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Featured Article
https://doi.org/10.12688/f1000research.9206.1
Opinion Article metrics
Top 10 metrics for life science software good practices
[version 1; peer review: 2 approved]
Haydee Artaza, Neil Chue Hong, Manuel Corpas, Angel Corpuz, Rob W.W. Hooft, Rafael C. Jiménez, Brane Leskošek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vařeková, Thomas Van Parys, Daniel Vaughan
Peer Reviewers Invited
PUBLISHED 16 Aug 2016
https://doi.org/10.12688/f1000research.163833.1
Software Tool Article metrics AWAITING PEER REVIEW
LitSieve: An integrated literature search and triage tool for biocuration
[version 1; peer review: awaiting peer review]
Matt Jeffryes, Melissa Harrison, Henning Hermjakob, Johanna McEntyre
Peer Reviewers Invited
  • Funders
  • European Molecular Biology Laboratory
  • HORIZON EUROPE Marie Sklodowska-Curie Actions
PUBLISHED 11 Jul 2025
https://doi.org/10.12688/f1000research.157778.1
Opinion Article metrics
Foundational Competencies and Responsibilities of a Research Software Engineer
[version 1; peer review: 2 approved]
Florian Goth, Renato Alves, Matthias Braun, Leyla Jael Castro, Gerasimos Chourdakis, Simon Christ, Jeremy Cohen, Stephan Druskat, Fredo Erxleben, Jean-Noël Grad, Magnus Hagdorn, Toby Hodges, Guido Juckeland, Dominic Kempf, Anna-Lena Lamprecht, Jan Linxweiler, Frank Löffler, Michele Martone, Moritz Schwarzmeier, Heidi Seibold, Jan Philipp Thiele, Harald von Waldow, Samantha Wittke
Peer Reviewers Miranda Mundt; Uwe Schmitt
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Deutsche Forschungsgemeinschaft
  • European High Performance Computing Joint Undertaking
  • Hessisches Ministerium für Wissenschaft und Kunst
  • Engineering and Physical Sciences Research Council
PUBLISHED 26 Nov 2024
https://doi.org/10.12688/f1000research.153895.1
Opinion Article metrics
From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure
[version 1; peer review: 3 approved with reservations]
Bogdan Mirăuță, Cătălina Zenoaga-Barbăroșie, Monica Abrudan, Marius Mihășan, Mădălina Giurgiu, Daria Mihalachi, Michalis-Daniel Lazăr, RSBI Members, Horia L. Banciu
Peer Reviewers Francis Ouellette; Federico Zambelli; Carol Goble
  • Funder
  • EEA Grants/Norway Grants (Bioinformatics Capacity Building Human Genomics, an RSBI and ELIXIR Norway bilateral project)
PUBLISHED 03 Sep 2024
https://doi.org/10.12688/f1000research.74416.2
Software Tool Article metrics
Revised
BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data
[version 2; peer review: 1 approved, 2 approved with reservations]
Alan O'Callaghan, Nils Eling, John C. Marioni, Catalina A. Vallejos
Peer Reviewers Oliver M. Crook; Andrew McDavid; Michel S Naslavsky
  • Funders
  • Cancer Research UK
  • University of Edinburgh
  • European Molecular Biology Laboratory
LATEST VERSION PUBLISHED 07 May 2024
https://doi.org/10.12688/f1000research.144515.1
Opinion Article metrics
Establishing the ELIXIR Microbiome Community
[version 1; peer review: 1 approved, 1 approved with reservations]
Robert D. Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J. Cox, Claudio Donati, Vitor Martins dos Santos, Bruno Fosso, John Hancock, Katharina F. Heil, Naveed Ishaque, Varsha Kale, Benoit J. Kunath, Claudine Médigue, Evangelos Pafilis, Graziano Pesole, Lorna Richardson, Monica Santamaria, Tim Van Den Bossche, Juan Antonio Vizcaíno, Haris Zafeiropoulos, Nils P. Willassen, Eric Pelletier, Bérénice Batut
Peer Reviewers Charlie Pauvert; Almut Heinken
  • Funders
  • CnrBiomics
  • Fundação para a Ciência e a Tecnologia
  • ELIXIRxNextGenIT
  • National Research Fund Luxembourg
  • Research Foundation Flanders
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 08 Jan 2024
https://doi.org/10.12688/f1000research.123934.1
Software Tool Article metrics
ENA Source Attribute Helper: An Application Programming Interface to facilitate accurate reference to biological source data
[version 1; peer review: 1 approved, 1 not approved]
Vikas Gupta, Joana Paupério, Josephine Burgin, Suran Jayathilaka, Guy Cochrane
Peer Reviewers Sujeevan Ratnasingham; Begoña Aguado and Sandra Gonzalez
  • Funder
  • Horizon 2020 Research and Innovation Action
PUBLISHED 13 Sep 2022
https://doi.org/10.12688/f1000research.109080.2
Opinion Article metrics
Revised
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
[version 2; peer review: 2 approved]
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, Paul J. Kersey, Stephan Weise, Richard Finkers, Baron Koylass, Timothee Cezard, Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
Peer Reviewers Boas Pucker and Alenka Hafner; Micha M. Bayer
  • Funders
  • ELIXIR
  • Bundesministerium für Bildung und Forschung
  • Horizon 2020 Framework Programme
LATEST VERSION PUBLISHED 19 May 2022
https://doi.org/10.12688/f1000research.118082.1
Case Study metrics
IT Service management system for EMBL’s European Bioinformatics Institute’s IT department
[version 1; peer review: 2 approved with reservations]
Montserrat González Ferreiro, Steven Newhouse
Peer Reviewers Álvaro López García; Muhammad Hafizhuddin Hilman
PUBLISHED 10 May 2022
https://doi.org/10.12688/f1000research.121363.1
Case Study metrics
Data protection record of processing activities and privacy notice generator toolkit by EMBL’s European Bioinformatics Institute
[version 1; peer review: 2 approved with reservations]
Montserrat González Ferreiro, Steven Newhouse
Peer Reviewers Mikael Linden; Harshvardhan Pandit
PUBLISHED 05 May 2022
https://doi.org/10.12688/f1000research.53698.1
Review metrics
Approaches for containerized scientific workflows in cloud environments with applications in life science
[version 1; peer review: 2 not approved]
Ola Spjuth, Marco Capuccini, Matteo Carone, Anders Larsson, Wesley Schaal, Jon Ander Novella, Oliver Stein, Morgan Ekmefjord, Paolo Di Tommaso, Evan Floden, Cedric Notredame, Pablo Moreno, Andreas Hellander, Payam Emami Khoonsari, Stephanie Herman, Kim Kultima, Samuel Lampa
Peer Reviewers Maciej Malawski; Roberto Vera Alvarez
  • Funders
  • Nordic e-Infrastructure Collaboration (NeIC)
  • Swedish Foundation for Strategic Research
  • Åke Wiberg Foundation
  • European Commission's Horizon 2020 programme
  • Swedish Research Council FORMAS
  • Swedish e-Science Research Centre (SeRC)
PUBLISHED 29 Jun 2021
https://doi.org/10.12688/f1000research.53408.1
Editorial metrics NOT PEER REVIEWED
Highlights from the 16th International Society for Computational Biology Student Council Symposium 2020
[version 1; peer review: not peer reviewed]
Wim L. Cuypers, Handan Melike Dönertaş, Jasleen K. Grewal, Nazeefa Fatima, Chase Donnelly, Arvind Singh Mer, Spencer Krieger, Bart Cuypers, Farzana Rahman
PUBLISHED 04 Jun 2021
https://doi.org/10.12688/f1000research.52531.1
Opinion Article metrics
Developing open-source software for bioimage analysis: opportunities and challenges
[version 1; peer review: 2 approved]
Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Peer Reviewers Loïc A. Royer; Nico Stuurman
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Institut National de la Santé et de la Recherche Médicale
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.29032.2
Method Article metrics
Revised
Sustainable data analysis with Snakemake
[version 2; peer review: 2 approved]
Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
Peer Reviewers Michael Reich; Caroline C. Friedel
  • Funders
  • Netherlands Organisation for Scientific Research (NWO)
  • Deutsche Stiftung für Herzforschung
  • United States National Science Foundation Graduate Research Fellowship Program (NSF-GRFP)
  • Google LLC
LATEST VERSION PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.40666.1
Editorial metrics NOT PEER REVIEWED
6th European Student Council Symposium (ESCS): overcoming obstacles to enhance virtuality, connectivity, inclusivity and community engagement
[version 1; peer review: not peer reviewed]
Gabriel J. Olguín-Orellana, Sofia Papadimitriou, Alberto Langtry Yáñez, Pradeep Eranti, Rosario del Carmen Flores-Vallejo, Ana I. Castillo-Orozco, Kalaumari Mayoral-Peña, R. Gonzalo Parra
  • Funder
  • ISCB Student Council; Information Technology for Translational Medicine (ITTM) Solutions
PUBLISHED 22 Jan 2021
https://doi.org/10.12688/f1000research.28330.1
Editorial metrics NOT PEER REVIEWED
4th ISCB Latin American Student Council Symposium: a virtual and inclusive experience during COVID-19 times
[version 1; peer review: not peer reviewed]
Camila Castillo-Vilcahuaman, Catalina Valdivia, Cleidy Osorio-Mogollón, Claudia Silva-Andrade, Rafael Puche-Quiñonez, Sebastián Ayala-Ruano, Yesid Cuesta-Astroz, R. Gonzalo Parra
  • Funder
  • ISCB Student Council
PUBLISHED 15 Dec 2020
https://doi.org/10.12688/f1000research.25413.2
Research Article metrics
Revised
Biocuration - mapping resources and needs
[version 2; peer review: 2 approved]
Alexandra Holinski, Melissa L. Burke, Sarah L. Morgan, Peter McQuilton, Patricia M. Palagi
Peer Reviewers Tanya Berardini; Luana Licata
  • Funder
  • ELIXIR
LATEST VERSION PUBLISHED 02 Dec 2020
https://doi.org/10.12688/f1000research.24427.1
Research Article metrics
Annotation and curation of human genomic variations: an ELIXIR Implementation Study
[version 1; peer review: 2 approved with reservations]
Alessia David, Valérie Barbié, Marcella Attimonelli, Roberto Preste, Enni Makkonen, Heidi Marjonen, Mats Lindstedt, Kati Kristiansson, Sarah E. Hunt, Fiona Cunningham, Ilkka Lappalainen, Michael J.E. Sternberg
Peer Reviewers Lina Ma; Osamu Ogasawara
  • Funders
  • ELIXIR
  • Imperial College London
  • European Molecular Biology Laboratory
PUBLISHED 08 Oct 2020
https://doi.org/10.12688/f1000research.25235.1
Method Article metrics
Modelling structural rearrangements in proteins using Euclidean distance matrices
[version 1; peer review: 2 approved with reservations]
Aleix Lafita, Alex Bateman
Peer Reviewers Sergey Ovchinnikov; Henry Wolkowicz and Haesol Im
  • Funder
  • European Molecular Biology Laboratory
PUBLISHED 20 Jul 2020
https://doi.org/10.12688/f1000research.20559.1
Opinion Article metrics
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)
[version 1; peer review: 1 approved, 3 approved with reservations]
Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital, Modesto Orozco, Anastassis Perrakis, Matthias Rarey, Claudio Soares, Joel L. Sussman, Janet M. Thornton, Pierre Tuffery, Gabor Tusnady, Rikkert Wierenga, Tiina Salminen, Bohdan Schneider
Peer Reviewers Sjoerd Jacob De Vries and Isaure Chauvot de Beauchene; Silvio C.E Tosatto; Roland L. Dunbrack; Andras Fiser
  • Funder
  • ELIXIR
PUBLISHED 22 Apr 2020
https://doi.org/10.12688/f1000research.17927.4
Software Tool Article metrics
Revised
Biobtree: A tool to search and map bioinformatics identifiers and special keywords
[version 4; peer review: 2 approved]
Tamer Gur
Peer Reviewers Maxim N. Shokhirev; Samuel Lampa
LATEST VERSION PUBLISHED 20 Jan 2020
1-20 of 53 ARTICLES
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