Advances in Xmipp for cryo-electron microscopy: from Xmipp to Scipion

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Strelak, David and Jiménez Moreno, Amaya and Vilas, José Luis and Ramírez Aportela, Erney and Sánchez García, Rubén and Maluenda, David and Vargas Balbuena, Javier and Herreros, David and Fernández Giménez, Estrella and Isidro Gómez, Federico P. de and Horacek, Jan and Myska, David and Horacek, Martin and Conesa, Pablo and Fonseca-Reyna, Yunior C. and Jiménez, Jorge and Martínez, Marta and Harastani, Mohamad and Jonic, Slavica and Filipovic, Jiri and Marabini, Roberto and Carazo, José María and Sorzano, Carlos O. S (2021) Advances in Xmipp for cryo-electron microscopy: from Xmipp to Scipion. Molecules, 26 (20). ISSN 1420-3049

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Official URL: http://dx.doi.org/10.3390/molecules26206224




Abstract

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.


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© 2021 by the authors.
Artículo firmado por más de 10 autores.
The project that gave rise to these results received the support of a fellowship from the “la Caixa” Foundation (ID 100010434). The fellowship code is LCF/BQ/DI18/11660021. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 713673. The work was supported by European Regional Development Fund-Project "CERIT Scientific Cloud" (No.CZ.02.1.01/0.0/0.0/16_013/0001802). The authors would like to acknowledge economic support from: The Spanish Ministry of Economy and Competitiveness through Grants PID2019-104757RB-I00 (AEI/FEDER, UE) and SEV 2017-0712, the “Comunidad Autónoma de Madrid” through Grant: S2017/BMD-3817. European Union (EU) and Horizon 2020 through grants: EOSC Life (Proposal: 824087), HighResCells (Proposal: 810057), IM-paCT (Proposal: 857203), EOSC-Synergy (Proposal: 857647) and iNEXT-Discovery (Proposal: 871037). Authors acknowledge the support and the use of resources of Instruct, a Landmark ESFRI project. J.V thanks economical support from the Spanish Ministry of Science and Innovation through the call 2019 Proyectos de I+D+i–RTI Tipo A (PID2019-108850RA-I00). We acknowledge the support of the French National Research Agency—ANR (ANR-11-BSV8-010-04, ANR-19-CE11-0008-01, and ANR-20-CE11-0020-03 to S.J.), the French National Center for Scientific Research and the Spanish National Research Council (CSIC2009FR0015 and PICS 2011 to S.J. and C.O.S.S.), and access to HPC resources of CINES and IDRIS granted by GENCI (2010-2016 project No. 072174, A0100710998, A0070710998, AP010712190, AD011012188 to S.J.).

Uncontrolled Keywords:Single-particle analysis; Local resolution; Quality assessment; Reconstruction; Alignment; Software; Accurate; Protein; 3dem; Integration
Subjects:Sciences > Physics > Optics
ID Code:68855
Deposited On:18 Jan 2022 19:45
Last Modified:05 Aug 2022 14:18

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