#+title: Promoting platform interoperability with portable bcbio workflows
#+author: Brad Chapman \newline Bioinformatics Core, Harvard Chan School \newline https://bcb.io \newline http://j.mp/bcbiolinks
#+date: 8 July 2016

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* Talk

** Blue Collar Bioinformatics

[[./images/bcbio.png]]

#+BEGIN_CENTER
\LARGE
http://bcb.io
#+END_CENTER

** Good quality high throughput sequencing analyses
\Large
- Variant calling: SNPs and indels
- Structural variation
- Cancer heterogeneity
- RNA-seq
- small RNA
- Quality control

** Validate and move quickly

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[[./images/grading-summary-24385.png]]
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** Infrastructure Goals
\Large
- Free, open source, community developed
- Welcoming to contributions
- Local machines
- Clusters: SLURM, SGE, Torque, PBS, LSF
- Clouds: Amazon, Google, Azure
- Clinical environments
- User interface for researchers
- Integrate with LIMS
- Accessible to the general public

** Open source communities not yet optimal

[[./images/fitness.png]]

\tiny
https://en.wikipedia.org/wiki/Fitness_landscape

** Better abstractions = more interoperability

[[./images/abstractions.png]]

https://bcbio-nextgen.readthedocs.io/en/latest/contents/cwl.html
