Software

Users of the Polonator G.007 will fall into one of two categories: those who simply want to obtain genomic sequence data as quickly and efficiently as possible, and those who wish to exploit the totally open nature of the Polonator to either extend the current biochemistry, or develop their own protocols from scratch. It’s a bit early, but based upon our initial customer discussions, we anticipate that this will break at somewhere around 90% : 10%. That is, the majority of users will in fact operate the Polonator as a “black box”, following the published protocols, loading standard flow cells, and publishing their results. That said, it is absolutely essential that we provide maximal support to both the large datacenters with the resources to redirect the Polonator, as well as those leading-edge researchers who will blaze entirely new trails in sequencing.

The Church Lab has written the extensive software suite that operates the Polonator, and multiple programmer-years have gone into this development. The software is compartmentalized into two basic subsets, each of which has a dedicated, leading-edge, dual core CPU and hardware at its disposal. Three terabytes of local storage are provided, along with a gigabit Ethernet interface. One of the two computers within the instrument is dedicated to image acquisition and instrument control, while the other is singularly focused on image processing and basecalling. All time-critical routines are coded in C, with Python and Perl scripts used to orchestrate the instrument’s lower speed hardware features (see bullets under the Instrument section). In addition, real-time quality metrics are generated continuously during a run; these can either be exported to a network resource capable of running them, or users can load a copy of MatLab onto the Polonator, in which case Perl scripts provide real-time visual feedback on the data quality during a run.

We have gone to great lengths to ensure that ALL features of the Polonator are totally open and accessible. The operating sequence, the choice of specific reagents, their volume in microliters, flow rates, temperatures, rates of temperature change, duration within the flow cell, multi-axis motion, exposure, camera integration, EM gain, shutter blanking, filter selection, ALL system-wide parameters are fully accessible. For those intrepid souls willing to slip into the driver’s seat, the Polonator is completely open and at your disposal. Beyond buckling up, our only request is that you respect the open nature of the Polonator system, and promptly publish (or, better yet, communicate immediately via our user community forums) any enhancements that you might develop. It is through your creativity that the Polonator system will evolve.

Owing to the large number of hardware enhancements between our internal prototype version and the commercially available G.007, the lads in the coding pits are still beavering away, with the open source publication date set for early May, 2008.