U of Cambridge
Many biological models consider biochemical reaction networks. However, as these grow in size they also produce large amount of equations which needs to be transcribed into computer code. This is a monotonous task of little fun and which is prone to generating bugs (and finding these bugs is even less entertaining). Fortunately we have been able to automate it. By using Julia’s capability of meta programming we have created a DSL (domain-specific language) allowing its user to input their reaction network as chemical equations (as opposed to mathematical ones). This format both look aesthetically pleasing and efficiently handles features such as coupled noise. The DSL generates an IR (intermediate representation) which have been constructed with Julia’s high-performance DifferentialEquations.jl library in mind. It can be used to create ODE, SDE and JumpProblems, all of which can be solved using DifferentialEquations’ solvers. Taken in total this can significantly cut the amount of code required, as well as making what remains much prettier.
Torkel is a mathematician and first year Ph.D. student at the University of Cambridge. With the use of mathematical models he investigates how B. Subtilis responds to various forms of stress by producing alternative sigma factors.
