Bio::GMOD::Admin::Monitor::blat - Monitor a BLAT server
Check the installed version of a MOD
use Bio::GMOD::Util::CheckVersions.pm my $gmod = Bio::GMOD::Util::CheckVersions->new(-mod=>'WormBase'); my $version = $gmod->live_version;
Update a MOD installation
use Bio::GMOD::Update; my $gmod = Bio::GMOD::Update->new(-mod=>'WormBase'); $gmod->update();
Build archives of MOD releases (coming soon...)
Do some common datamining tasks (coming soon...)
Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN.
MODs are highly curated resources of biological knowledge. MODs typically incorporate the typical information found at common community sites such as NCBI. However, they greatly extend this information, placing it within a framework of experimental and published observations of biological function gleaned from experiments in model organisms.
Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. Furthermore, the quickly-evolving nature of these projects have made installing a MOD locally and keeping it up-to-date a delicate and time-consuming experience.
Bio::GMOD aims to solve these problems by:
1. Making MODs easy to install 2. Making MODs easy to upgrade 3. Enabling cross-MOD data mining through a unified API 4. Insulating programmatic end users from model changes
Bio::GMOD.pm uses a generically subclass-able architecture that lets MOD developers support various features as needed or desired. For example, a developer may wish to override the default methods for Update.pm by building a Bio::GMOD::Update::FlyBase package that provides an update() method, as well as various supporting methods.
Currently, the only participating MOD is WormBase. The authors hope that this will change in the future!