Created
April 28, 2010 22:36
-
-
Save chapmanb/382835 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment