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Literature DB >> 28407023

Ten simple rules for making research software more robust.

Abstract

Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer's computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.

Entities: Disease Gene Species

Mesh：

Year: 2017 PMID： 28407023 PMCID： PMC5390961 DOI： 10.1371/journal.pcbi.1005412

Source DB: PubMed Journal: PLoS Comput Biol ISSN： 1553-734X Impact factor: 4.475

16 in total

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Authors: Pjotr Prins; Joep de Ligt; Artem Tarasov; Ritsert C Jansen; Edwin Cuppen; Philip E Bourne
Journal: Nat Biotechnol Date: 2015-07 Impact factor: 54.908

Review 2. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.

Authors: Anton Nekrutenko; James Taylor
Journal: Nat Rev Genet Date: 2012-09 Impact factor: 53.242

3. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Authors: Mihaela Pertea; Daehwan Kim; Geo M Pertea; Jeffrey T Leek; Steven L Salzberg
Journal: Nat Protoc Date: 2016-08-11 Impact factor: 13.491

4. A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

Authors: Michelle D Brazas; David Yim; Winston Yeung; B F Francis Ouellette
Journal: Nucleic Acids Res Date: 2012-06-14 Impact factor: 16.971

5. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

Authors: Teresa K Attwood; Teresa K Atwood; Erik Bongcam-Rudloff; Michelle E Brazas; Manuel Corpas; Pascale Gaudet; Fran Lewitter; Nicola Mulder; Patricia M Palagi; Maria Victoria Schneider; Celia W G van Gelder
Journal: PLoS Comput Biol Date: 2015-04-09 Impact factor: 4.475

6. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

Authors: Brendan Lawlor; Paul Walsh
Journal: Bioengineered Date: 2015-05-21 Impact factor: 3.269

7. Ten recommendations for creating usable bioinformatics command line software.

Authors: Torsten Seemann
Journal: Gigascience Date: 2013-11-13 Impact factor: 6.524

8. Best practices for scientific computing.

Authors: Greg Wilson; D A Aruliah; C Titus Brown; Neil P Chue Hong; Matt Davis; Richard T Guy; Steven H D Haddock; Kathryn D Huff; Ian M Mitchell; Mark D Plumbley; Ben Waugh; Ethan P White; Paul Wilson
Journal: PLoS Biol Date: 2014-01-07 Impact factor: 8.029

9. A Quick Introduction to Version Control with Git and GitHub.

Authors: John D Blischak; Emily R Davenport; Greg Wilson
Journal: PLoS Comput Biol Date: 2016-01-19 Impact factor: 4.475

10. A quick guide to organizing computational biology projects.

Authors: William Stafford Noble
Journal: PLoS Comput Biol Date: 2009-07-31 Impact factor: 4.475

29 in total

1. Software engineering for scientific big data analysis.

Authors: Björn A Grüning; Samuel Lampa; Marc Vaudel; Daniel Blankenberg
Journal: Gigascience Date: 2019-05-01 Impact factor: 6.524

2. Digital twins for predictive oncology will be a paradigm shift for precision cancer care.

Authors: Tina Hernandez-Boussard; Paul Macklin; Emily J Greenspan; Amy L Gryshuk; Eric Stahlberg; Tanveer Syeda-Mahmood; Ilya Shmulevich
Journal: Nat Med Date: 2021-12 Impact factor: 87.241

3. Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.

Authors: Peter Georgeson; Anna Syme; Clare Sloggett; Jessica Chung; Harriet Dashnow; Michael Milton; Andrew Lonsdale; David Powell; Torsten Seemann; Bernard Pope
Journal: Gigascience Date: 2019-09-01 Impact factor: 6.524

4. Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites.

Authors: William Digan; Aurélie Névéol; Antoine Neuraz; Maxime Wack; David Baudoin; Anita Burgun; Bastien Rance
Journal: J Am Med Inform Assoc Date: 2021-03-01 Impact factor: 4.497

5. Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research.

Authors: Patrick D Schloss
Journal: mBio Date: 2018-06-05 Impact factor: 7.867