What’s the answer? (GMOD tools)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question:

What is your experience with GMOD tools or alternatives?

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!

Michael Dondrup

I was surprised to see my somewhat snarky answer rated up today when I went to look! I suggested that the user community ought to be asked what they want built. And I relayed the story of how MaizeGDB had surveyed their community to see what the needs were. And soon after the lead author of the MaizeGDB paper on exactly that came by to share their experience. It was a nice exchange overall–I hope it was a win for end users and for developers!

It’s a conversation that  is going to have to go on over and over again as new species and new data sets come through the next-gen big data wave we are having. I think it’s important. Go see what everyone said. And offer your thoughts if you have had experience with these tools.