Sep 25 – 29, 2023
Centro de Ciencias de Benasque
Europe/Madrid timezone

Towards an integral, FAIR and cloud-enabled solution for cryoEM data acquisition and processing

Sep 28, 2023, 2:15 PM
Centro de Ciencias de Benasque

Centro de Ciencias de Benasque

Av. de Francia, 17, 22440   Benasque Huesca, Spain   42.603194, 0.523222
Presentation (15' + 5' for questions) Research applications in advanced Digital Infrastructures IBERGRID


Mikel Iceta Tena (Biocomputing Unit @ CNB-CSIC)


Instruct is the pan-European Research Infrastructure for structural biology, centered in bringing high-end technologies and methods to European researchers. The Instruct Image Processing Center (I2PC) has actively been promoting FAIR practices for cryoEM data acquisition and processing workflows. Efforts carried in the scope of projects such as EOSC-Life, BY_COVID and EOSC-Synergy are driving the implementation of the Data Management Plan of Instruct-ERIC and defining the future of an integrated CryoEM workflow. The image acquisitions at the microscope facilities are controlled by SmartScope (an open-source software used in the field) and registered in a Laboratory Information Management System (LIMS) while the project details and metadata will be FAIR-ly available through ARIA (the project management application developed inside Instruct) and the information is stored through a data space (with distributed tools such as iRODS). The processing can easily be deployed in federated computing infrastructures (such as EGI Cloud Compute or the IFCA cloud) by using ScipionCloud. Eventually, the data is made publicly available through EMPIAR (the electron microscopy public archive). The effort will culminate with a fully-connected and integrated system, offering a solution for the whole pipeline in CryoEM (and other) techniques, respecting FAIR principles and ensuring the availability of information.

Primary authors

Mr Alberto García Mena (Biocomputing Unit @ CNB-CSIC) Prof. Ales Krenek (CEITEC-MU) Prof. Carlos Óscar Sorzano Sánchez (Biocomputing Unit @ CNB-CSIC) Mr Daniel Alejandro Marchán Torres (Biocomputing Unit @ CNB-CSIC) Mrs Irene Sánchez López (Biocomputing Unit @ CNB-CSIC) Dr Jiri Novacek (CEITEC-MU) Prof. José María Carazo García (Biocomputing Unit @ CNB-CSIC) Ms Laura del Caño Novales (Biocomputing Unit @ CNB-CSIC) Mikel Iceta Tena (Biocomputing Unit @ CNB-CSIC) Mr Radek Veverka (CEITEC-MU) Tomas Svoboda (Masaryk University)

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