Articlehybrid2016

BioPartsDB: a synthetic biology workflow web-application for education and research

Giovanni Stracquadanio · Kun Yang · Jef D. Boeke · Joel S. Bader

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Scientific Computing and Data Management Microbial Metabolic Engineering and Bioproduction Genetics, Bioinformatics, and Biomedical Research

Abstract

Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones. AVAILABILITY AND IMPLEMENTATION: BioPartsDB is released under the MIT license and available for download at https://github.com/baderzone/biopartsdb Additional documentation and video tutorials are available at https://github.com/baderzone/biopartsdb/wiki An Amazon Web Services image is available from the AWS Market Place (ami-a01d07c8). CONTACT: joel.bader@jhu.edu.

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2018Visual Life Sciences Workflow Design Using Distributed and Heterogeneous Resources

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