Towards high-level executable specifications of heterogeneous systems with systemC-AMS: Application to a manycore PCR-CE lab on chip for DNA sequencing

The paper presents the systemC/systemC-AMS implentation of a for DNA analysis lab-on-chip that encompasses several disciplines such as analog, digital, chemical kinetic reactions, optics and embedded software. The corresponding system virtual prototype takes as input an initial DNA concentration as well as the expression of the gene as a DNA string, and is able to compare the input string to a huge database of reference samples, thus providing a way to efficiently detect mutation and pathologies. The presented model is composed of three parts: (1) DNA amplification by Polymerase Chain Reaction (PCR), (2) molecular separation by Capillary Electrophoresis (CE) and optical detection of fluorescently labeled molecules, (3) automated DNA sequencing on a digital manycore architecture running a highly multi-threaded software. The platform also digitally assists the two former AMS parts. The simulated model can be used as a simulatable specification at a very high level of abstraction and can be seen as the first refinement step towards the design of complex heterogeneous bio-compatible designs.