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Ten Simple Rules for Taking Advantage of Git and GitHub.
Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA. Perez-Riverol Y, et al. Among authors: katz ds. PLoS Comput Biol. 2016 Jul 14;12(7):e1004947. doi: 10.1371/journal.pcbi.1004947. eCollection 2016 Jul. PLoS Comput Biol. 2016. PMID: 27415786 Free PMC article. No abstract available.
FAIR-USE4OS: Guidelines for creating impactful open-source software.
Sonabend R, Gruson H, Wolansky L, Kiragga A, Katz DS. Sonabend R, et al. Among authors: katz ds. PLoS Comput Biol. 2024 May 9;20(5):e1012045. doi: 10.1371/journal.pcbi.1012045. eCollection 2024 May. PLoS Comput Biol. 2024. PMID: 38722873 Free PMC article.
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. Among authors: katz ds. F1000Res. 2017 Jun 13;6:ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017. F1000Res. 2017. PMID: 28751965 Free PMC article.
Managing genomic variant calling workflows with Swift/T.
Ahmed AE, Heldenbrand J, Asmann Y, Fadlelmola FM, Katz DS, Kendig K, Kendzior MC, Li T, Ren Y, Rodriguez E, Weber MR, Wozniak JM, Zermeno J, Mainzer LS. Ahmed AE, et al. Among authors: katz ds. PLoS One. 2019 Jul 9;14(7):e0211608. doi: 10.1371/journal.pone.0211608. eCollection 2019. PLoS One. 2019. PMID: 31287816 Free PMC article.
Journal of Open Source Software (JOSS): design and first-year review.
Smith AM, Niemeyer KE, Katz DS, Barba LA, Githinji G, Gymrek M, Huff KD, Madan CR, Mayes AC, Moerman KM, Prins P, Ram K, Rokem A, Teal TK, Guimera RV, Vanderplas JT. Smith AM, et al. Among authors: katz ds. PeerJ Prepr. 2018;4:e147. doi: 10.7717/peerj-cs.147. Epub 2018 Feb 12. PeerJ Prepr. 2018. PMID: 32704456 Free PMC article.
A multi-disciplinary perspective on emergent and future innovations in peer review.
Tennant JP, Dugan JM, Graziotin D, Jacques DC, Waldner F, Mietchen D, Elkhatib Y, B Collister L, Pikas CK, Crick T, Masuzzo P, Caravaggi A, Berg DR, Niemeyer KE, Ross-Hellauer T, Mannheimer S, Rigling L, Katz DS, Greshake Tzovaras B, Pacheco-Mendoza J, Fatima N, Poblet M, Isaakidis M, Irawan DE, Renaut S, Madan CR, Matthias L, Nørgaard Kjær J, O'Donnell DP, Neylon C, Kearns S, Selvaraju M, Colomb J. Tennant JP, et al. Among authors: katz ds. F1000Res. 2017 Jul 20;6:1151. doi: 10.12688/f1000research.12037.3. eCollection 2017. F1000Res. 2017. PMID: 29188015 Free PMC article. Review.
FAIR for AI: An interdisciplinary and international community building perspective.
Huerta EA, Blaiszik B, Brinson LC, Bouchard KE, Diaz D, Doglioni C, Duarte JM, Emani M, Foster I, Fox G, Harris P, Heinrich L, Jha S, Katz DS, Kindratenko V, Kirkpatrick CR, Lassila-Perini K, Madduri RK, Neubauer MS, Psomopoulos FE, Roy A, Rübel O, Zhao Z, Zhu R. Huerta EA, et al. Among authors: katz ds. Sci Data. 2023 Jul 26;10(1):487. doi: 10.1038/s41597-023-02298-6. Sci Data. 2023. PMID: 37495591 Free PMC article.
331 results