Bioboxes: standardised containers for interchangeable bioinformatics software

Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD (2015)
GigaScience 4: 47.

Download
No fulltext has been uploaded. References only!
Journal Article | Original Article | Published | English

No fulltext has been uploaded

Author
; ; ; ; ;
Abstract
Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.
Publishing Year
eISSN
PUB-ID

Cite this

Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD. Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience. 2015;4: 47.
Belmann, P., Dröge, J., Bremges, A., McHardy, A. C., Sczyrba, A., & Barton, M. D. (2015). Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience, 4, 47. doi:10.1186/s13742-015-0087-0
Belmann, P., Dröge, J., Bremges, A., McHardy, A. C., Sczyrba, A., and Barton, M. D. (2015). Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience 4:47.
Belmann, P., et al., 2015. Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience, 4: 47.
P. Belmann, et al., “Bioboxes: standardised containers for interchangeable bioinformatics software”, GigaScience, vol. 4, 2015, : 47.
Belmann, P., Dröge, J., Bremges, A., McHardy, A.C., Sczyrba, A., Barton, M.D.: Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience. 4, : 47 (2015).
Belmann, Peter, Dröge, Johannes, Bremges, Andreas, McHardy, Alice C, Sczyrba, Alexander, and Barton, Michael D. “Bioboxes: standardised containers for interchangeable bioinformatics software”. GigaScience 4 (2015): 47.
This data publication is cited in the following publications:
This publication cites the following data publications:

15 Citations in Europe PMC

Data provided by Europe PubMed Central.

Tissue specificity of in vitro drug sensitivity.
Yao F, Madani Tonekaboni SA, Safikhani Z, Smirnov P, El-Hachem N, Freeman M, Manem VSK, Haibe-Kains B., J Am Med Inform Assoc 25(2), 2018
PMID: 29016819
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Droge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jorgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvociute M, Hansen LH, Sorensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Goker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC., Nat. Methods 14(11), 2017
PMID: 28967888
Systematic integration of biomedical knowledge prioritizes drugs for repurposing.
Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE., Elife 6(), 2017
PMID: 28936969
Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.
Kim B, Ali T, Lijeron C, Afgan E, Krampis K., Gigascience 6(8), 2017
PMID: 28854616
MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.
Piro VC, Matschkowski M, Renard BY., Microbiome 5(1), 2017
PMID: 28807044
General guidelines for biomedical software development.
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J., F1000Res 6(), 2017
PMID: 28443186
Nextflow enables reproducible computational workflows.
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C., Nat. Biotechnol. 35(4), 2017
PMID: 28398311
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.
O'Connor BD, Yuen D, Chung V, Duncan AG, Liu XK, Patricia J, Paten B, Stein L, Ferretti V., F1000Res 6(), 2017
PMID: 28344774
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.
Gorgolewski KJ, Alfaro-Almagro F, Auer T, Bellec P, Capota M, Chakravarty MM, Churchill NW, Cohen AL, Craddock RC, Devenyi GA, Eklund A, Esteban O, Flandin G, Ghosh SS, Guntupalli JS, Jenkinson M, Keshavan A, Kiar G, Liem F, Raamana PR, Raffelt D, Steele CJ, Quirion PO, Smith RE, Strother SC, Varoquaux G, Wang Y, Yarkoni T, Poldrack RA., PLoS Comput. Biol. 13(3), 2017
PMID: 28278228
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.
Narayanasamy S, Jarosz Y, Muller EE, Heintz-Buschart A, Herold M, Kaysen A, Laczny CC, Pinel N, May P, Wilmes P., Genome Biol. 17(1), 2016
PMID: 27986083
Big Data and Uveitis.
Lee CS, Lee AY, Holland GN, Van Gelder RN, Tufail A., Ophthalmology 123(11), 2016
PMID: 27772646
Tools and techniques for computational reproducibility.
Piccolo SR, Frampton MB., Gigascience 5(1), 2016
PMID: 27401684
BioShaDock: a community driven bioinformatics shared Docker-based tools registry.
Moreews F, Sallou O, Menager H, Le Bras Y, Monjeaud C, Blanchet C, Collin O., F1000Res 4(), 2015
PMID: 26913191

10 References

Data provided by Europe PubMed Central.

Rise and demise of bioinformatics? Promise and progress.
Ouzounis CA., PLoS Comput. Biol. 8(4), 2012
PMID: 22570600
Core services: Reward bioinformaticians.
Chang J., Nature 520(7546), 2015
PMID: 25855439
Creating a bioinformatics nation.
Stein L., Nature 417(6885), 2002
PMID: 12000935
Scholarly context not found: one in five articles suffers from reference rot.
Klein M, Van de Sompel H, Sanderson R, Shankar H, Balakireva L, Zhou K, Tobin R., PLoS ONE 9(12), 2014
PMID: 25541969

AUTHOR UNKNOWN, 0
An introduction to Docker for reproducible research, with examples from the R environment
Boettiger C., 2014
The impact of Docker containers on the performance of genomic pipelines
Di P, Palumbo E, Chatzou M, Prieto P, Heuer ML, Notredame C., 2015

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 26473029
PubMed | Europe PMC

Search this title in

Google Scholar