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Codefest 2010

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Revision as of 12:49, 16 June 2010 by Chapmanb (talk) (→‎Location)
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OpenBio Codefest 2010 will take place July 7th and 8th, 2010 in conjunction with BOSC 2010. This is an opportunity for OpenBio developers from projects like BioPerl, BioJava, Biopython, BioRuby, and EMBOSS to work collaboratively on improving Open Source Bioinformatics code.

Goals

OpenBio projects are typically coordinated remotely, with users from all over the world contributing and organizing themselves through mailing lists and IRC chats. Additionally, contributors work on these projects in their spare time, coordinating improving the projects with their day jobs and life outside of the computer. The objective of the Codefest is to give these talented developers a chance to be fully focused on the projects for a few days, interacting in real time. Previous Hackathons have been immensely successful at producing new high quality code and innovative project developments.

The general aim of the Codefest is improving the accessibility, functionality and interoperability of the existing libraries. The specific goals are determined based on the interests of attending members and inputs of sponsors. Some current areas of topic discussion are:

Cloud computing

Improving the presence of OpenBio libraries on distributed computing environments like Amazon Elastic Compute Cloud and Eucalyptus. Ntino has written up an excellent project proposal available for download in pdf format.

Initial work has started to develop an automated build environment that incorporates the Cloud BioLinux and bioperl-max efforts. See the blog post for full details. Code and configuration files are available from a GitHub repository. The post outlines several areas of improvements which could be targets for focused work at the Codefest.

Location

  • July 7, 2010 -- Harvard School of Public Health 655 Huntington Avenue, Boston, MA
  • July 8, 2010 -- Massachusetts General Hospital (MGH), Simches Research Building, Room 3130 185 Cambridge Street, Boston, MA
    • Getting there: The three closest MBTA stops are 'Charles/MGH' (Red Line), 'Bowdoin' (Blue line) and 'Government Center' (Green line). All three are located next to Cambridge Street. From the Red Line stop, walk away from the river; walk towards the river from either the Blue or Green line. Simches is located slightly off Cambridge Street -- the closest landmark on Cambridge Street is a big yellow Au Bon Pain. Walk up the stairs next to the Au Bon Pain and you'll be in a parking lot: the Simches building is located immediately to the right of the Whole Foods and CVS.

Resources

  • Amazon Web Services -- We will be able to use EC2 and other Amazon services thanks to Amazon grant support for a proposal put together by Steffan Moellar. Many thanks to Amazon for supporting the initiative and Steffan for putting together the application.
  • Eucalyptus -- The Universitätsklinikum Schleswig-Holstein is sponsoring a 12 node local Eucalyptus cloud for testing and development. Thanks again to Steffan for making this available.

Sponsorship

Space and internet for the Codefest are kindly provided by the Harvard School of Public Health and Massachusetts General Hospital. We are actively seeking sponsors to help supplement the travel, lodging and meal costs for developers. If you're interested in contributing to Open Source development in Bioinformatics and helping to direct the focus on the Codefest, please contact Brad.

ToDo List

Add your goals and plans for the Codefest here. This is a brainstorming section to help us organize ourselves.

Cloud computing

Work for the current community bioinformatics image (framework on GitHub):

  • Perl library support and useful package list
  • Java library organization and expand useful packages
  • Provide packaging for missing programs. See comments at the end of the Package config for some targets.
  • Documentation: especially targeted at new users.
  • Produce an automated manifest for an AMI, listing versions of all installed packages and libraries.
  • Automation to build AMI and roll out to Amazon on a bi-weekly/monthly basis based on latest code.
  • Website with documentation, AMI history, other goals.
  • Testing and work on Eucalyptus cloud

Attendees

Feel free to add yourself if you are interested. We are happy to have you.

Discussion

We welcome any thoughts from interested participants. Please direct discussion to the BOSC mailing list: open-bio-l@lists.open-bio.org.

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