2nd Scipion Facilities Course (online edition). Madrid, 2020.

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)