Teaching the fundamentals of biological data integration using classroom games.

by Maria Victoria Schneider, Rafael C Jimenez
Published 2012-01-01

KEGGViewer, a BioJS component to visualize KEGG Pathways [v1; ref status: indexed, http://f1000r.es/2uq]

by Jose M. Villaveces, Rafael C. Jimenez, Bianca H. Habermann
Published 2014-02-01

PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers [v1; ref status: indexed, http://f1000r.es/2up]

by Jose M. Villaveces, Rafael C. Jimenez, Bianca H. Habermann
Published 2014-02-01

General guidelines for biomedical software development [version 2; referees: 2 approved]

by Luis Bastiao Silva, Rafael C. Jimenez, Niklas Blomberg, José Luis Oliveira
Published 2017-07-01

General guidelines for biomedical software development [version 1; referees: 2 approved]

by Luis Bastiao Silva, Rafael C. Jimenez, Niklas Blomberg, José Luis Oliveira
Published 2017-03-01

wigExplorer, a BioJS component to visualise wig data [version 3; referees: 1 approved, 2 approved with reservations, 1 not approved]

by Anil S. Thanki, Rafael C. Jimenez, Gemy G. Kaithakottil, Manuel Corpas, Robert P. Davey
Published 2016-08-01

myKaryoView: a light-weight client for visualization of genomic data.

by Rafael C Jimenez, Gustavo A Salazar, Bernat Gel, Joaquin Dopazo, Nicola Mulder, Manuel Corpas
Published 2011-01-01

MyDas, an extensible Java DAS server.

by Gustavo A Salazar, Leyla J García, Philip Jones, Rafael C Jimenez, Antony F Quinn, Andrew M Jenkinson, Nicola Mulder, Maria Martin, Sarah Hunter, Henning Hermjakob
Published 2012-01-01

Top 10 metrics for life science software good practices [version 1; referees: 2 approved]

by Haydee Artaza, Neil Chue Hong, Manuel Corpas, Angel Corpuz, Rob Hooft, Rafael C. Jimenez, Brane Leskošek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vařeková, Thomas Van Parys, Daniel Vaughan
Published 2016-08-01

Future opportunities and future trends for e-infrastructures and life sciences: going beyond grid to enable life science data analysis

by Fotis ePsomopoulos, Fotis ePsomopoulos, Afonso Miguel Duarte, Christophe eBlanchet, Alexandre M.J.J. Bonvin, Manuel eCorpas, Alain eFranc, Rafael C. Jimenez, Jesus eMarco de Lucas, Tommi eNyrönen, Gergely eSipos, Stephanie B. Suhr
Published 2015-06-01

Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations]

by 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
Published 2019-03-01

A community proposal to integrate proteomics activities in ELIXIR [version 1; referees: 2 approved]

by 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
Published 2017-06-01

The future of metabolomics in ELIXIR [version 1; referees: 2 approved, 1 approved with reservations]

by 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, 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
Published 2017-09-01

The future of metabolomics in ELIXIR [version 2; referees: 2 approved, 1 approved with reservations]

by 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
Published 2017-10-01

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

by Julie A McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C Ison, Rafael C Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L Snoep, Stian Soiland-Reyes, Natalie J Stanford, Neil Swainston, Nicole Washington, Alan R Williams, Sarala M Wimalaratne, Lilly M Winfree, Katherine Wolstencroft, Carole Goble, Christopher J Mungall, Melissa A Haendel, Helen Parkinson
Published 2017-06-01

Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]

by 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
Published 2017-06-01