ScipionTomo : Towards cryo-electron tomography software integration, reproducibility, and validation
Jiménez de la Morena, Jorge (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Conesa Mingo, Pablo (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Fonseca-Reyna, Yunior César (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
de Isidro-Gómez, Federico P. (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Herreros, David (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Fernández-Giménez, Estrella (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Střelák, David (Masaryk University)
Moebel, Emmanuel (Institut National de Recherche en Informatique et en Automatique)
Buchholz, Tim Oliver (Center for Systems Biology Dresden)
Jug, Florian (Fondazione Human Technopole)
Martínez-Sánchez, Antonio (University of Oviedo. Department of Computer Sciences)
Harastani, Mohamad (Sorbonne Université)
Jonic, Slavica (Sorbonne Université)
Conesa, José Javier (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Cuervo, Ana (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Losana, Patricia (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Sánchez-Caballero, Ignacio (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Iceta Tena, Mikel (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
del Cano, Laura (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Gragera, Marcos (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Melero, Roberto (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Sharov, Grigory (MRC Laboratory of Molecular Biology. Structural Studies Division)
Castaño-Díez, Daniel (University of Basel. Biozentrum)
Koster, Abraham J. (University of Leiden. Ultrastructural and Molecular Imaging)
Piccirillo, Jonathan G. (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Vilas, Jose Luis (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Oton, Joaquin (ALBA Laboratori de Llum de Sincrotró)
Marabini, Roberto (Universidad Autònoma de Madrid. Escuela Politécnica Superior)
Sorzano, Carlos Oscar S. (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)
Carazo Garcia, José María (Consejo Superior de Investigaciones Científicas. National Center of Biotechnology)

Data:	2022
Resum:	Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.
Ajuts:	Agencia Estatal de Investigación PID2019-104757RB-I00 European Commission 713673 European Commission 810057 European Commission 824087 "la Caixa" Foundation 100010434
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Publicat a:	Journal of structural biology, Vol. 214, Issue 3 (September 2022) , art. 107872, ISSN 1095-8657

DOI: 10.1016/j.jsb.2022.107872
PMID: 35660516

14 p, 13.9 MB

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