workshop

Dates: November 5-7th 2024 (3 EU afternoons or 3 east US mornings)

Venue: Hybrid format

Aim: The aim of this meeting is to gather feedback and showcase how facilities are using Scipion, demonstrating its capabilities and benefits for Cryo-EM facilities. The event will feature talks and ample time for discussion, aiming to share experiences with Scipion, discuss operational methodologies, and highlight new developments that can enhance our community’s daily workflow.

Conditions: The workshop will be held at the Spanish National Centre for Biotechnology in Madrid, Spain. For the practical session on November 5, in-person attendance is required, and you must select this option on the registration page to ensure we prepare a machine for you. The main workshop on November 6-7 can be attended either in person or remotely.
No programming skills are required. We will use in-house bigbluebutton conference system. Verify your browser works at https://demo.bigbluebutton.org/

Program:

We start at:
San Francisco – 05:00 // Minneapolis – 07:00 // New York – 08:00 // São Paulo – 09:00 // Madrid – 14:00 // London – 13:00
Beijing – 20:00 // Tokyo – 21:00 // Sydney – 23:00

PRACTICAL COURSE

Tuesday 5th November – In person

14:00 – 14:30     Course Overview – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain.
14:30 – 15:30     On-the-fly processing – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
15:30 – 16:00     Coffee break
16:00 – 17:00     Processing workflows and templates – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
17:00 – 17:45     Scipion with queue systems – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
17:45 – 18:30     Build your own workflow – Support from CNB staff

WORKSHOP

Wednesday 6th November – Hybrid

14:00 (CET)      Welcome – Jose María Carazo , Biocomputing Unit CNB – Madrid, Spain.
14:15 – 14:45     An Overview of Scipion in Facilities – Pablo Conesa, Biocomputing Unit CNB – Madrid, Spain.
14:45 – 15:15     Automated on-the-fly data processing in EMhub is fantastic, but what’s next? – Jose Miguel de la Rosa Trevin, St Jude Children’s Research Hospital – Memphis, USA.
15:15 – 15:45     Lab Management with CEITEC: LIMS Demo and Key Features – Radek Veverka, Central European Institute of Technology at Masaryk University – Brno, Czech Republic.
15:45 – 16:15     Coffee break
16:15 – 16:45     Smart Data Collection with Smartscope – Jonathan Bouvette, Princeton University – New Jersey, USA.
16:45 – 17:15     Enhancing Smart Acquisition: Integrating SPA Processing Feedback with the Scipion-EM-SmartScope Plugin – Alberto Garcia, Biocomputing Unit CNB – Madrid, Spain.
17:15 – 18:00     Discussion and user input gathering

Thursday 7th November – Hybrid

14.00 (CET)      Enhancing Efficiency: Best Practices and Automations for On-the-Fly Processing in SPA Workflows – Daniel Marchan, Biocomputing Unit CNB – Madrid, Spain.
14:30 – 15:00     NextPyP: A scalable platform for single-particle cryo-EM/ET image analysis – Alberto Bartesaghi Duke University – Durham , USA.
15:00 – 15:30    Using Scipion to enable diverse cryo-ET workflows to explore Neurodegeneration at UCSF – Eric Tse, Institute for Neurodegenerative Diseases UCSF – San Francisco, USA.
15:30 – 16:00     Coffee break
16:00 – 16:30     Scipion use Case: Stream processing at CNB Facility –  Javier Chichon, CryoEM Facility CNB – Madrid, Spain.
16:30 – 17:00     Expanding access to cryo-EM through specimen preparation robotics and platform-independent remote imaging – Mario Borgnia, National Institute of Environmental Health Sciences – Durham, USA
17:00 – 18:00     Discussion and conclusions