Using BioDepot-workflow-builder to Access Public Databases in a Containerized Environment

Modern day analyses of biomedical data typically involves a series of computational tasks called workflows. Each of these modules could be written by different laboratories and thus, potentially requires different computing environments. Reproducible analyses of biomedical data is a growing field of...

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Vydáno v:2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) s. 1243
Hlavní autoři: Scott, Christin, Hung, Ling-Hong, Lloyd, Wes, Yeung, Ka Yee
Médium: Konferenční příspěvek
Jazyk:angličtina
Vydáno: IEEE 01.11.2019
Témata:
Bioinformatics
bioinformatics workflows
Containers
Docker
GEO
Laboratories
reproducibility of research
Reproducibility of results
Software
software development
Software development management
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Shrnutí:Modern day analyses of biomedical data typically involves a series of computational tasks called workflows. Each of these modules could be written by different laboratories and thus, potentially requires different computing environments. Reproducible analyses of biomedical data is a growing field of interest [1]. This makes it important to develop tools to facilitate analyses in a reproducible manner. Software containers have been used to increase reproducibility in bioinformatics analyses [2]. However, these software containers often use command line tools, requiring expertise that make them inaccessible to many biomedical scientists.
DOI:10.1109/BIBM47256.2019.8983263