[3dem] Very Vague Question

Tue Aug 12 08:16:40 PDT 2025

Hi all,

Valuable input from Marcus/Ayil/Steven.

At our facility (protein production + structural biology, but we do not have the microscopes), the cryo-EM pipeline covers protein production (if needed), freezing, screening, data collection (with support from another dedicated cryo-EM team), and processing with a user.

We require a dedicated person on the user’s side—usually a PhD student or postdoc—especially for new targets or difficult cases. They must be involved in data collection, processing, interpretation, and data management. This ensures clear communication, aligned goals, and that the project stays with the lab, not the facility. For simpler or familiar cases, we decide on a case-by-case basis. We don’t aim to turn users into structural biologists, but give them enough skills to work independently under our supervision.

Without this setup, demand would exceed our capacity. It also avoids us having to interpret biological results or design follow-up experiments, which fall outside our scope.

GPU and storage resources are centralized at the institution, with clusters that support cryo-EM workloads without GPU reservations. Users are responsible for their own data. We run CryoSPARC and SBGrid on the clusters, minimizing software maintenance for staff.

All staff have postdoc experience in X-ray, single particle, or tomography. We support the university community without charging for precisely all the time, giving us flexibility. We don’t require authorship but expect at least acknowledgement.

A typical workflow: we collect data, create a shared CryoSPARC workspace, and the trainee duplicates and continues jobs independently. We monitor progress and step in if needed, following this approach through to model building and interpretation.

Best

Kelvin

--
Kelvin Lau
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Scientist - Protein production and structure core facility – PTPSP
Co-President – EPFL Scientific Staff Association – ELSA

EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin.lau at epfl.ch<mailto:kelvin.lau at epfl.ch>
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If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267>

On 12.08.2025, 16:13, "3dem on behalf of Marcus FISLAGE via 3dem" <3dem-bounces at ncmir.ucsd.edu<mailto:3dem-bounces at ncmir.ucsd.edu> on behalf of 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>> wrote:

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

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________________________________
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
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