- https://www.sincrotronalba.es/ca/actualitat/agenda/esdeveniments-publics-dalba/emhub-and-scipion-bridging-data-management-with-on-the-fly-data-processing
- EMhub and Scipion: bridging data management with on-the-fly data processing
- 2024-05-15T12:00:00+02:00
- 2024-05-15T13:00:00+02:00
- By Jose Miguel de la Rosa; Scientific Software developer for Cryo-EM
- Què
- events
- Quan
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Mai 15, 2024
de 12:00 a 13:00 (Europe/Madrid / UTC200) - On
- ALBA Synchrotron, Maxwell Auditorium
- Nom de contacte
- Joaquín Otón
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- Lloc web relacionat
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Abstract
I will present EMhub (https://3dem.github.io/emdocs/emhub/) a web platform designed to serve scientific facilities needs such as instrument bookings, data management, and reporting. EMhub has been used in the last few years at the Swedish National CryoEM Facility and has been useful for managing users, applications, bookings, invoicing, and project tracking. A central component of this application is a booking calendar which allows booking microscopes and instruments or even services such as bi-weekly facility drop-ins. Users are grouped by laboratories and universities, which is convenient for evaluating yearly applications and generating invoices for specific periods. Another helpful feature is the implementation of projects and their associated entries. This documents the whole process of grids preparation, screening, and data collection. Moreover, different processes can be attached to the application via a REST API to automate various tasks (e.g. folder creation, user and password generation, etc) and for monitoring on-the-fly data processing independently of the software used. Emhub has also been installed in the CryoEM center at the Structural Biology Department at St. Jude Children's Research Hospital in Memphis, TN. There, it has been more centered on on-the-fly data processing and analysis. Currently, a fully automated pipeline is in place that goes until 2D classification and selection of best classes. The CryoEM pipeline has been implemented using Scipion, a software framework for integration, reproducibility, and analysis (https://scipion.i2pc.es/).
