Introduction
ReCSiP is an FPGA-Based, ultra high-throughput biochemical pathway simulator.
Project Goal
ReCSiP's goal is to provide a desktop, accelerated biochemical simulation environment to replace PC/WS clusters. By replacing PC/WS clusters with FPGAs, reduction of space and cost will be possible. This means biologists will be enabled to explore the large parameter space of their interested biochemical systems, on their own desktop, but not on existing shared high-performance systems such as PC/WS clusters or vector machines.
Where We Are
Research for both of ODE-based and stochastic simulator is going on. Currently, the explicit ODE-based simulator is our main task, but project for stochastic version is also running.
Basic mechanism of ODE-based version is already fixed, and we have already proven that FPGA can achieve about 50 to 100-fold speedup compared to modern microprocessors. We're now developing a simulation "system" which has software interfaces to modeling and analysis. This will be the first challenge in the world, to utilize FPGAs in mathematical modeling and simulation of biochemical systems.
On the other hand, some other groups are developing stochastic biochemical simulators on FPGAs. However, the systems (including ours) cannot simulate large biochemical networks because they have no scalability to the target systems. We're now planning to develop a scalable stochastic simulator on FPGAs (This will appear in late 2005 or early 2006).