Simulation of electrochemical and stochastic systems using Just in Time compiled declarative languages

Computational biology is a relatively new discipline which sits at the intersection of computer science, physics, chemistry and biology. One of the primary goals of computational biology is to develop predictive algorithmic and mathematical models of biological processes.;A model description in a declarative language such as SBML express the structure of the model without having the specify the explicit control flow. Declarative descriptions have numerous advantages over lower level programming languages. The SBML language is specifically oriented towards describing biochemical systems: one simply has to list reactants and the relationships, as opposed to lower level procedural languages, where one would have to explicitly specify the computational details. Models may also be readily exchanged and reused in a variety of applications.;A number of interpreters exist for simulating SBML models, but to our knowledge, there are no Just In Time (JIT) compilers. Compiled languages often offer hundred fold performance improvements over interpreters. As simulations of cellular systems become more complex, particularly in multicellular models, the need for reusable and high performance simulation engines is becoming clear.;This thesis will describe the SBML JIT compiler, simulation and analysis library that was developed. The library has been designed to be extensible and offers superior performance to standard desktop simulators and supports a variety of analyses including time course simulation and a wide range of analysis features such as steady state and metabolic control analysis.;The library was used to develop a physically based model of the first component of the mitochondrial electron transport chain. Mitochondria play a essential role in cellular biology, and there exists a need for a physically accurate and interchangeable models of mitochondrial processes. Additionally, to demonstrate the stochastic capabilities of the library, a stochastic bistable chemical system was modeled and analyzed.