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Hackathon 2007 info

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Accomplishments

Apollo

  • Created an example organism-specific webstart build of Apollo and an accompanying ant build file for repeating the build.
  • Verified that the triggers required for the original JDBC connector work with PostgreSQL 8.1 (they work in Pg 7.4 but not in 8.0).
  • Wrote an alternative set of triggers in plperl (converted from plpgsql)

Needs to be done still:

  • Document the process for creating an organism specific release

Core

  • Created a webpage outlining the various configuration parameters that need to be adjusted to make it organism-specific.
  • Created tools for users to upload GAME-XML files and for admins to load the XML files into Chado.
  • Tested the GBrowse Chado adaptor with the GBrowse DAS server to verify that the Chado adaptor can work as a DAS-1 source.

Needs to be done still:

MediaWiki

See Hackathon_wikidb

  • Did most of a new release of TableEdit to conform better to MW coding standards
  • Wiki Chado round trip partly successful
    • Chado2Wiki worked via dumps to intermediate flatfile formats
    • Wiki2Chado worked for simple case with Modware
    • Wiki2Chado via Chado XML and XORT - close but not completed before we left

Location info

Dates

August 23-24

Agenda

Thursday 8:40 Meet in the lobby of the hotel to walk over to NU

9:00 Introductions and network administrivia

9:30 The current state of things:

  • Chado
  • Wiki/TableEdit  : working notes at Hackathon_wikidb
  • Apollo
  • Documentation`

10:15 Sorting out who wants to do what

10:30 Hack!

Location

Center For Genetic Medicine Northwestern University Chicago Campus
in Downtown Chicago, IL
Lurie Building Room 6-127 (6th floor)
303 E Superior St
Google Map of Location

Elevators are located on the south side of the lobby. There is a security guard who may stop you on the way to the elevator, you will have to sign in and mention that you are with the GMOD hackathon.

This is on the Northwestern University Medical School Campus in DOWNTOWN CHICAGO, not to be confused with the main campus in Evanston

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.

Public Transportation

If you are taking the Chicago CTA (a.k.a the 'El') the closest stop is Chicago Ave. on the RED LINE. Google map of route from Red line to Hackathon Location

Lodging

There is a room block at the Red Roof Inn Chicago - (312) 787-3580 for August 22nd checking out on the 25th. This one of the least expensive hotels in the area, but it is clean, secure, and very close to the Hackathon venue. We blocked 5 doubles (so people can room share if they like) and 5 kings at a rate of $109 and $119. When you are booking, please mention that you are with the 'HACKATHON' group in order to get our group rate. (code:b281hack)

If you are interested in other hotels, there are a couple of very conveniently located hotels:

Lastly, because of Chicago's public transportation system, anywhere that is relatively near an 'El' stop is convenient!

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 TableEdit, 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:

Core:

  • 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.

Apollo:

  • An easy to understand Apollo configuration set up. Will we need a new release of Apollo (I'm betting yes)
  • A good example config that works with the dicty example database.

MediaWiki/TableEdit:

All of this should be saved in the schema cvs, in the hackathon_2007 directory: http://gmod.cvs.sourceforge.net/gmod/schema/hackathon_2007/

Possible Goals considered

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

  • Improving Apollo-Chado round tripping (documentation, examples, tutorials, configuration files, installation procedures, etc)
Justin: I've written Apollo-Chado Integration at BovineBase: Bugs and Suggestions containing a list of bugs and suggestions from our developers and Apollo users, compiled during our construction of a Chado<->Apollo setup for the Bovine genome annotation effort.
  • 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 Chado XML
  • 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?) (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.
    Scott 20:46, 30 July 2007 (EDT): I don't think the admin stuff needs to be a priority
  • A printer (maybe--do people use paper anymore?)
  • A computer projector

Prep for attendees:

  • All attendees should have SourceForge accounts and have them added as GMOD developers since we will be using a SourceForge GMOD cvs repository for work at the hackathon. Email Scott Cain with your SourceForge account name so he can add you.
  • Get a developer's cvs checkout of the GMOD schema repository (if you already have one, do an "update -d" to get the new directory for the hackathon).
  • Get a developer's cvs checkout of Apollo (in the GMOD cvs reposotiry), and try to build it. See apollo/doc/README.developers for pointers on running/building Apollo.

Attendees

Possible:

  • 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)