Difference between revisions of "Hackathon 2007 info"

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(Preparation)
(Attendees)
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*Josh Goodman, FlyBase, IndianaU
 
*Josh Goodman, FlyBase, IndianaU
 
*Mike Wong, SFSU, www.dhgp.org
 
*Mike Wong, SFSU, www.dhgp.org
 +
*Brian O'Connor, UCLA, biopackages.net
  
 
Possible:
 
Possible:

Revision as of 18:36, 23 July 2007

Location info

Dates

August 23-24

Location

Northwestern University Chicago Campus
in Downtown Chicago, IL
Building/Room TBA

Transportation

Airports

There are two major airports in Chicago: Midway and O'Hare. Both are about equally convenient to Northwestern's Chicago Campus

Driving


Be aware that above driving directions for South and East travel take you through I-90/94. This stretch of interstate is currently undergoing major construction and you might encounter significant delays. See http://www.danryanexpressway.com/ for more information and suggested alternate routes.

Lodging

WE ARE WORKING ON A ROOM BLOCK. CHECK BACK SOON.

Leading candidate goal

Several people have expressed interest in tuning the Apollo<->Chado interaction. With that in mind, I would like to propose this goal: to produce a VMware image that has Chado and associated tools, Apollo, and MediaWiki with the Table Editor, with the point of producing a server that could be picked up and used for a nascent model organism database for use with community annotation.

Other things that would make sense to put in the VMware image but are secondary to the goal are GBrowse and GMODWeb. Other things that could be worked on during the hackathon are rebuilding rpm packages for biopackages.net, tuning MODWare for the newer Chado schema, and tuning PostgreSQL to get better performance.

Possible Goals

While definitive goals have not been established yet, here are some possiblities. Please feel free to add more.

  • Improving Apollo-Chado round tripping (documentation, examples, tutorials, configuration files, installation procedures, etc)
  • Beginning work on Apollo-Ensembl round tripping
  • Merging the ClassDBI classes the ModWare and GMODWeb use (Chado::AutoDBO and Turnkey::AutoDBI)
  • Giving a small MOD a 'GMOD make over'
  • Work on perl XML::DOM tools for writing ChadoXML
  • Building VMware instances for distribution
  • Rebuilding RPM packages for updated GMOD software
  • Polishing a gmod 0.5 release
  • Modify Apollo to annotate with GO terms and enable chado round tripping of feature_cvterms
  • improving analysis plugins for chado via modware or gbrowse
  • performance tuning.
  • community wiki development/wiki table editor work

Preparation

Things we'll need provided either by Eric (the host) or various people coming:

  • A server that a few VMware instances can go on (this could potentially be a fast laptop with a fair amount of memory)
  • A base VMware instance to start working with (Scott will provide--what distro to use? Ubuntu server (its a bit of a hassle and the lack of a gui may turn some people off)? Ubuntu desktop? Fedora 7?)
  • A VMWare instance with Chado already installed and some sample data (what to use? a few chromosomes of worm, or a few chromosomes of fly, something else? Perhaps a 'younger' organism that someone attending works on?) (Scott will provide provided we can )
  • A printer (maybe--do people use paper anymore?)
  • A computer projector

Attendees

  • Scott Cain, CSHL
  • Eric Just, DictyBase, Northwestern
  • Jim Hu, Ecoliwiki, TAMU
  • Don Gilbert, euGenes, IndianaU
  • Mark Gibson, Apollo, Berkeley?
  • Josh Goodman, FlyBase, IndianaU
  • Mike Wong, SFSU, www.dhgp.org
  • Brian O'Connor, UCLA, biopackages.net

Possible:

  • Sanjay Chellapilla, Kansas State University
  • Emmanuelle Morin, Sea urchin, CalTech
  • Kris Khamvongsa, Sea urchin, CalTech
  • Dave Emmert, FlyBase, Harvard
  • Jonathan Crabtree, Apollo, The institute that was TIGR
  • Justin Reese, Georgetown U. (via Skype)
  • Debra Buerhans(?), CSHL, Dolan Center
  • Cornel Ghiban, CSHL, Dolan Center