<p>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'.</p>

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

<ul>
<li>ontologies (anatomy, developmental stage, etc.) </li>
<li>phenotype-genotype data, including images of phenotypes and stages </li>
<li>authentication/authorization</li>
<li>some users should be able to contribute by doing remote annotation</li>
<li>RNA-seq and other experimental data should be visualized as tracks</li>
<li>there should be private and public tracks for the genome</li>
<li>Blast interface to the genome</li>
</ul>

<p>So I thought the <a href='http://gmod.org/wiki/Main_Page'>GMOD tools</a> will do the trick, as what we are trying to build is pretty much similar to <a href='http://flybase.org/'>FlyBase</a> or <a href='http://www.wormbase.org/'>WormBase</a>, etc. Now my questions, excuse me if it is a bit vague:</p>

<p>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?</p>

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

<p><strong><em>*cough</em></strong>* </p>
<p>Have you asked your main local end users what they prefer? I mean, of course they want everything, but they might have some preference for one or the other.</p>
<p>But I will also point you to an interesting survey that was done by the MaizeGDB folks when they were considering this question too: <a href="http://blog.openhelix.eu/?p=4206">Choosing a genome browser for your organism…</a></p>
<p>And they put it all into a paper too. <a href="http://database.oxfordjournals.org/content/2010/baq007">Choosing a genome browser for a Model Organism Database: surveying the Maize community</a></p>