Container-based bioinformatics with Pachyderm | Zendy

Jon Ander Novella | Zendy; Payam Emami Khoonsari | Zendy; Stephanie Herman | Zendy; Daniel Whitenack | Zendy; Marco Capuccini | Zendy; Joachim Burman | Zendy; Kim Kultima | Zendy; Ola Spjuth | Zendy

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Container-based bioinformatics with Pachyderm

Author(s) -

Jon Ander Novella,

Payam Emami Khoonsari,

Stephanie Herman,

Daniel Whitenack,

Marco Capuccini,

Joachim Burman,

Kim Kultima,

Ola Spjuth

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty699

Subject(s) - computer science , container (type theory) , bioinformatics , computational biology , biology , engineering , mechanical engineering

Computational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a reliable way to run processing stages in any computational environment, (ii) a well-defined way to orchestrate those processing stages and (iii) a data management layer that tracks data as it moves through the processing pipeline.

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