An open platform approach to cyberinfrastructure

C. Titus Brown

ctb@msu.edu

Asst Professor, Michigan State University

(Microbiology, Computer Science, and BEACON)

khmer softwareAn efficient, sensitive, and specific pipeline component for extremely scalable shotgun sequencing analysis

github.com/ged-lab/khmer

Estimate 50% drop-off at each junction.

Academic software development is really, really hard!

Considerations of “remixing” are in addition to:

• Interesting science

• Sufficient compute

• User interface

• Liability and other legal issues

• Integration

Towards an “ecology” of components

• We don’t need “one true pipeline.”

• We need flexible, reusable, and competing

pipeline components.

• This is not a concern:

• It’s how science works! http://xkcd.com/927/

• Want flexible, sustainable CI? Build open platforms, openly, with open source approaches.

– The OSS community has lots of experience in doing this, & working within incentive structures.

– Note, traditional academic incentives don’t align well.

• Agile methodologies (iterative, use-case driven, organic) ensure that software doesn’t go too far astray; must directly involve (& be driven by) domain research groups.

• Too much of software that is produced is not even reusable in theory, much less in practice. This needs to change!!!Blog post will be at: http://ivory.idyll.org/blog/2013-gbmf-mmi.html

Other things I’m doing• Scalable/sensitive/specific algorithms for shotgunomics.

• Benchmarking shotgun metagenome assembly.

• CI education (NIH/ngs; NSF/data + compute;

Sloan/Software Carpentry; BEACON/intro computing for

grad)

• Hobbies/windmills:

– Open science and open data.

– Replication and reproducible research.

– Changing publication and peer review culture in biology.

Exploratory interfaces for data& executable notebooks