Task 3.1 Development of a web service for stochastic simulations of biochemical reacting systems

As part of this research we have designed and developed a pilot web service resource for parallel stochastic simulation of biological systems over the Internet. The pilot web service allows remote authorized users to perform efficient stochastic simulations of biological systems, which are supplied in standard SBML (Systems Biology Markup Language) file format, by using the application-specific back-end we have developed (the SSA SoCs developed in WP1) without having to worry about how to configure the back-end for optimal performance of their specific simulation job. In this way we achieve great ease of use, since people who have no knowledge of computer usage can supply requests.

To achieve this level of flexibility and transparency we designed and implemented the pilot web service using the web programming language PHP, the development framework Symfony2, and an array of different technologies, libraries and development tools. With the help of these we implemented efficiently three main functionalities related to: a) users authentication and authorization of the system to ensure that the service can be accessed only by registered users with an account in the system, b) entry, storage and management of biomodels uploaded as SBML files, and c) introduction and management of the flow of stochastic simulation jobs in the system. The latter depends on the parameters that the user provides in a form, the stochastic simulation algorithm (FRM / NRM) selected and the mode of parallel operation (SSIP / MSIP). These choices directly influence the automatic selection of the most appropriate SoC instance (from a library of presynthesized SoC instances) that will eventually perform the stochastic simulation run(s) of the user job in the FPGA board (system back-end). When a simulation job completes the user is notified and can download the results. The IP cores used to synthesize the SoC instances in the library have been designed based on the work performed in WP1.

Such a web server did not exist to date and is an important novelty and a very useful service for the scientific community of systems biology as it allows very efficient and accelerated stochastic simulations of biomodels without the user having knowledge of the specific high performance backend. As shown in Task 1.3, the SoCs for stochastic simulation that we have designed and implemented on FPGA devices perform simulations of biological systems much more efficiently than any available simulation software (e.g. COPASI). The pilot web service created was successfully tested by the project team with a variety of biomodels developed and used in Tasks 1.3 and 2.2.

Access to the web service is in the initial phase of use for registered users through a temporarily generated domain name: webstoch.ddns.net while in the future we intend to proceed with registration and use of a permanent domain name like stochsocs.org.

Deliverables (technical report)

D3.1 A web server for processing biomodel simulation queries submitted over the internet