06 Feb 2012 MiniLIMS Ion Torrent plugin sneak peek
The great conflagration of genomic luminaries known as AGBT is once again upon us. Getting it in just under the wire, we’ll be releasing the Ion Torrent plugin for the MiniLIMS platform at this meeting.
If you’ve been following my previous posts about the PHP API (starting here) you know a little bit about how MiniLIMS is exchanging data with the Torrent Server via the nicely designed RESTful JSON interface. What I’d like to show you here is how that data exchange is materializing in the MiniLIMS plugin.
First, I want to show you really quickly how you install the Ion Torrent plugin (assuming you have MiniLIMS installed at /var/www/minilims):
$ cd /var/www/minilims/plugins $ sudo cp ~/Downloads/IonTorrent.tar.gz . $ tar xzvf IonTorrent.tar.gz
That’s it. Using the runtime integration capabilities of PHP, the Ion Torrent plugin will be loaded the next time you access a MiniLIMS page.
Our 1.0 plugin release isn’t particularly glitzy, but it takes advantage of the Torrent Server API to provide some of the key things that our early users have been interested in: planned experiment posting; run and report retrieval; instrument status; and file and quality results delivery.
Planned experiments are a nice facility provided by the Torrent Server that allows you to define a PGM run outside of the tiny console on the instrument itself. By setting them up in MiniLIMS and posting to the Torrent Server, you can maintain data integrity by selecting predefined Sample and Project records.
Once saved, the Planned Experiment can be posted to the Torrent Server and, therefore, selected from the console.
As most lab scientists will attest to, the same basic experiment is run repeatedly with just a different sample and/or project. PGM Planned Experiments can be saved as PGM Experiment Templates that can be reused for common experiment types. When creating a new planned experiment, just chose a template from the available list and your form will be populated with it’s values.
Like the Illumina and Roche 454 MiniLIMS plugins, the Ion Torrent offering features a run loader. The Ion Torrent run loader retrieves Experiments (runs), Results (reports), Quality Metrics and Lib Metrics from the Torrent Server. As described in the previous postings, the data types closely follow the API arrangement. Data can either be retrieved via the regular cron job or by using the “Refresh data” button on the Torrent Server page.
MiniLIMS also provides lab personnel with a quick overview of the state of the instrument run and analysis based on the data from the most recent run. FTP status of the run and status of the currently running report (if there is one) is shown along with a list of the most recent runs and results.
End user results delivery is also made simpler by MiniLIMS. MiniLIMS projects, typically used to group user Samples, now include a summary of the results associated with your project. The summary has just about everything a discerning scientist would need: links to FASTQ and SFF files (zipped versions), drill-down links to full PGM Experiment and PGM Result pages, the full analysis reports on the Torrent Server and q17 and q20 read numbers.
Remember when looking at these examples of the PGM plugin pages that MiniLIMS is end-user configurable. Though the data types used to supply a table result like the one above are fixed, specific columns can be added or removed, filters and sorting can be applied and new properties can be added to the Project definition to match your lab workflow.
Those are pretty much the key elements of the 1.0 plugin. We expect to have a couple more releases this year as MiniLIMS grows and we incorporate feedback from customers. If you’re going to AGBT, come find us.