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BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. da Veiga Leprevost F, et al. Among authors: jimenez rc. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. Bioinformatics. 2017. PMID: 28379341 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.
Dasty3, a WEB framework for DAS.
Villaveces JM, Jimenez RC, Garcia LJ, Salazar GA, Gel B, Mulder N, Martin M, Garcia A, Hermjakob H. Villaveces JM, et al. Among authors: jimenez rc. Bioinformatics. 2011 Sep 15;27(18):2616-7. doi: 10.1093/bioinformatics/btr433. Epub 2011 Jul 28. Bioinformatics. 2011. PMID: 21798964 Free PMC article.
Discovering and linking public omics data sets using the Omics Discovery Index.
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Perez-Riverol Y, et al. Among authors: jimenez rc. Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. Nat Biotechnol. 2017. PMID: 28486464 Free PMC article. No abstract available.
BioJS: an open source JavaScript framework for biological data visualization.
Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC. Gómez J, et al. Among authors: jimenez rc. Bioinformatics. 2013 Apr 15;29(8):1103-4. doi: 10.1093/bioinformatics/btt100. Epub 2013 Feb 23. Bioinformatics. 2013. PMID: 23435069 Free PMC article.
Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H. Jimenez RC, et al. Bioinformatics. 2008 Sep 15;24(18):2119-21. doi: 10.1093/bioinformatics/btn387. Epub 2008 Aug 11. Bioinformatics. 2008. PMID: 18694895
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM. Reeves GA, et al. Among authors: jimenez rc. Bioinformatics. 2008 Dec 1;24(23):2767-72. doi: 10.1093/bioinformatics/btn528. Epub 2008 Oct 20. Bioinformatics. 2008. PMID: 18936051 Free PMC article.
iAnn: an event sharing platform for the life sciences.
Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M. Jimenez RC, et al. Bioinformatics. 2013 Aug 1;29(15):1919-21. doi: 10.1093/bioinformatics/btt306. Epub 2013 Jun 5. Bioinformatics. 2013. PMID: 23742982 Free PMC article.
Tools and data services registry: a community effort to document bioinformatics resources.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Ison J, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3. Nucleic Acids Res. 2016. PMID: 26538599 Free PMC article.
55 results