The Objectives of WP3 are (technical reports) :
1) Development of a pilot web service that will allow remote users to submit biomodels for stochastic simulation
2) Preparation of information material for remote users of the service
Development of Web accessible computing platform for large biological network simulation
To the best of our knowledge, there is currently no computing resource with an FPGA based back-end that accepts as input user queries, in the form of SBML descriptions of biomodels, parses them, simulates the network stochastically for a number of repetitions, and returns results (e.g. time series of species counts). For large-scale networks, users are limited to developing their own model-specific implementations for CPUs or GPUs (programmed in C++, Cuda C, Matlab etc), a time consuming process that only expert programmers can handle. We designed and developed a pilot web-accessible easy to port and deploy computing platform which allows practitioners with just an internet connection, but no programming skills, to submit biomodels in SBML for efficient stochastic simulation. Simulation jobs are handled efficiently because the user query is parsed, analyzed and executed using the most appropriate pre-synthesized SoC implementation for the task at hand in the FPGA back-end of the platform (e.g. currently a medium size Kindex 7 Xilinx FPGA can implement SoCs with up to N=16 processors, able to handle biomodels with up to m=4K reactions, each reaction being up to 3rd order with as many as 5 products). This is the first attempt to produce a platform with an FPGA backend for the flexible yet efficient stochastic simulation of large-scale biomodels submitted as SBML files, without requiring any effort whatsoever from the end-user.
Currently the pilot resource is fully functional and accessible here and requires user registration. We encourage research groups that want to use it to provide feedback and possibly collaborate with us on systems biology research that will benefit from its use to contact us.
The Deliverables of WP3 are (technical reports):
D3.1 A web server for processing biomodel simulation queries submitted over the internet
D3.2 Information material for using the web server