Evidence map›Paper›PMID 34684805›Full record

ArticleMolecules (Basel, Switzerland)2021

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.

David Strelak, Amaya Jiménez-Moreno, José L Vilas, Erney Ramírez-Aportela, Ruben Sánchez-García, David Maluenda, Javier Vargas, David Herreros, Estrella Fernández-Giménez, Federico P de Isidro-Gómez and 13 more

Abstract read
In one paragraph

Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

  1. Article
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  10. Article
  11. Computational methods forFrontiers in cellular and infection microbiology · 2023
    Review
  12. Article
  13. Protein Structural Analysis by Cryogenic Electron Microscopy.Methods in molecular biology (Clifton, N.J.) · 2023
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

23 authors.

David StrelakFaculty of Informatics, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic.ORCID 0000-0003-4513-4718
Amaya Jiménez-MorenoSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
José L VilasSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Erney Ramírez-AportelaSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Ruben Sánchez-GarcíaOxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, UK.
David MaluendaDepartament de Física Aplicada, Universitat de Barcelona (UB), Martí i Franquès 1, 08028 Barcelona, Spain.ORCID 0000-0002-4385-7798
Javier VargasDepartamento de Óptica, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040 Madrid, Spain.ORCID 0000-0001-7519-6106
David HerrerosSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Estrella Fernández-GiménezSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Federico P de Isidro-GómezSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.ORCID 0000-0003-2289-2364
Jan HoracekInstitute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic.
David MyskaInstitute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic.
Martin HoracekInstitute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic.
Pablo ConesaSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Yunior C Fonseca-ReynaSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Jorge JiménezSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Marta MartínezSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.ORCID 0000-0002-8435-5540
Mohamad HarastaniIMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, 4 Place Jussieu, 75005 Paris, France.ORCID 0000-0001-9154-1109
Slavica JonićIMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, 4 Place Jussieu, 75005 Paris, France.ORCID 0000-0001-5112-2743
Jiri FilipovicInstitute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic.ORCID 0000-0002-5703-9673
Roberto MarabiniSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
José M CarazoSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Carlos O S SorzanoSpanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.ORCID 0000-0002-9473-283X

Funding

NEUROBEHAVIORAL MECHANISMS OF DRUG ADDICTIONR01DA003817 · NIDA · ALBANY MEDICAL COLLEGE · PI GLICK, STANLEY D · 1985 to 2001
$370k
CERIT Scientific Cloud CZ.02.1.01/0.0/0.0/16_013/0001802Comunidad Autónoma de Madrid S2017/BMD-3817European Union (EU) and Horizon 2020 EOSC Life (Proposal: 824087)European Union (EU) and Horizon 2020 EOSC - Synergy (Proposal: 857647)European Union (EU) and Horizon 2020 HighResCells (Proposal: 810057)European Union (EU) and Horizon 2020 IMpaCT (Proposal: 857203)European Union (EU) and Horizon 2020 iNEXT-Discovery (Proposal: 871037)European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement 713673French National Center for Scientific Research and the Spanish National Research Council CSIC2009FR0015 and PICS 2011French National Research Agency ANR-11-BSV8-010-04French National Research Agency ANR-19-CE11-0008-01French National Research Agency ANR-20-CE11-0020-03Grand Équipement National de Calcul Intensif (France) 2010-2016 project No. 072174Grand Équipement National de Calcul Intensif (France) A0070710998Grand Équipement National de Calcul Intensif (France) A0100710998Grand Équipement National de Calcul Intensif (France) AD011012188Grand Équipement National de Calcul Intensif (France) AP010712190Horizon 2020 EOSC Life (Proposal: 824087)la Caixa Foundation ID 100010434la Caixa Foundation LCF/BQ/DI18/11660021Spanish Ministry of Science and Innovation 2019 Proyectos de I+D+i -- RTI Tipo A (PID2019-108850RA-I00)The Spanish Ministry of Economy and Competitiveness PID2019-104757RB-I00 (AEI/FEDER, UE)The Spanish Ministry of Economy and Competitiveness SEV 2017-0712
6 · The paper itself

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.

Indexed as

Cryo-EMScipionsingle-particle analysisXmipp

Identifiers

PMID34684805
PMCPMC8537808

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.