Dates:
Tuesday 27 Oct – Friday 30, 4 days, afternoon from 16:00-18:00 CET
Aim
The aim of this meeting is to show what scipion offers to a Cryo-em facility. The course will have a strong “practical component”, since workflows will be running live on the Amazon cloud.
I2PC is organising a Cryo-EM Scipion course specifically for Facilities. Scipion team and collaborators have been working in the last years in what we call streaming processing. We understand the importance of monitoring the acquisition in real time to take early decisions to improve the acquisition performance. In addition, Scipion incorporates new techniques to automate the real time image processing pipeline until 2D classification and even an initial estimation of 3D heterogeneity. Moreover, Scipion is equipped with several consensus protocols to get combined results from different EM-packages to screen and select the best micrographs, CTFs, particles or 2D-classes. All with the benefit of Scipion flexibility and ”mix and match” capabilities. Scipion is also able to gather all the processing information and present it in a HTML report that could be served over the web and automatically refreshed. It also offers automatic tools for direct submission to databases, like EMPIAR, when appropriate.
No programming skills are required.
Target Audience:
Cryo em facility operators wanting to do or already doing on the fly processing. The course will address both Single Particle Analysis (SPA) and Tomography, although the stress will be in SPA.
Conditions:
Course will be online, so attendees should connect remotely and have internet connection and a modern browser.
No programming skills are required.
AWS machines will be provided by us.
Content
Day | Time (CET time zone) | Description | Speakers |
Tuesday 27th October | 16:00-17:00 | Welcome, introduction , agenda, logistics. | Jose Maria, Pablo |
17:00-19:00 | On AWS: running streaming demo – intro, file formats, installation – plugins – configuration. | Pablo Conesa | |
Wednesday 28th October | 16:00-19:00 | Available functionality: guided practice: from movies to …X. Consensus. Breaking the stream. | Marcos, Coss |
Thursday 29th October | 16:00-18:00 | Monitoring – HTML – Grafana (customization) | Roberto |
18:00-19:00 | Catch-up, personal work | All | |
Friday 30th October | 16:00-17:30 | Kicking off scipion (templates) – passing data to user. | Jorge, David |
17:30-18:30 | Submission to EMPIAR, Json summary. | Laura | |
18:30-19:00 | What do you miss in the Scipion/your pipeline? Feedback, open discussion, closing session. | All |
Key dates:
01 – 30 September, 2020: Submission of the course application
01 – 15 October, 2020: Communication of awarded applications
Fill your application here. (Registration will be open soon)