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diff --git a/abstract-bio.txt b/abstract-bio.txt new file mode 100644 index 0000000..e4963df --- /dev/null +++ b/abstract-bio.txt @@ -0,0 +1,34 @@ +Title: + +BioNix: functional, reproducible bioinformatics workflows + +Abstract: + +A challenge for computational biologists is to make our analyses +reproducible - that is, easy to rerun, combine, and share, with the +assurance that equivalent runs will generate identical results. Current +best practice aims at this using a combination of package managers, +workflow engines, and containers. + +In this talk I will present BioNix, a lightweight library built on the Nix +deployment system. BioNix manages software dependencies, computational +environments, and workflow stages together using a single abstraction: +pure functions. BioNix lets users specify workflows in a clean, uniform +way, with strong reproducibility guarantees. + +I will also discuss the application of BioNix to the Stafford Fox Rare +Cancer project. Within this project BioNix has been used to manage a +complicated workflow across >100 whole genome and whole exome sequences. I +will discuss lessons learnt from this application and the future direction +of BioNix. + +Bio: + +Dr Justin Bedő is the Stafford Fox Centenary Fellow in Bioinformatics +and Computational Biology for Rare Cancers at the WEHI. He was awarded +a PhD by the ANU in 2009 in Machine Learning. His PhD investigated novel +machine learning algorithms to solve bioinformatics problems arising +in plant breeding and cancer genomics. After his PhD he obtained +Postdoctoral experience at NICTA and IBISC (Genopole, Paris) as well as +industrial research experience at IBM Research Australia. His interests +span machine learning, diagnostic genomics, and bioinformatics. |