BioSANS: A software package for symbolic and numeric biological simulation

Abstract

Modeling biochemical systems can provide insights into behaviors that are difficult to observe or understand. It requires software, programming, and understanding of the system to build a model and study it. Softwares exist for systems biology modeling, but most support only certain types of modeling tasks. Desirable features including ease in preparing input, symbolic or analytical computation, parameter estimation, graphical user interface, and systems biology markup language (SBML) support are not seen concurrently in one software package. In this study, we developed a python-based software that supports these features, with both deterministic and stochastic propagations. The software can be used by graphical user interface, command line, or as a python import. We also developed a semi-programmable and intuitively easy topology input method for the biochemical reactions. We tested the software with semantic and stochastic SBML test cases. Tests on symbolic solution and parameter estimation were also included. The software we developed is reliable, well performing, convenient to use, and compliant with most of the SBML tests. So far it is the only systems biology software that supports symbolic, deterministic, and stochastic modeling in one package that also features parameter estimation and SBML support. This work offers a comprehensive set of tools and allows for better availability and accessibility for studying kinetics and dynamics in biochemical systems.