF67318F2E94 at bcm.edu>
> Content-Type: text/plain; charset="utf-8"
> 
> Our core gets pressured on this point all of the time (by advisors, etc.). The issue is that users want data processing/reconstruction/computing help but they don't want to pay for it, and it is _very_ expensive, often more per hour than the instrument. Even if you install something easy-to-use like CryoSparc on a workstation and let them use it, novice users will still need some training, and even then may take whatever first structure it dumps out and assume it's "the answer" and just figure they can go straight to publication. There is a lack of understanding among new users of what has to go in to turning CryoEM images into a publication with a biological or structural conclusion, and I've never found a good solution to the problem other than gradual education. When we set up someone who could help users with computation as a fee-for-service, it is virtually unused, and instead we get people who offer to "collaborate" with the person instead of paying. Most users who don't want t
> o learn how to actually analyze CryoEM/ET data will wind up collaborating with someone who does have the experience (like a core director or a prominent user).
> 
> ---
> Steven Ludtke, Ph.D. <sludtke at bcm.edu>                      Baylor College of Medicine
> Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry
> Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
> Academic Director, CryoEM Core
> Co-Director CIBR Center
> 
> 
> On Aug 12, 2025, at 8:45?AM, Chipman,Paul via 3dem <3dem at ncmir.ucsd.edu> wrote:
> 
> ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
> ________________________________
> Hi All,
> 
> We recently acquired a TFS Glacios and have started to pump out large amounts of data.  Many of our customers are completely unfamiliar with image processing.  I?m interested to hear how any other core facilities or similar have dealt with this issue.  Since we are an expected revenue neutral core I?m a bit challenged on how to best help our users.  Should we hire someone to deal with processing? What would be an expected salary? Post doc?  We have a bioinformatics core that might be helpful as well or positioned to have a joint appointment.  Just looking for thoughts.
> 
> Best,
> Paul
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=oktMcYr87tI6glFiYbF0qckVrDx_H-bUFTGeUH5_j07Mze68isPi-6ULWAeW17GL&s=emp3SXmDg_BbgCieUb6rT2IxGtKZG-JjALshT--8hBQ&e=  
> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20250812/239f0f2b/attachment-0001.html >
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 12 Aug 2025 10:12:09 -0400
> From: Ayil Perrott <perrotta2 at vcu.edu>
> To: "Chipman,Paul" <pchipman at ufl.edu>
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Very Vague Question
> Message-ID:
> <CADd7EQQG=z8MdFYYEJVhUJ3vrsht26g+pdFN5FzuSH8ruPqidw at mail.gmail.com <mailto:z8MdFYYEJVhUJ3vrsht26g%2BpdFN5FzuSH8ruPqidw at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi, Paul. I hope all is well with you!
> 
> In conjunction with what Steven has so eloquently said, it will really
> depend on the needs of your collaborators and your available resources. How
> it worked for me in my previous experience was that we worked with
> collaborators directly to gradually show them the ropes of the processing
> software and what to look out for while working with the data, with the
> goal of having them conduct processing on their own and come to us with
> questions if they were confused. I helped teach numerous collaborators and
> new hires about processing, and worked with senior leadership in the core
> to help them better understand and be more creative with their pipelines.
> 
> Translating to your facility, one of the big questions revolves around how
> involved you and your core members want to be with your collaborators in
> this respect, and how involved they want to be in the learning process. Are
> they able and open to learn how to do image processing, and eventually do
> it on their own? If you have the people that are well-experienced with
> processing and are willing to teach/directly assist with it, that could
> potentially be a great way to help your collaborators with their projects
> while also building stronger connections with the core, though of course
> there is the problem of proper compensation. My core allowed for its
> members to become more involved with collaborators and get on some papers,
> though deep involvement with multiple projects personally did not work for
> me as a core member.
> 
> There are also a slew of amazing resources to provide to collaborators if
> they are not entirely familiar with the concepts of cryo-EM that are
> critical for processing. One of these is cryoem101.org, a website created
> to teach the concepts of cryo-EM and cryo-ET from sample prep to image
> processing, all of which I feel is critical for understanding how to work
> with the data.
> 
> I hope this helps!
> 
> Sincerely,
> Ayil Perrott
> (they/them)
> --
> Doctoral Student
> Physiology and Biophysics
> Virginia Commonwealth University
> Richmond, VA
> 
> 
> On Tue, Aug 12, 2025 at 9:45?AM Chipman,Paul via 3dem <3dem at ncmir.ucsd.edu>
> wrote:
> 
> > Hi All,
> >
> >
> >
> > We recently acquired a TFS Glacios and have started to pump out large
> > amounts of data.  Many of our customers are completely unfamiliar with
> > image processing.  I?m interested to hear how any other core facilities or
> > similar have dealt with this issue.  Since we are an expected revenue
> > neutral core I?m a bit challenged on how to best help our users.  Should we
> > hire someone to deal with processing? What would be an expected salary?
> > Post doc?  We have a bioinformatics core that might be helpful as well or
> > positioned to have a joint appointment.  Just looking for thoughts.
> >
> >
> >
> > Best,
> >
> > Paul
> > _______________________________________________
> > 3dem mailing list
> > 3dem at ncmir.ucsd.edu
> > https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem  
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20250812/6f5cd0cb/attachment-0001.html >
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 12 Aug 2025 14:12:21 +0000
> From: Marcus FISLAGE <Marcus.Fislage at vub.be>
> To: "Chipman,Paul" <pchipman at ufl.edu>, "3dem at ncmir.ucsd.edu"
> <3dem at ncmir.ucsd.edu>
> Subject: Re: [3dem] Very Vague Question
> Message-ID:
> <AM0PR01MB437151A40079AF72671B3882F42BA at AM0PR01MB4371.eurprd01.prod.exchangelabs.com>
> 
> Content-Type: text/plain; charset="windows-1252"
> 
> Hi Paul,
> 
> I think an important aspect is what type of customer do you serve industrial or academics.
> For your academic users I would not recommend that the facility is doing the processing for the users. We invested heavily in training of our local base with seminars and hands on support. This hands-on support can be quite a lot in the beginning as your users will make many dumb mistakes and do not see what went wrong. In that early period a dedicated staff scientist can be very helpful. And for that you probably need someone with post-doc level skills. A technical staff could do the job but may need significant training first,bringing you back to square one. For processing training of your academic users, you can also send them on many of the professional workshops organized throughout the country. From there on the knowledge should normally start to propagate withing the local groups.
> What I found very helpful is to take over the maintenance of the computing infratsructure for the academic groups. We host all the group owned GPU stations (they don;t want to share) and provide them at the same time with secure long and short term data storage as well as software packages hosted by us that are available to all users. Therfore the users only have to learn how to use the software, not how to maintain a system. Depending on the size of the user base this can be done by a half or full FTE. It is very helpful if that IT FTE has knowledge about cryoEM, so the person can translate computer-user/user-computer.
> 
> The more industrial clients you have the more a dedicated staff and in house processing can be very useful. Like that you can easily counter-finance the computing person for the academic groups which would otherwise complain about the costs. However, I also have met several industrial people that just want data. So here it is very important I think to listen to your industrial user base. Providing them with processing option could be a good way of tying them to you, but it is hard/important to define what a successull result in processing data is.
> 
> Cheers
> Marcus
> 
> 
> 
> ______________________________________
> 
> Dr. Marcus Fislage
> 
> 
> Upcoming days out of office:
> 
> 18-29/08
> 
> 
> 
> EM Manager
> 
> BECM
> VIB-Center for Structural Biology
> VUB (Vrije Universiteit Brussel)
> Building P1T, room 0.01
> 
> Pleinlaan 2
> 
> 1050 BRUSSELS
> 
> https://urldefense.com/v3/__http://www.becm.be__;!!Mih3wA!Co8p7iKuiS-U1cIbudZ4eeQay5A_NSJGwItG255Z-ImYDM3a91WmWsAbl2WRYACqz9OcSzRzUd7dgsJdw8k7TGoIWR2D$ <https://urldefense.com/v3/__http://www.becm.be__;!!Mih3wA!Co8p7iKuiS-U1cIbudZ4eeQay5A_NSJGwItG255Z-ImYDM3a91WmWsAbl2WRYACqz9OcSzRzUd7dgsJdw8k7TGoIWR2D$ >
> 
> ________________________________
> From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Chipman,Paul via 3dem <3dem at ncmir.ucsd.edu>
> Sent: Tuesday, August 12, 2025 3:45 PM
> To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> Subject: [3dem] Very Vague Question
> 
> 
> Hi All,
> 
> 
> 
> We recently acquired a TFS Glacios and have started to pump out large amounts of data.  Many of our customers are completely unfamiliar with image processing.  I?m interested to hear how any other core facilities or similar have dealt with this issue.  Since we are an expected revenue neutral core I?m a bit challenged on how to best help our users.  Should we hire someone to deal with processing? What would be an expected salary? Post doc?  We have a bioinformatics core that might be helpful as well or positioned to have a joint appointment.  Just looking for thoughts.
> 
> 
> 
> Best,
> 
> Paul
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20250812/65998395/attachment.html >
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem 
> 
> 
> ------------------------------
> 
> End of 3dem Digest, Vol 216, Issue 9
> ************************************
> 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20250812/66f1be6d/attachment.html>