GMODWeb, Biopackages, & Virtual Machines Brian O'Connor Nelson Lab, UCLA 1/16/2009.

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Presentation transcript:

GMODWeb, Biopackages, & Virtual Machines Brian O'Connor Nelson Lab, UCLA 1/16/2009

Turnkey is... A website auto-generator SQL: Create table foo...

GMODWeb is... GMODWeb = Turnkey + Chado + Integration w/ other projects (GBrowse, Amigo, etc) SQL: Create table foo... Chado GMODWeb

Active Code Generation SQL: Create table foo... SQL::Translator Directed Graph Mapping Layer XML Layout & Templates SQL Schema Data Objects

Strengths & Weaknesses Strengths Good prototyping tool Great tool for active code generation Quickly build up-to-date webapps integrated with other GMOD tools Weaknesses Perl dependencies are ridiculous and the source of all pain Early design decision to use custom Perl rendering engine limits performance and appeal to users

Status Turnkey 1.4 is available and addresses some bugs since the release of the paper GMODWeb: a web framework for the Generic Model Organism Database. Genome Biol ; 9(6). Try the virtual machines at: Working on Updated RPMs

Biopackages.net is... A repository of software compiled for CentOS (mostly CentOS4) and Fedora “yum install chado” Wanted to make it easy to install software dependencies

Biopackages Dependency resolution is a huge part of the work

Biopackages Build Farm Goal is to build as much in an automated way as possible

Status Previously focused on CentOS4 RPM packages for the Nelson Lab Transitioning now to CentOS5 Currently packaging Chado DBs using the 1.0 schema: Base DB with ontologies Human hg18 DB Possibly others (mm9, rn4, panTro2, rheMac2...) DAS/2 reference server Dependencies

Virtual Machines On paper RPMs solve many problems However, machines can be tainted by other repositories, source-based installs, other customizations Virtual machines can be used to: A mechanism to quickly try the GMOD catalog of tools A mechanism to distribute clean testing and development environments

Status Idea is to have a virtual machine with all the Biopackages-provided tools pre-installed Currently based on CentOS4 Have a prototype CentOS4 machine with Chado 1.0 schema, recent BioPerl, and Turnkey/GMODWeb 1.4 Working with Dave Clements on RPMs to create an updated CentOS5 VM

Status

Contact Me... Turnkey/GMODWeb: looking to expand Java producer to eliminate Perl dependency problem Biopackages: looking for RPM developers (or deb package builders for Ubuntu) Virtual Machines: looking to create CentOS5 machines Pre-configured GMOD demo/dev kit Pre-configured Biopackages dev kit Anyone using GMOD tools for Next Gen Sequencing???