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Page 1
General guidelines for biomedical software development.
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J. Silva LB, et al. Among authors: jimenez rc. F1000Res. 2017 Mar 15;6:273. doi: 10.12688/f1000research.10750.2. eCollection 2017. F1000Res. 2017. PMID: 28443186 Free PMC article. Review.
Four simple recommendations to encourage best practices in research software.
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. Jiménez RC, et al. F1000Res. 2017 Jun 13;6:ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017. F1000Res. 2017. PMID: 28751965 Free PMC article.
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H. McMurry JA, et al. Among authors: jimenez rc. PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun. PLoS Biol. 2017. PMID: 28662064 Free PMC article.
Top 10 metrics for life science software good practices.
Artaza H, Chue Hong N, Corpas M, Corpuz A, Hooft R, Jimenez RC, Leskošek B, Olivier BG, Stourac J, Svobodová Vařeková R, Van Parys T, Vaughan D. Artaza H, et al. Among authors: jimenez rc. F1000Res. 2016 Aug 16;5:ELIXIR-2000. doi: 10.12688/f1000research.9206.1. eCollection 2016. F1000Res. 2016. PMID: 27635232 Free PMC article.
BioJS: an open source standard for biological visualisation - its status in 2014.
Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H. Corpas M, et al. F1000Res. 2014 Feb 13;3:55. doi: 10.12688/f1000research.3-55.v1. eCollection 2014. F1000Res. 2014. PMID: 25075290 Free PMC article.
Recommendations for the packaging and containerizing of bioinformatics software.
Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC; BioContainers Community; Perez-Riverol Y. Gruening B, et al. Among authors: jimenez rc. F1000Res. 2018 Jun 14;7:ISCB Comm J-742. doi: 10.12688/f1000research.15140.2. eCollection 2018. F1000Res. 2018. PMID: 31543945 Free PMC article.
KEGGViewer, a BioJS component to visualize KEGG Pathways.
Villaveces JM, Jimenez RC, Habermann BH. Villaveces JM, et al. Among authors: jimenez rc. F1000Res. 2014 Feb 13;3:43. doi: 10.12688/f1000research.3-43.v1. eCollection 2014. F1000Res. 2014. PMID: 24715980 Free PMC article.
A community proposal to integrate proteomics activities in ELIXIR.
Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O. Vizcaíno JA, et al. Among authors: jimenez rc. F1000Res. 2017 Jun 13;6:ELIXIR-875. doi: 10.12688/f1000research.11751.1. eCollection 2017. F1000Res. 2017. PMID: 28713550 Free PMC article.
54 results