PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology

[摘要] A Python package called PySUNDIALS has been developed which providesan interface to the suite of nonlinear di erential/algebraic equation solvers(SUNDIALS) using ctypes as a foreign function interface (FFI). SUNDIALS isa C implementation of a set of modern algorithms for integrating and solvingvarious forms of the initial value problem (IVP). Additionally, arbitrary root nding capabilities, time dependent sensitivity analysis, and the solution ofdi erential and algebraic systems are available in the various modules providedby SUNDIALS. A signi cant focus of the project was to ensure the pythonpackage conforms to Python language standards and syntactic expectations.Multiple examples of the SUNDIALS modules (CVODE, CVODES, IDA andKINSOL) are presented comparing PySUNDIALS to C SUNDIALS (for veri cationof correctness), and comparing PySUNDIALS to various other comparablesoftware packages. The examples presented also provide benchmark comparisonsfor speed, and code length. Speci c uses of the features of the SUNDIALSpackage are illustrated, including the modelling of discontinuous events usingrootnding, time dependent sensitivity analysis of oscillatory systems, andthe modelling of equilibrium blocks using a complete set of implicit di erentialand algebraic equations.PySUNDIALS is available as open source software for download. It is beingintegrated into the systems biology software PySCeS as an optional solver set,on an ongoing basis. A brief discussion of potential methods of optimizationand the continuation of the project to wrap the parallel processing modulesof SUNDIALS is presented.

[发布机构] Stellenbosch University