Difference between revisions of "Hackathon 2007 info"

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*Mike Wong, SFSU, www.dhgp.org
*Mike Wong, SFSU, www.dhgp.org
*Brian O'Connor, UCLA, biopackages.net
*Brian O'Connor, UCLA, biopackages.net
*Ben Faga, CSHL

Revision as of 18:07, 30 July 2007

Location info


August 23-24


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



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


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.



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.

More specific subgoals:


  • A cgi file upload/drop box for community created GAMEXML/ChadoXML files (perhaps the wiki could handle this, since it would also take care of user identification, though it would almost certainly make the script below a little more complicated).
  • A script for periodically loading uploaded XML files to Chado (this could use command line Apollo or XORT).
  • A set up script that will prompt the user for items specific to the user/community and will make appropriate chages to everything, including:
    • Modifying mediawiki's LocalSettings.php with names, email addresses and icons
    • Inserting organism data into Chado (allowing for the possiblity of multiple organisms)
    • Modifying appropriate Apollo config files that would then be downloadable by members of the community
    • Modifying the default organism in /usr/local/gmod/conf/default.conf.
  • An easy to understand 'Getting started' guide that gives an overview of the contents and how to get started (presumably, this would go in the wiki so that the users would have the ability to edit the contents for their community)
  • An easy to understand guide on how to update any software when necessary--mediawiki, extentions, GBrowse, Chado. More than anything, these should be pointers to where to get further information.


  • An easy to understand Apollo configuration set up. Will we need a new release of Apollo (I'm betting yes)

MediaWiki/Table Editor:

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


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?) (Eric already created a vmware appliance with Chado populated with Dicty data--I'll probably use that.)
  • Also in the vmware instance: phpmyadmin, phppgadmin, mediawiki all configured and ready to use.
  • A printer (maybe--do people use paper anymore?)
  • A computer projector


  • 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
  • Ben Faga, CSHL


  • 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