All Stories

  1. Bio-Aurac – an open-source browser plugin to better navigate literature content

    Article • September 2022, Cold Spring Harbor Laboratory Press

    Mr Rafael C Jimenez

  2. Ten simple rules to run a successful BioHackathon

    Article • PLoS Computational Biology, May 2020, PLOS

    Mr Rafael C Jimenez

  3. Harnessing the Potential of Digital Technologies for the Early Detection of Neurodegenerative Diseases

    Article • October 2019, Center for Open Science

    Mr Rafael C Jimenez

  4. The bio.tools registry of software tools and data resources for the life sciences

    Article • August 2019, Springer Science + Business Media

    Mr Rafael C Jimenez, Matúš Kalaš

  5. Implementation and relevance of FAIR data principles in biopharmaceutical R&D

    Article • Drug Discovery Today, April 2019, Elsevier

    Mr Rafael C Jimenez

  6. FAIRsharing as a community approach to standards, repositories and policies

    Article • Nature Biotechnology, April 2019, Springer Science + Business Media

    Mr Rafael C Jimenez

  7. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, March 2019, Faculty of 1000, Ltd.

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  8. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez, Björn Grüning, Susheel Varma, Pablo Moreno, Dr. Yasset Perez-Riverol

  9. Uniform resolution of compact identifiers for biomedical data

    Article • Scientific Data, May 2018, Springer Science + Business Media

    Mr Rafael C Jimenez

  10. The future of metabolomics in ELIXIR

    Article • F1000Research, October 2017, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez

  11. Metabolomics, ELIXIR Platforms and Use Cases

    Article • F1000Research, September 2017, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez, Martin Reczko, Ola Spjuth, Philippe Rocca-Serra, Kairi Koort, Nicholas Moschonas, Maria Klapa, Alejandra Gonzalez-Beltran

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

    Article • July 2017, PeerJ

    Ms Haydee H Artaza, Dr John M Hancock, Mr Rafael C Jimenez

  13. General guidelines for biomedical software development

    Article • F1000Research, July 2017, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez, Dr Niklas U Blomberg

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

    Article • PLoS Biology, June 2017, PLOS

    Mr Rafael C Jimenez, Dr Niklas U Blomberg

  15. Four simple recommendations to encourage best practices in research software

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Dr Monther Alhamdoosh, Mr Rafael C Jimenez, Mr Neil P Chue Hong, Professor Josep Ll. Gelpi, Prof Carole A Goble, Rob Hooft, Daniel S Katz, Mr Federico López Gómez, Dr Sonika Tyagi, Sonika Tyagi, Mateusz Kuzak, Allegra Via, Xiaochuan (Harry) Wang, Montserrat Gonzalez, Björn Grüning, Andrew Treloar, Nathan Watson-Haigh, Dr. Yasset Perez-Riverol

  16. A community proposal to integrate proteomics activities in ELIXIR

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Dr Magnus Palmblad, Mr Rafael C Jimenez, DR Juan Antonio Vizcaino, Peter Horvatovich, Lennart Martens, Albert Heck

  17. Discovering and linking public omics data sets using the Omics Discovery Index

    Article • Nature Biotechnology, May 2017, Nature

    DR Juan Antonio Vizcaino, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  18. BioCIDER: a Contextualisation InDEx for biological Resources discovery

    Article • Bioinformatics, April 2017, Oxford University Press (OUP)

    Dr John M Hancock, Mr Rafael C Jimenez

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

    Article • Bioinformatics, March 2017, Oxford University Press (OUP)

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  20. General guidelines for biomedical software development

    Article • F1000Research, March 2017, Faculty of 1000, Ltd.

    Dr Niklas U Blomberg, José Luis Oliveira, Luís António Bastião Silva, Mr Rafael C Jimenez

  21. A global perspective on bioinformatics training needs

    Article • February 2017, Cold Spring Harbor Laboratory Press

    Catherine Brooksbank, Mr Rafael C Jimenez

  22. Uniform Resolution of Compact Identifiers for Biomedical Data

    Article • January 2017, Cold Spring Harbor Laboratory Press

    Mr Rafael C Jimenez

  23. How to measure whether software is produced "professionally"

    Article • F1000Research, August 2016, Faculty of 1000, Ltd.

    Ms Haydee H Artaza, Mr Neil P Chue Hong, Rob Hooft, Brett G Olivier, Mr Rafael C Jimenez

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

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Mr Rafael C Jimenez, Björn Grüning, Dr Tunca Dogan, Matúš Kalaš

  25. Data integration in biological research: an overview

    Article • Journal of Biological Research-Thessaloniki, September 2015, Springer Science + Business Media

    Mr Rafael C Jimenez

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

    Article • Frontiers in Genetics, June 2015, Frontiers

    Dr Fotis E. Psomopoulos, Mr Rafael C Jimenez, Dr. Alexandre M.J.J. Bonvin

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

    Article • Database, February 2015, Oxford University Press (OUP)

    Mr Rafael C Jimenez

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

    Article • Bioinformatics, September 2014, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  29. Sequence, a BioJS component for visualising sequences

    Article • F1000Research, February 2014, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez

  30. KEGGViewer, a BioJS component to visualize KEGG Pathways

    Article • F1000Research, February 2014, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez

  31. PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers

    Article • F1000Research, February 2014, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez

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

    Article • F1000Research, February 2014, Faculty of 1000, Ltd.

    alex garcia, Staff Scientist Suzanna E Lewis, Dr William Spooner, Mr Rafael C Jimenez

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

    Article • Nucleic Acids Research, November 2013, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  34. Best practices in bioinformatics training for life scientists

    Article • Briefings in Bioinformatics, June 2013, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  35. iAnn: an event sharing platform for the life sciences

    Article • Bioinformatics, June 2013, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  36. A new reference implementation of the PSICQUIC web service

    Article • Nucleic Acids Research, May 2013, Oxford University Press (OUP)

    Mr Rafael C Jimenez

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

    Article • Bioinformatics, February 2013, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  38. Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories

    Article • January 2013, Springer Science + Business Media

    DR Juan Antonio Vizcaino, Mr Rafael C Jimenez

  39. Bioinformatics Workflows and Web Services in Systems Biology Made Easy for Experimentalists

    Article • January 2013, Springer Science + Business Media

    Mr Rafael C Jimenez

  40. Teaching the Fundamentals of Biological Data Integration Using Classroom Games

    Article • PLoS Computational Biology, December 2012, PLOS

    Mr Rafael C Jimenez

  41. MyDas, an Extensible Java DAS Server

    Article • PLoS ONE, September 2012, PLOS

    Mr Rafael C Jimenez

  42. Low budget analysis of Direct-To-Consumer genomic testing familial data

    Article • F1000Research, July 2012, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez

  43. The IntAct molecular interaction database in 2012

    Article • Nucleic Acids Research, November 2011, Oxford University Press (OUP)

    Mr Rafael C Jimenez

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

    Article • Briefings in Bioinformatics, November 2011, Oxford University Press (OUP)

    Mr Rafael C Jimenez, Catherine Brooksbank

  45. myKaryoView: A Light-Weight Client for Visualization of Genomic Data

    Article • PLoS ONE, October 2011, PLOS

    Mr Rafael C Jimenez

  46. Dasty3, a WEB Framework for DAS

    Article • Bioinformatics, July 2011, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  47. PSICQUIC and PSISCORE: accessing and scoring molecular interactions

    Article • Nature Methods, June 2011, Springer Science + Business Media

    Sylvie RICARD-BLUM, Professor Gary D Bader, Mr Rafael C Jimenez

  48. DAS Writeback: A Collaborative Annotation System

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    Mr Rafael C Jimenez

  49. easyDAS: Automatic creation of DAS servers

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    Mr Rafael C Jimenez

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

    Article • Bioinformatics, October 2008, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  51. Dasty2, an Ajax protein DAS client

    Article • Bioinformatics, August 2008, Oxford University Press (OUP)

    Mr Rafael C Jimenez

  52. Integrating biological data – the Distributed Annotation System

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Mr Rafael C Jimenez

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

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Mr Rafael C Jimenez