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https://doi.org/10.12688/f1000research.20136.1
Opinion Article metrics
An intrinsically disordered proteins community for ELIXIR
[version 1; peer review: 2 approved]
Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas, John M. Hancock, Jen Harrow, Desmond Higgins, Cy M. Jeffries, Philippe Le Mercier, Balint Mészáros, Marco Necci, Cedric Notredame, Sandra Orchard, Christos A. Ouzounis, Rita Pancsa, Elena Papaleo, Roberta Pierattelli, Damiano Piovesan, Vasilis J. Promponas, Patrick Ruch, Gabriella Rustici, Pedro Romero, Sirarat Sarntivijai, Gary Saunders, Benjamin Schuler, Malvika Sharan, Denis C. Shields, Joel L. Sussman, Jonathan A. Tedds, Peter Tompa, Michael Turewicz, Jiri Vondrasek, Wim F. Vranken, Bonnie Ann Wallace, Kanin Wichapong, Silvio C. E. Tosatto
Peer Reviewers Iva Pritisanac and Julie Forman-Kay; Osman Ugur Sezerman
  • Funders
  • Vetenskapsrådet
  • BBSRC
  • European Molecular Biology Laboratory
  • Carlsberg Foundation Distinguished Fellowship
  • National Institutes of Health
  • Israel I-CORE Project
  • ELIXIR
  • Danmarks Grundforskningsfond
  • Instruct-ERIC
  • Swiss Federal Government
  • Marie Skłodowska-Curie
  • COST Action BM1405 NGP-net
  • Wellcome Trust
PUBLISHED 15 Oct 2019
https://doi.org/10.12688/f1000research.19427.1
Research Article metrics
Understanding life sciences data curation practices via user research
[version 1; peer review: 1 approved, 1 approved with reservations]
Aravind Venkatesan, Nikiforos Karamanis, Michele Ide-Smith, Jonathan Hickford, Johanna McEntyre
Peer Reviewers Lynette Hirschman; Cecilia N. Arighi
  • Funder
  • European Commission
PUBLISHED 11 Sep 2019
https://doi.org/10.12688/f1000research.20408.1
Editorial metrics NOT PEER REVIEWED
Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers
[version 1; peer review: not peer reviewed]
Sayane Shome, R. Gonzalo Parra, Nazeefa Fatima, Alexander Miguel Monzon, Bart Cuypers, Yumna Moosa, Nilson Da Rocha Coimbra, Juliana Assis, Carla Giner-Delgado, Handan Melike Dönertaş, Yesid Cuesta-Astroz, Geetha Saarunya, Imane Allali, Shruti Gupta, Ambuj Srivastava, Manisha Kalsan, Catalina Valdivia, Gabriel J. Olguin-Orellana, Sofia Papadimitriou, Daniele Parisi, Nikolaj Pagh Kristensen, Leonor Rib, Marouen Ben Guebila, Eugen Bauer, Gaia Zaffaroni, Amel Bekkar, Efejiro Ashano, Lisanna Paladin, Marco Necci, Nicolás N. Moreyra, Martin Rydén, Jordan Villalobos-Solís, Nikolaos Papadopoulos, Candice Rafael, Tülay Karakulak, Yasin Kaya, Yvonne Gladbach, Sandeep Kumar Dhanda, Nikolina Šoštarić, Aishwarya Alex, Dan DeBlasio, Farzana Rahman
  • Funder
  • International Society for Computational Biology
PUBLISHED 02 Sep 2019
https://doi.org/10.12688/f1000research.15140.2
Opinion Article metrics
Revised
Recommendations for the packaging and containerizing of bioinformatics software
[version 2; peer review: 2 approved, 1 approved with reservations]
Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol
Peer Reviewers Ka Yee Yeung and Daniel Kristiyanto; Monther Alhamdoosh; Evan Floden
  • Funders
  • Horizon 2020
  • National Institutes of Health
LATEST VERSION PUBLISHED 20 Mar 2019
https://doi.org/10.12688/f1000research.17315.1
Method Article metrics
Rapid identification of novel protein families using similarity searches
[version 1; peer review: 2 approved]
Matt Jeffryes, Alex Bateman
Peer Reviewers Daniel J. Rigden; Desmond G Higgins
  • Funder
  • European Molecular Biology Laboratory
PUBLISHED 24 Dec 2018
https://doi.org/10.12688/f1000research.14509.2
Opinion Article metrics
Revised
The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
[version 2; peer review: 2 approved]
Alexandre Angers-Loustau, Mauro Petrillo, Johan Bengtsson-Palme, Thomas Berendonk, Burton Blais, Kok-Gan Chan, Teresa M. Coque, Paul Hammer, Stefanie Heß, Dafni M. Kagkli, Carsten Krumbiegel, Val F. Lanza, Jean-Yves Madec, Thierry Naas, Justin O'Grady, Valentina Paracchini, John W.A. Rossen, Etienne Ruppé, Jessica Vamathevan, Vittorio Venturi, Guy Van den Eede
Peer Reviewers Enrico Lavezzo and Giorgio Palù; Jason C. Kwong
  • Funder
  • European Commission
LATEST VERSION PUBLISHED 07 Dec 2018
https://doi.org/10.12688/f1000research.12344.2
Opinion Article metrics
Revised
Best practice data life cycle approaches for the life sciences
[version 2; peer review: 2 approved]
Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi, Jeffrey H. Christiansen, Saravanan Dayalan, Simon Gladman, Sandra B. Hangartner, Helen L. Hayden, William W.H. Ho, Gabriel Keeble-Gagnère, Pasi K. Korhonen, Peter Neish, Priscilla R. Prestes, Mark F. Richardson, Nathan S. Watson-Haigh, Kelly L. Wyres, Neil D. Young, Maria Victoria Schneider
Peer Reviewers Johannes Starlinger; Sven Nahnsen
  • Funders
  • Bioplatforms Australia
  • University of Melbourne
LATEST VERSION PUBLISHED 04 Jun 2018
https://doi.org/10.12688/f1000research.14399.1
Software Tool Article metrics
Authoring Bioconductor workflows with BiocWorkflowTools
[version 1; peer review: 2 approved with reservations]
Mike L. Smith, Andrzej K. Oleś, Wolfgang Huber
Peer Reviewers Justin Kitzes; Laurent Gatto
  • Funders
  • Bundesministerium für Bildung und Forschung
  • Horizon 2020
  • German Network for Bioinformatics Infrastructure
PUBLISHED 06 Apr 2018
https://doi.org/10.12688/f1000research.14050.1
Method Article metrics
Gene Unprediction with Spurio: A tool to identify spurious protein sequences
[version 1; peer review: 2 approved]
Wolfram Höps, Matt Jeffryes, Alex Bateman
Peer Reviewers Arne Elofsson; Daniel H. Haft
  • Funder
  • European Molecular Biology Laboratory
PUBLISHED 02 Mar 2018
https://doi.org/10.12688/f1000research.13482.1
Research Note metrics
Improving communication for interdisciplinary teams working on storage of digital information in DNA
[version 1; peer review: 2 approved]
Emily E. Hesketh, Jossy Sayir, Nick Goldman
Peer Reviewers Robert Grass; Jeffrey R. Sampson
  • Funders
  • European Molecular Biology Laboratory
  • European Bioinformatics Institute
  • Biotechnology and Biological Sciences Research Council
PUBLISHED 10 Jan 2018
https://doi.org/10.12688/f1000research.12342.2
Opinion Article metrics
Revised
The future of metabolomics in ELIXIR
[version 2; peer review: 3 approved]
Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-Garcia, Rafael C. Jimenez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Pablo Moreno, Nicholas K. Moschonas, Steffen Neumann, Claire O’Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph Steinbeck
Peer Reviewers Charles F. Burant; Carl Brunius; Emmanuel Mikros
  • Funder
  • Horizon 2020 Framework Programme
LATEST VERSION PUBLISHED 30 Oct 2017
https://doi.org/10.12688/f1000research.12168.1
Method Article metrics
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data
[version 1; peer review: 2 approved]
Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino Da Silva Santos, Jeroen Belien, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond Fijneman, J. Dylan Spalding, Sanne Abeln
Peer Reviewers Hervé Ménager; Gilbert S. Omenn
  • Funders
  • CTMM-TraIT
  • Horizon 2020
PUBLISHED 16 Aug 2017
https://doi.org/10.12688/f1000research.11407.1
Opinion Article metrics
Four simple recommendations to encourage best practices in research software
[version 1; peer review: 3 approved]
Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch
Peer Reviewers Roberto Di Cosmo; Gregory V. Wilson; Stefanie Betz
  • Funders
  • ELIXIR-EXCELERATE
  • EMBL-ABR
  • Netherlands eScience Center
  • CORBEL
  • Software Sustainability Institute
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.11751.1
Opinion Article metrics
A community proposal to integrate proteomics activities in ELIXIR
[version 1; peer review: 2 approved]
Juan Antonio Vizcaíno, Mathias Walzer, Rafael C. Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J.R. Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane, Kris Laukens, Fredrik Levander, Frederique Lisacek, Petr Novak, Magnus Palmblad, Damiano Piovesan, Alfred Pühler, Veit Schwämmle, Dirk Valkenborg, Merlijn van Rijswijk, Jiri Vondrasek, Martin Eisenacher, Lennart Martens, Oliver Kohlbacher
Peer Reviewers Felix Elortza; Chuming Chen
  • Funder
  • Horizon 2020
PUBLISHED 13 Jun 2017
https://doi.org/10.12688/f1000research.9656.2
Method Article metrics
Revised
Identifying ELIXIR Core Data Resources
[version 2; peer review: 2 approved]
Christine Durinx, Jo McEntyre, Ron Appel, Rolf Apweiler, Mary Barlow, Niklas Blomberg, Chuck Cook, Elisabeth Gasteiger, Jee-Hyub Kim, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Alfonso Valencia
Peer Reviewers Helen M. Berman; Maryann E. Martone
LATEST VERSION PUBLISHED 09 Mar 2017
https://doi.org/10.12688/f1000research.10443.1
Method Article metrics
ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services
[version 1; peer review: 1 approved, 2 approved with reservations]
Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen
Peer Reviewers Marla I. Trindade and Leonardo van Zyl; Takashi Gojobori; Anders Blomberg
  • Funders
  • ELIXIR
  • EMBL-EBI
  • Universitetet i Tromsø
PUBLISHED 23 Jan 2017
https://doi.org/10.12688/f1000research.10221.1
Software Tool Article metrics
Integration of EGA secure data access into Galaxy
[version 1; peer review: 2 approved]
Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, Dylan Spalding, Sanne Abeln
Peer Reviewers Hervé Ménager; Anton Nekrutenko
  • Funders
  • ELIXIR
  • ELIXIR-EXCELERATE
  • CTMM-TraIT
  • European Molecular Biology Laboratory
PUBLISHED 12 Dec 2016
https://doi.org/10.12688/f1000research.9501.2
Software Tool Article metrics
Revised
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
[version 2; peer review: 3 approved, 2 approved with reservations]
Aaron T.L. Lun, Davis J. McCarthy, John C. Marioni
Peer Reviewers Diana H.P. Low; Hongkai Ji; Andrew McDavid; David duVerle; Antonio Rausell
LATEST VERSION PUBLISHED 31 Oct 2016
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 Pedro L. Fernandes; Bruno Gaëta
PUBLISHED 16 Aug 2016
https://doi.org/10.12688/f1000research.3-53.v3
Software Tool Article metrics
Revised
wigExplorer, a BioJS component to visualise wig data
[version 3; peer review: 1 approved, 2 approved with reservations, 1 not approved]
Anil S. Thanki, Rafael C. Jimenez, Gemy G. Kaithakottil, Manuel Corpas, Robert P. Davey
Peer Reviewers Robert Buels; Phil Lord; Stefan Thomas Lang; Chunlei Wu and Jiwen Xin
LATEST VERSION PUBLISHED 09 Aug 2016
21-40 of 53 ARTICLES
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