Dear OpenEM members,

This past year has been a whirlwind for the OpenEM project! We wanted to take this opportunity to thank the participants for their hard work, provide some updates on the current project status, and of course wish all of you a Joyeux Noël, Happy Holidays, Frohe Weihnachten, and Buon Anno!

Website & Communication

We are happy to announce that the website can now be reached at https://www.openem.ch. Links to the previous github address should continue to function. If you haven’t visited lately, please look over updated content on the project plan, news, and documentation.

In order to keep you continuously informed about the project status, we will be sending out regular newsletters in future. Please invite any colleagues who you think might be interested to subscribe to the mailing list.

Completed Milestones

We have now completed four of our seven milestones, with major deliverables achieved from all workpackages. We published the first dataset in September as part of MS-III: Proof of Concept, and with the recently completed MS-IV: Alpha Release the service is running at Uni Basel for initial testing.

We have been active along with the OSC-EM consortium in developing an interoperable metadata schema. Most metadata is automatically extracted during acquisition and then can be reviewed by users when ingesting data into the PSI SciCat Data Catalog. Data is stored on either the CSCS Petabyte Archive or ETHZ Long Term Storage systems. A new page has been developed on the Data Catalog website for managing data ingestion, which communicates with an ingestor service running at your facility for secure data access and transfer.

Integration with other services is also essential for open data. A new tool is now available to aid depositing datasets in the EMDB. Just upload refined maps and models for cryoEM datasets and the system will pre-fill metadata for publication in EMDB. (EMPIAR support planned in 2025!)

Intermediate Reports

Intermediate reports were submitted for both OpenEM funding sources. Following constructive feedback from the ETH review board last May, we worked intensively on improving the documentation, being more transparent with the project plan, and completing the initial milestones on schedule. A second intermediate report was submitted Nov 20 and received favorable review and approval for the second phase of funding.

A report to swissuniversities was submitted in Feb 2024. This resulted in a project extension so that university partners will continue to participate through next June. This aligns with the official OpenEM release date, while ETH-funded partners will continue the project through Dec 2025 to provide training, hand over duties to facility staff, and respond to user feedback.

Upcoming

The alpha version has been deployed to limited users at University of Basel. This will serve as a model environment in which we can gain experience in deploying OpenEM. The next milestone will focus on expanding access to this to all OpenEM facilities. While not all features are fully completed, we want to get as much feedback from the facilities as possible. This will be an opportunity to customize the experience to each facility and ensure that all use cases are covered by the OpenEM workflows. Based on this experience in the alpha, we will refine the system requirements and installation documentation and carry out initial real-world tests.

All-Hands Workshop

On Dec 9 we sent out the invitations for our upcoming OpenEM workshop, which will take place on Feb 13, 2025 at the University of Bern. This will take place in hybrid mode, but we encourage you to join us in-person for a demo, feedback session, and apéro.

The workshop is free and open to project members, facility operators, interested researchers, and other stakeholders. Microscope operators and IT specialists who will interact routinely with OpenEM are particularly invited to attend. In-person registration is limited, so please sign up soon on the following page:

OpenEM Workshop (13 February 2025): Registration · Indico

Seasons Greetings

The entire OpenEM team wishes you happy holidays and a good start to the new year!

Best regards,

OpenEM-Team