aws_cloud_brainstorming

Developing an open source community for cloud bioinformatics

- Main points
  = Developing open source code in biology especially difficult.
  = Most productive target for work is developer resources.
  = Community emerging to develop and maintain images.

- Open source background:
  = OpenBio, Bio* projects, Biopython
  = Grad school -- developed distributed system with BSP. Never reused: why
    later

- Work background:
  = Automated biological pipelines at startup.
  = Democratization of analysis in research/hospital setting.

- Filters in biology make finding open source developers hard 
  = Filter: belief that someone else might be working on problem.
  = Filter: interest in sharing and developing open source code.
  = Filter: working in same biological area.
  = Filter: your software intuitive enough to get started with
  = Filter: have technical capabilities.
  = How many people are left at the end? Not many.

- Academic rewards system does not encourage code reuse
  = Most successful software from research institutes
  = Community work not easy to recognize through publication system.

- Successful examples of community based bioinformatics work
  = BioPerl
  = Bioconductor
  = Aimed at developers, instead of end users.

- Other attributes of success
  = Easy to get running: Galaxy versus Gbrowse
  = Building blocks for specific, custom biological work: can publish

- Cloud lowers barriers (maybe too obvious; for cutting/quicky)
  = No installation; ready to try AMI
  = Common platform to scale with

- Developing community to provide bioinformatics images
  = Integrate existing work: 
    ^ biolinux
    ^ bioperl-max
    ^ MachetEC2
    ^ Debian Med
  = Software: http://github.com/chapmanb/bcbb/tree/master/ec2/biolinux/

- Provide ready to use biological data along with software
  = Data: http://github.com/chapmanb/bcbb/blob/master/galaxy/galaxy_fabfile.py

- Organize interested developers
  = CodeFest: http://www.open-bio.org/wiki/Codefest_2010

- Community goals
  = Easy to add new packages: plain text config file based
  = Inclusive but configurable. Aim to cover a wide scope of areas but make
    it easy to install only a few.
  = Aim at developers initially; bootstrap more contributors