Ken Brewer
Senior Developer Advocate at Seqera
San Francisco, California, United States
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Ken Brewer is a Senior Developer Advocate at Seqera, where he supports the scientific community in adopting modern software tooling and best practices. Prior to joining Seqera, he was one of the first computational biologists to join the early-stage startup ProFound Therapeutics, where he helped build out a computational platform for exploring the unannotated human proteome. He then joined GeneDx where he provided technical leadership in building a bioinformatics platform designed to meet the data-intensive needs of the future of genetic medicine. Ken has a B.A. in Chemistry from Harvard College and a Ph.D. in Molecular Biophysics and Biochemistry from Yale University, where he developed computational methods for discovering structured noncoding RNA families in bacteria. He is passionate about open-source science and is a member of the Cytomining and nf-core organizations, which are dedicated to providing high-quality software for analyzing microscopy images using machine learning and building bioinformatics pipelines, respectively.
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How to NOT contribute to nf-core: Best practices for using nf-core tooling in closed-source contexts
Even when developing code that can’t be contributed to open-source, it pays great dividends for Nextflow developers to build their pipelines compatible with nf-core tooling. As a result, many organizations maintain repositories containing a mix of open-source and proprietary code.
To support this common scenario, this talk will explore the practicalities of using nf-core pipelines and tooling in hybrid-source environments. It will include an overview of strategies for adding custom code and configurations, from the lightweight (and still-open) option of creating an institutional pipeline configuration to the heavier lift (and fully closed) option of maintaining private pipeline forks and private module libraries. Additionally, the talk will discuss the benefits of empowering bioinformatics teams with open-source contribution policies and guidelines that allow them to contribute code in the environment (in nf-core or not) that best balances the short and long-term needs of a commercial organization participating in a broader scientific community.
Ken Brewer
Senior Developer Advocate at Seqera
San Francisco, California, United States
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