Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to
Scipion

J 2021

Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

STŘELÁK, David, Amaya JIMÉNEZ-MORENO, José VILAS, Erney RAMÍREZ-APORTELA, Ruben SÁNCHEZ-GARCÍA et. al.

Basic information

Original name

Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

Authors

STŘELÁK, David (203 Czech Republic, guarantor, belonging to the institution), Amaya JIMÉNEZ-MORENO (724 Spain), José VILAS (724 Spain), Erney RAMÍREZ-APORTELA (724 Spain), Ruben SÁNCHEZ-GARCÍA (724 Spain), David MALUENDA (724 Spain), Javier VARGAS (724 Spain), David HERREROS (724 Spain), Estrella FERNÁNDEZ-GIMÉNEZ (724 Spain), Federico DE ISIDRO-GÓMEZ (724 Spain), Jan HORÁČEK (203 Czech Republic, belonging to the institution), David MYŠKA (203 Czech Republic, belonging to the institution), Martin HORÁČEK (203 Czech Republic, belonging to the institution), Pablo CONESA (724 Spain), Yunior FONSECA-REYNA (724 Spain), Jorge JIMÉNEZ, Marta MARTÍNEZ (724 Spain), Mohamad HARASTANI (250 France), Slavica JONIĆ (250 France), Jiří FILIPOVIČ (203 Czech Republic, belonging to the institution), Roberto MARABINI (724 Spain), José CARAZO (724 Spain) and Carlos SORZANO (724 Spain)

Edition

Molecules, Mayer und Muller, 2021, 1420-3049

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.927

RIV identification code

RIV/00216224:14330/21:00122593

Organization unit

Faculty of Informatics

DOI

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

UT WoS

000714566400001

Keywords in English

Xmipp; Cryo-EM; Scipion; single-particle analysis

Abstract

V originále

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.

Links

EF16_013/0001802, research and development project

Name: CERIT Scientific Cloud

MUNI/A/1411/2019, interní kód MU

Name: Aplikovaný výzkum: softwarové architektury kritických infrastruktur, bezpečnost počítačových systémů, zpracování přirozeného jazyka a jazykové inženýrství, vizualizaci velkých dat a rozšířená realita.

Investor: Masaryk University, Category A

MUNI/A/1549/2020, interní kód MU

Name: Zapojení studentů Fakulty informatiky do mezinárodní vědecké komunity 21 (Acronym: SKOMU)

Investor: Masaryk University

Citovat

STŘELÁK, David, Amaya JIMÉNEZ-MORENO, José VILAS, Erney RAMÍREZ-APORTELA, Ruben SÁNCHEZ-GARCÍA, David MALUENDA, Javier VARGAS, David HERREROS, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, Jan HORÁČEK, David MYŠKA, Martin HORÁČEK, Pablo CONESA, Yunior FONSECA-REYNA, Jorge JIMÉNEZ, Marta MARTÍNEZ, Mohamad HARASTANI, Slavica JONIĆ, Jiří FILIPOVIČ, Roberto MARABINI, José CARAZO and Carlos SORZANO. Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion. Molecules. Mayer und Muller, 2021, vol. 26, No 20, p. 1-14. ISSN 1420-3049. Available from: https://dx.doi.org/10.3390/molecules26206224.

@article{1798282,
   author = {Střelák, David and JiménezandMoreno, Amaya and Vilas, José and RamírezandAportela, Erney and SánchezandGarcía, Ruben and Maluenda, David and Vargas, Javier and Herreros, David and FernándezandGiménez, Estrella and de IsidroandGómez, Federico and Horáček, Jan and Myška, David and Horáček, Martin and Conesa, Pablo and FonsecaandReyna, Yunior and Jiménez, Jorge and Martínez, Marta and Harastani, Mohamad and Jonić, Slavica and Filipovič, Jiří and Marabini, Roberto and Carazo, José and Sorzano, Carlos},
   article_number = {20},
   doi = {http://dx.doi.org/10.3390/molecules26206224},
   keywords = {Xmipp; Cryo-EM; Scipion; single-particle analysis},
   language = {eng},
   issn = {1420-3049},
   journal = {Molecules},
   title = {Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion},
   url = {https://www.mdpi.com/1420-3049/26/20/6224},
   volume = {26},
   year = {2021}
}

TY  - JOUR
ID  - 1798282
AU  - Střelák, David - Jiménez-Moreno, Amaya - Vilas, José - Ramírez-Aportela, Erney - Sánchez-García, Ruben - Maluenda, David - Vargas, Javier - Herreros, David - Fernández-Giménez, Estrella - de Isidro-Gómez, Federico - Horáček, Jan - Myška, David - Horáček, Martin - Conesa, Pablo - Fonseca-Reyna, Yunior - Jiménez, Jorge - Martínez, Marta - Harastani, Mohamad - Jonić, Slavica - Filipovič, Jiří - Marabini, Roberto - Carazo, José - Sorzano, Carlos
PY  - 2021
TI  - Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion
JF  - Molecules
VL  - 26
IS  - 20
SP  - 1-14
EP  - 1-14
PB  - Mayer und Muller
SN  - 14203049
KW  - Xmipp
KW  - Cryo-EM
KW  - Scipion
KW  - single-particle analysis
UR  - https://www.mdpi.com/1420-3049/26/20/6224
N2  - 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.
ER  -

STŘELÁK, David, Amaya JIMÉNEZ-MORENO, José VILAS, Erney RAMÍREZ-APORTELA, Ruben SÁNCHEZ-GARCÍA, David MALUENDA, Javier VARGAS, David HERREROS, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, Jan HORÁČEK, David MYŠKA, Martin HORÁČEK, Pablo CONESA, Yunior FONSECA-REYNA, Jorge JIMÉNEZ, Marta MARTÍNEZ, Mohamad HARASTANI, Slavica JONI$\backslash$'C, Jiří FILIPOVIČ, Roberto MARABINI, José CARAZO and Carlos SORZANO. Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion. \textit{Molecules}. Mayer und Muller, 2021, vol.~26, No~20, p.~1-14. ISSN~1420-3049. Available from: https://dx.doi.org/10.3390/molecules26206224.

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