ScipionTomo: Towards cryo-electron tomography software
integration, reproducibility, and validation

J 2022

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation

JIMÉNEZ DE LA MORENA, Jorge, Pablo CONESA, Yunior FONSECA, Federico DE ISIDRO-GÓMEZ, David HERREROS et. al.

Základní údaje

Originální název

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation

Autoři

JIMÉNEZ DE LA MORENA, Jorge, Pablo CONESA, Yunior FONSECA, Federico DE ISIDRO-GÓMEZ, David HERREROS, Estrella FERNÁNDEZ-GIMÉNEZ, David STŘELÁK (203 Česká republika, garant, domácí), Emmanuel MOEBEL, Tim-Oliver BUCHHOLZ, Florian JUG, Antonio MARTINEZ-SANCHEZ, Mohamad HARASTANI, Slavica JONIC, Jose CONESA, Ana CUERVO, Patricia LOSANA, Irene SÁNCHEZ, Mikel ICETA, Laura DEL CANO, Marcos GRAGERA, Roberto MELERO, Grigori SHAROV, Daniel CASTAÑO-DÍEZ, Aart KOSTER, Jonathan PICCIRILLO, Jose Luis VILAS, Joaqin OTÓN, Roberto MARABINI, Carlos Oscar SANCHEZ SORZANO a Jose Maria CARAZO

Vydání

Journal of Structural Biology, Elsevier, 2022, 1047-8477

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.000

Kód RIV

RIV/00216224:14330/22:00125969

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1016/j.jsb.2022.107872

UT WoS

000823355700001

Klíčová slova anglicky

ELECTRONRECONSTRUCTIONRESOLUTIONALIGNMENT

Změněno: 6. 4. 2023 11:13, RNDr. Pavel Šmerk, Ph.D.

Anotace

V originále

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 (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). 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.

Citovat

JIMÉNEZ DE LA MORENA, Jorge, Pablo CONESA, Yunior FONSECA, Federico DE ISIDRO-GÓMEZ, David HERREROS, Estrella FERNÁNDEZ-GIMÉNEZ, David STŘELÁK, Emmanuel MOEBEL, Tim-Oliver BUCHHOLZ, Florian JUG, Antonio MARTINEZ-SANCHEZ, Mohamad HARASTANI, Slavica JONIC, Jose CONESA, Ana CUERVO, Patricia LOSANA, Irene SÁNCHEZ, Mikel ICETA, Laura DEL CANO, Marcos GRAGERA, Roberto MELERO, Grigori SHAROV, Daniel CASTAÑO-DÍEZ, Aart KOSTER, Jonathan PICCIRILLO, Jose Luis VILAS, Joaqin OTÓN, Roberto MARABINI, Carlos Oscar SANCHEZ SORZANO a Jose Maria CARAZO. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. Journal of Structural Biology. Elsevier, 2022, roč. 214, č. 3, s. 1-14. ISSN 1047-8477. Dostupné z: https://dx.doi.org/10.1016/j.jsb.2022.107872.

@article{1859097,
   author = {Jiménez de la Morena, Jorge and Conesa, Pablo and Fonseca, Yunior and de IsidroandGómez, Federico and Herreros, David and FernándezandGiménez, Estrella and Střelák, David and Moebel, Emmanuel and Buchholz, TimandOliver and Jug, Florian and MartinezandSanchez, Antonio and Harastani, Mohamad and Jonic, Slavica and Conesa, Jose and Cuervo, Ana and Losana, Patricia and Sánchez, Irene and Iceta, Mikel and del Cano, Laura and Gragera, Marcos and Melero, Roberto and Sharov, Grigori and CastañoandDíez, Daniel and Koster, Aart and Piccirillo, Jonathan and Vilas, Jose Luis and Otón, Joaqin and Marabini, Roberto and Sanchez Sorzano, Carlos Oscar and Carazo, Jose Maria},
   article_number = {3},
   doi = {http://dx.doi.org/10.1016/j.jsb.2022.107872},
   keywords = {ELECTRONRECONSTRUCTIONRESOLUTIONALIGNMENT},
   language = {eng},
   issn = {1047-8477},
   journal = {Journal of Structural Biology},
   title = {ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation},
   url = {http://dx.doi.org/10.1016/j.jsb.2022.107872},
   volume = {214},
   year = {2022}
}

TY  - JOUR
ID  - 1859097
AU  - Jiménez de la Morena, Jorge - Conesa, Pablo - Fonseca, Yunior - de Isidro-Gómez, Federico - Herreros, David - Fernández-Giménez, Estrella - Střelák, David - Moebel, Emmanuel - Buchholz, Tim-Oliver - Jug, Florian - Martinez-Sanchez, Antonio - Harastani, Mohamad - Jonic, Slavica - Conesa, Jose - Cuervo, Ana - Losana, Patricia - Sánchez, Irene - Iceta, Mikel - del Cano, Laura - Gragera, Marcos - Melero, Roberto - Sharov, Grigori - Castaño-Díez, Daniel - Koster, Aart - Piccirillo, Jonathan - Vilas, Jose Luis - Otón, Joaqin - Marabini, Roberto - Sanchez Sorzano, Carlos Oscar - Carazo, Jose Maria
PY  - 2022
TI  - ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation
JF  - Journal of Structural Biology
VL  - 214
IS  - 3
SP  - 1-14
EP  - 1-14
PB  - Elsevier
SN  - 10478477
KW  - ELECTRONRECONSTRUCTIONRESOLUTIONALIGNMENT
UR  - http://dx.doi.org/10.1016/j.jsb.2022.107872
N2  - 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 (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). 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.
ER  -

JIMÉNEZ DE LA MORENA, Jorge, Pablo CONESA, Yunior FONSECA, Federico DE ISIDRO-GÓMEZ, David HERREROS, Estrella FERNÁNDEZ-GIMÉNEZ, David STŘELÁK, Emmanuel MOEBEL, Tim-Oliver BUCHHOLZ, Florian JUG, Antonio MARTINEZ-SANCHEZ, Mohamad HARASTANI, Slavica JONIC, Jose CONESA, Ana CUERVO, Patricia LOSANA, Irene SÁNCHEZ, Mikel ICETA, Laura DEL CANO, Marcos GRAGERA, Roberto MELERO, Grigori SHAROV, Daniel CASTAÑO-DÍEZ, Aart KOSTER, Jonathan PICCIRILLO, Jose Luis VILAS, Joaqin OTÓN, Roberto MARABINI, Carlos Oscar SANCHEZ SORZANO a Jose Maria CARAZO. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. \textit{Journal of Structural Biology}. Elsevier, 2022, roč.~214, č.~3, s.~1-14. ISSN~1047-8477. Dostupné z: https://dx.doi.org/10.1016/j.jsb.2022.107872.

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