Literature DB >> 26154002

Toward effective software solutions for big biology.

Pjotr Prins1, Joep de Ligt2, Artem Tarasov3, Ritsert C Jansen4, Edwin Cuppen5, Philip E Bourne6.   

Abstract

Mesh：

Year:  2015        PMID： 26154002     DOI： 10.1038/nbt.3240

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  5 in total

1.  Biology: The big challenges of big data.

Authors:  Vivien Marx
Journal:  Nature       Date:  2013-06-13       Impact factor: 49.962

2.  Big data, but are we ready?

Authors:  Oswaldo Trelles; Pjotr Prins; Marc Snir; Ritsert C Jansen
Journal:  Nat Rev Genet       Date:  2011-02-08       Impact factor: 53.242

3.  Toward effective sharing of high-dimensional immunology data.

Authors:  Berend Snijder; Richard Kumaran Kandasamy; Giulio Superti-Furga
Journal:  Nat Biotechnol       Date:  2014-08       Impact factor: 54.908

4.  Policy: NIH plans to enhance reproducibility.

Authors:  Francis S Collins; Lawrence A Tabak
Journal:  Nature       Date:  2014-01-30       Impact factor: 49.962

5.  Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Authors:  Steffen Möller; Enis Afgan; Michael Banck; Raoul J P Bonnal; Timothy Booth; John Chilton; Peter J A Cock; Markus Gumbel; Nomi Harris; Richard Holland; Matúš Kalaš; László Kaján; Eri Kibukawa; David R Powel; Pjotr Prins; Jacqueline Quinn; Olivier Sallou; Francesco Strozzi; Torsten Seemann; Clare Sloggett; Stian Soiland-Reyes; William Spooner; Sascha Steinbiss; Andreas Tille; Anthony J Travis; Roman Guimera; Toshiaki Katayama; Brad A Chapman
Journal:  BMC Bioinformatics       Date:  2014-11-27       Impact factor: 3.169
  5 in total
  15 in total

1.  Ten simple rules for making research software more robust.

Authors:  Morgan Taschuk; Greg Wilson
Journal:  PLoS Comput Biol       Date:  2017-04-13       Impact factor: 4.475

2.  BioShaDock: a community driven bioinformatics shared Docker-based tools registry.

Authors:  François Moreews; Olivier Sallou; Hervé Ménager; Yvan Le Bras; Cyril Monjeaud; Christophe Blanchet; Olivier Collin
Journal:  F1000Res       Date:  2015-12-14

3.  Highlights from the Era of Open Source Web-Based Tools.

Authors:  Kristin R Anderson; Julie A Harris; Lydia Ng; Pjotr Prins; Sara Memar; Bengt Ljungquist; Daniel Fürth; Robert W Williams; Giorgio A Ascoli; Dani Dumitriu
Journal:  J Neurosci       Date:  2021-01-20       Impact factor: 6.167

4.  Imagining the future of bioimage analysis.

Authors:  Erik Meijering; Anne E Carpenter; Hanchuan Peng; Fred A Hamprecht; Jean-Christophe Olivo-Marin
Journal:  Nat Biotechnol       Date:  2016-12-07       Impact factor: 54.908

5.  A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.

Authors:  Erik Garrison; Zev N Kronenberg; Eric T Dawson; Brent S Pedersen; Pjotr Prins
Journal:  PLoS Comput Biol       Date:  2022-05-31       Impact factor: 4.779

6.  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

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

Authors:  Yasset Perez-Riverol; Mingze Bai; Felipe da Veiga Leprevost; Silvano Squizzato; Young Mi Park; Kenneth Haug; Adam J Carroll; Dylan Spalding; Justin Paschall; Mingxun Wang; Noemi Del-Toro; Tobias Ternent; Peng Zhang; Nicola Buso; Nuno Bandeira; Eric W Deutsch; David S Campbell; Ronald C Beavis; Reza M Salek; Ugis Sarkans; Robert Petryszak; Maria Keays; Eoin Fahy; Manish Sud; Shankar Subramaniam; Ariana Barbera; Rafael C Jiménez; Alexey I Nesvizhskii; Susanna-Assunta Sansone; Christoph Steinbeck; Rodrigo Lopez; Juan A Vizcaíno; Peipei Ping; Henning Hermjakob
Journal:  Nat Biotechnol       Date:  2017-05-09       Impact factor: 54.908

8.  Collaborative analysis of multi-gigapixel imaging data using Cytomine.

Authors:  Raphaël Marée; Loïc Rollus; Benjamin Stévens; Renaud Hoyoux; Gilles Louppe; Rémy Vandaele; Jean-Michel Begon; Philipp Kainz; Pierre Geurts; Louis Wehenkel
Journal:  Bioinformatics       Date:  2016-01-10       Impact factor: 6.937

9.  hackseq: Catalyzing collaboration between biological and computational scientists via hackathon.

Authors: 
Journal:  F1000Res       Date:  2017-02-28

10.  Sharing and reusing cell image data.

Authors:  Assaf Zaritsky
Journal:  Mol Biol Cell       Date:  2018-06-01       Impact factor: 4.138
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