As many of you may know, about a year ago, The BioTeam began developing a LIMS platform called MiniLIMS to replace the highly successful WikiLIMS with a more effective and focused tool. With a stable of long term beta customers and a recent release of MiniLIMS 1.0, the software has become a valuable tool for lab data management. Though the combination of a super flexible persistence layer akin to Google’s BigTable or MediaWiki’s Semantic extension and a plugin application architecture can support any lab process, most demand has been around the MiniLIMS plugins for Next Generation Sequencing (NGS) instruments like the Roche 454 GS FLX and Illumina GA/HiSeq/MiSeq.
Recently, I started working on a plugin for the Ion Torrent Personal Genome Machine (PGM). Though MiniLIMS has been great for Roche and Illumina instruments, the marriage of MiniLIMS and the PGM is particularly compelling. The pricey, high complexity LIMS systems are justifiable when you’re spending hundreds of thousands on a machine and reagents, but make very little sense when you’re trying to help manage the data of a small lab with a PGM. The low cost of MiniLIMS and great end-user configuration capabilities make for a very low overhead solution.
Besides, the hardware experts at BioTeam are already providing hardware configuration and cloud instances for the Ion Torrent Server.
The plugin that I’ve started, and whose development this series of posts will follow, will be a union between the Ion Torrent Server API, a Djangoed, RESTful JSON system, and the MiniLIMS, property-oriented PHP classes. The Torrent Server information I’ll be using comes from the Developer portions of the Ion Torrent Community site. While the site’s social networking motif feels a bit gimmicky sometimes, it is a hell of an improvement over the old Applied BioSystems days (I think J. Edgar’s ghost used to haunt that place).
The MiniLIMS API has some documentation as well, but it’s, let’s say, “unfinished”. As things come up, I’ll try to fill in the details on that set of pages as well.
One of the reasons I’m kinda excited about working on this is that it should be an example of my favorite answer to the structure vs. flexibility argument for APIs- both. Also, I’m hoping that along the way, we’ll get a better understanding of both the MiniLIMS and Torrent server APIs.
Next post in this series: