Question: I am going to implement a (non)-model-organism (does that matter) genome database very soon. It will present a newly sequenced animal genome with annotation to the community. We are looking for software that will support the development of such a tool without 're-inventing the wheel'.

We will need a genome-browser for sure and a database backend for the annotation data.
We also will have use for integration of

ontologies (anatomy, developmental stage, etc.)

phenotype-genotype data, including images of phenotypes and stages

authentication/authorization

some users should be able to contribute by doing remote annotation

RNA-seq and other experimental data should be visualized as tracks

there should be private and public tracks for the genome

Blast interface to the genome

So I thought the GMOD tools will do the trick, as what we are trying to build is pretty much similar to FlyBase or WormBase, etc. Now my questions, excuse me if it is a bit vague:

How good is GMOD for this purpose and what are your experiences with it mainly as a developer? Are there good and viable alternatives to it (e.g. UCSC Genome browser + their data model)? I was planning to use G/JBROWSE and the CHADO database models, is that a good idea? Can such a system be administered by
1-1.5 persons?

We are still in the phase of summing up project requirements, but please contribute your valuable experiences, every input counts!

Answer: Hi Michael,

While I obviously have a biased opinion, I thought I'd at least share some information on what can be done with GMOD tools. I'll take your bullet points and give some explanation or guidance on each:

ontologies (anatomy, developmental stage, etc.) -- Chado is based on the use of ontologies and controlled vocabularies; that's where it gets its considerable flexibility. Tripal (which I will refer to a lot here) is a web front end for Chado that is based on Drupal that also has ontology awareness.

phenotype-genotype data, including images of phenotypes and stages -- Chado has a module for genotypes and phenotypes. While I don't think the Tripal modules that work with these Chado modules is publicly available yet, the Tripal group is actively working on them. I don't know much about what they are supporting interns of images, but I'm reasonably sure that they are supported.

authentication/authorization -- The nice thing about basing Tripal on Drupal is that it has all of the user stuff already built in.

some users should be able to contribute by doing remote annotation -- Apollo and Artemis are good for this for sequence annotation, and when WebApollo is available (based on JBrowse), it will be even better. Tripal allows authorized users to make changes to text-based annotations.

RNA-seq and other experimental data should be visualized as tracks -- GBrowse and JBrowse both support displaying nextgen sequence data via SAMtools (though I'm not positive the JBrowse support is public yet).

there should be private and public tracks for the genome -- GBrowse supports user authentication as well, and tracks can be configured to either be public or shown only to authorized users. The data upload functionality of GBrowse works the same way--it can be public, private, or shared with select users.

Blast interface to the genome -- This is a main missing item for the GMOD community. A tool called Mimosa was recently developed, though it hasn't been released and it's future is somewhat uncertain at the moment (due to developers' comings and goings).

What is important to realize about GMOD is that it is a collaborative community. Each one of the tools I mentioned above are developed by different groups, though we all communicate about what were doing and how to best interoperate. In fact, two good places to learn about the community are at community meetings (the next one is in DC in April and the GMOD Summer Schools (the next one will likely be in August in North Carolina, but the details aren't firm yet).