Rafael C. Jiménez

According to our database, Rafael C. Jiménez authored at least 34 papers between 2008 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2021

Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era.

Maria Victoria Schneider, Rafael C. Jiménez

Briefings Bioinform., 2021

2020

Ten simple rules to run a successful BioHackathon.

Leyla J. García, Erick Antezana, Alexander García Castro, Evan Bolton, Rafael C. Jiménez, Pjotr Prins, Juan M. Banda, Toshiaki Katayama

PLoS Comput. Biol., 2020

2019

Community Organizations: Changing the Culture in Which Research Software Is Developed and Sustained.

Daniel S. Katz, Lois Curfman McInnes, David E. Bernholdt, Abigail Cabunoc Mayes, Neil P. Chue Hong, Jonah Duckles, Sandra Gesing, Michael A. Heroux, Simon Hettrick, Rafael C. Jiménez, Marlon E. Pierce, Belinda Weaver, Nancy Wilkins-Diehr

Comput. Sci. Eng., 2019

2018

Recommendations for the packaging and containerizing of bioinformatics software.

Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol

F1000Research, 2018

Lesson Development for Open Source Software Best Practices Adoption.

Mateusz Kuzak, Jen Harrow, Rafael C. Jiménez, Paula Andrea Martínez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via

Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017

PIsCO: A Performance indicators framework for collection of bioinformatics resource metrics.

Haydee Artaza, John M. Hancock, Rafael C. Jiménez, Manuel Corpas

PeerJ Prepr., 2017

General guidelines for biomedical software development.

Luís Bastião Silva, Rafael C. Jiménez, Niklas Blomberg, José Luís Oliveira

F1000Research, 2017

The future of metabolomics in ELIXIR.

Merlijn N. van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra N. González-Beltrán, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-García, Rafael C. Jiménez, 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 P. 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

F1000Research, 2017

Four simple recommendations to encourage best practices in research software.

Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutiérrez, Neil P. Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla J. García, Josep Lluis Gelpí, Simon L. Gladman, Carole A. Goble, Montserrat González Ferreiro, Alejandra N. González-Beltrán, Philippa C. Griffin, Björn A. Grüning, Jonas Hagberg, Petr Holub, Rob W. W. Hooft, Jon C. Ison, Daniel S. Katz, Brane Leskosek, Federico López-Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola J. Mulder, Yasset Pérez-Riverol, Robert Pergl, Horst Pichler, Bernard J. Pope, Ferran Sanz, Maria Victoria Schneider, Victoria Stodden, Radoslaw Suchecki, Radka Svobodová Vareková, Harry-Anton Talvik, Ilian T. Todorov, Andrew E. Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch

F1000Research, 2017

BioContainers: an open-source and community-driven framework for software standardization.

Felipe da Veiga Leprevost, Björn A. Grüning, Saulo Aflitos, Hannes L. Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo A. Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C. Jiménez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I. Nesvizhskii, Yasset Pérez-Riverol

Bioinform., 2017

BioCIDER: a Contextualisation InDEx for biological Resources discovery.

Carlos Horro, Martin Cook, Teresa K. Attwood, Michelle D. Brazas, John M. Hancock, Patricia M. Palagi, Manuel Corpas, Rafael C. Jiménez

Bioinform., 2017

Bioschemas: From Potato Salad to Protein Annotation.

Alasdair J. G. Gray, Carole A. Goble, Rafael C. Jiménez

Proceedings of the ISWC 2017 Posters & Demonstrations and Industry Tracks co-located with 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 23rd - to, 2017

2016

Tools and data services registry: a community effort to document bioinformatics resources.

Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak

Nucleic Acids Res., 2016

Top 10 metrics for life science software good practices.

Haydee Artaza, Neil P. Chue Hong, Manuel Corpas, Angel Corpuz, Rob W. W. Hooft, Rafael C. Jiménez, Brane Leskosek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vareková, Thomas Van Parys, Daniel Vaughan

F1000Research, 2016

2015

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

Manuel Corpas, Rafael C. Jiménez, Erik Bongcam-Rudloff, Aidan Budd, Michelle D. Brazas, Pedro L. Fernandes, Bruno A. Gaëta, Celia W. G. van Gelder, Eija Korpelainen, Fran Lewitter, Annette McGrath, Daniel MacLean, Patricia M. Palagi, Kristian Rother, Jan Taylor, Allegra Via, Mick Watson, Maria Victoria Schneider, Teresa K. Attwood

Bioinform., 2015

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Jose M. Villaveces, Rafael C. Jiménez, Pablo Porras, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Sandra E. Orchard, H. Choi, Peipei Ping, N. C. Zong, Manor Askenazi, Bianca Habermann, Henning Hermjakob

Database J. Biol. Databases Curation, 2015

2014

The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases.

Sandra E. Orchard, Mais G. Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro, Margaret J. Duesbury, Marine Dumousseau, Eugenia Galeota, Ursula Hinz, Marta Iannuccelli, Sruthi Jagannathan, Rafael C. Jiménez, Jyoti Khadake, Astrid Lægreid, Luana Licata, Ruth C. Lovering, Birgit Meldal, Anna N. Melidoni, Mila Milagros, Daniele Peluso, Livia Perfetto, Pablo Porras, Arathi Raghunath, Sylvie Ricard-Blum, Bernd Roechert, Andre Stutz, Michael Tognolli, Kim Van Roey, Gianni Cesareni, Henning Hermjakob

Nucleic Acids Res., 2014

<i>wigExplorer</i>, a BioJS component to visualise wig data.

Anil S. Thanki, Rafael C. Jiménez, Gemy G. Kaithakottil, Manuel Corpas, Robert P. Davey

F1000Research, 2014

<i>Sequence</i>, a BioJS component for visualising sequences.

John Gómez, Rafael C. Jiménez

F1000Research, 2014

BioJS: an open source standard for biological visualisation - its status in 2014.

Manuel Corpas, Rafael C. Jiménez, Seth Carbon, Alexander García Castro, Leyla Jael Castro, Tatyana Goldberg, John Gómez, Alex Kalderimis, Suzanna E. Lewis, Ian Mulvany, Aleksandra Pawlik, Francis Rowland, Gustavo A. Salazar, Fabian Schreiber, Ian Sillitoe, William Spooner, Anil S. Thanki, Jose M. Villaveces, Guy Yachdav, Henning Hermjakob

F1000Research, 2014

2013

A new reference implementation of the PSICQUIC web service.

Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Rafael C. Jiménez, Eugenia Galeota, Guillaume Launay, Johannes Goll, Karin Breuer, Keiichiro Ono, Lukasz Salwínski, Henning Hermjakob

Nucleic Acids Res., 2013

iAnn: an event sharing platform for the life sciences.

Rafael C. Jiménez, Juan P. Albar, Jong Bhak, Marie-Claude Blatter, Thomas Blicher, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Marc A. van Driel, Michael J. Dunn, Pedro L. Fernandes, Celia W. G. van Gelder, Henning Hermjakob, Vassilios Ioannidis, David Phillip Judge, Pascal Kahlem, Eija Korpelainen, Hans-Joachim Kraus, Jane E. Loveland, Christine Mayer, Jennifer McDowall, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Gustavo A. Salazar, Reinhard Schneider, Allegra Via, Jose M. Villaveces, Ping Yu, Maria Victoria Schneider, Teresa K. Attwood, Manuel Corpas

Bioinform., 2013

BioJS: an open source JavaScript framework for biological data visualization.

John Gómez, Leyla J. García, Gustavo A. Salazar, Jose M. Villaveces, Swanand P. Gore, Alexander García Castro, Maria Jesus Martin, Guillaume Launay, Rafael Alcántara, Noemi del-Toro, Marine Dumousseau, Sandra E. Orchard, Sameer Velankar, Henning Hermjakob, Chenggong Zong, Peipei Ping, Manuel Corpas, Rafael C. Jiménez

Bioinform., 2013

Best practices in bioinformatics training for life scientists.

Allegra Via, Thomas Blicher, Erik Bongcam-Rudloff, Michelle D. Brazas, Catherine Brooksbank, Aidan Budd, Javier De Las Rivas, Jacqueline Dreyer, Pedro L. Fernandes, Celia W. G. van Gelder, Joachim Jacob, Rafael C. Jiménez, Jane E. Loveland, Federico Morán, Nicola J. Mulder, Tommi H. Nyrönen, Kristian Rother, Maria Victoria Schneider, Teresa K. Attwood

Briefings Bioinform., 2013

2012

Teaching the Fundamentals of Biological Data Integration Using Classroom Games.

Maria Victoria Schneider, Rafael C. Jiménez

PLoS Comput. Biol., 2012

The IntAct molecular interaction database in 2012.

Samuel Kerrien, Bruno Aranda, Lionel Breuza, Alan J. Bridge, Fiona Broackes-Carter, Carol Chen, Margaret J. Duesbury, Marine Dumousseau, Marc Feuermann, Ursula Hinz, Christine Jandrasits, Rafael C. Jiménez, Jyoti Khadake, Usha Mahadevan, Patrick Masson, Ivo Pedruzzi, Eric Pfeiffenberger, Pablo Porras, Arathi Raghunath, Bernd Roechert, Sandra E. Orchard, Henning Hermjakob

Nucleic Acids Res., 2012

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

Maria Victoria Schneider, Peter Walter, Marie-Claude Blatter, James Watson, Michelle D. Brazas, Kristian Rother, Aidan Budd, Allegra Via, Celia W. G. van Gelder, Joachim Jacob, Pedro L. Fernandes, Tommi H. Nyrönen, Javier De Las Rivas, Thomas Blicher, Rafael C. Jiménez, Jane E. Loveland, Jennifer McDowall, Philip Jones, Brendan W. Vaughan, Rodrigo Lopez, Teresa K. Attwood, Catherine Brooksbank

Briefings Bioinform., 2012

2011

DAS Writeback: A Collaborative Annotation System.

Gustavo A. Salazar, Rafael C. Jiménez, Alexander García Castro, Henning Hermjakob, Nicola J. Mulder, Edwin H. Blake

BMC Bioinform., 2011

easyDAS: Automatic creation of DAS servers.

Bernat Gel, Andrew M. Jenkinson, Rafael C. Jiménez, Xavier Messeguer Peypoch, Henning Hermjakob

BMC Bioinform., 2011

Dasty3, a WEB framework for DAS.

Jose M. Villaveces, Rafael C. Jiménez, Leyla J. García, Gustavo A. Salazar, Bernat Gel, Nicola J. Mulder, Maria Jesus Martin, Alexander García Castro, Henning Hermjakob

Bioinform., 2011

2008

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.

Kieran O'Neill, Alexander García Castro, Anita Schwegmann, Rafael C. Jiménez, Dan Jacobson, Henning Hermjakob

BMC Bioinform., 2008

Integrating biological data - the Distributed Annotation System.

Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas A. Down, Robert D. Finn, Henning Hermjakob, Tim J. P. Hubbard, Rafael C. Jiménez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R. Macías, Gabrielle A. Reeves, Andreas Prlic

BMC Bioinform., 2008

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra E. Orchard, Rafael C. Jiménez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, Janet M. Thornton

Bioinform., 2008

Dasty2, an Ajax protein DAS client.

Rafael C. Jiménez, Antony F. Quinn, Alexander García Castro, Alberto Labarga, Kieran O'Neill, Fernando Martinez, Gustavo A. Salazar, Henning Hermjakob

Bioinform., 2008