March 3, 2017

Coining "Genome Content Management"

The services that Eagle Genomics provide are pretty simple, right? Support of open source bioinformatics software following the model of typical commercial Linux distros. One criticism that we often hear is: "Most molecular biology groups have access to/can hire bioinformaticians to install, manage and integrate everything that is needed; why use Eagle?". If you follow this argument, then it seems that professional bioinformaticians are spending a great deal of time installing, managing and integrating pretty much the same tools in pretty much the same way the world over. I admit that this has been a big part of my life, and that of many of my contemporaries, for many years.

Being an "operational bioinformatician" right now reminds me of my days as a "web developer" in the heady days of the dot-com bubble; things were moving fast and there was a lot to do! All online content was lovingly hand-crafted in HTML or generated by bespoke CGI scripts. At some point in the last 10 years (whilst I was diverted by my new-found love of genomics), web content management systems (CMS) emerged. Such systems have been adopted to such an extent that developers of web sites these days rarely resort to HTML let alone CGI. Interestingly, many of the most popular CMS systems, such as Joomla! and Wordpress, are open source!

So, will a technology emerge to fill the niche in bioinformatics that CMS systems fill in web development? I argue that development is well underway, with systems like Ensembl and Chado providing the data stores, Taverna and Galaxy the analysis workfows, and BioMart and InterMine the warehouses. What Eagle provides to this mix are the packages and templates that allow these powerful tools to work together, managing real-world genomic content.

So, we have a new phrase that sums up what these systems do, and the field in which Eagle are experts. And it's "genome content management".

Topics: Bioinformatics, Bioinformatics, BioMart, Chado, Ensembl, Galaxy, genome content management, InterMine, Open source, Taverna