EasyModel: a user-friendly GUI to build and analyze mathematical models of biological systems in Mathematica

2018 edition

Jordi Bartolome Tomas

There is a decades old tradition of using modeling and simulation to understand the dynamic behavior of biological networks from a systemic perspective. The use of these methods has been steadily growing through the years, and hundreds of software packages that facilitate their use have been developed. These packages fall within a wide range of user-friendliness that goes from “expert-only”, with full functional flexibility, to fully user-friendly, often at the cost of quite limited package functionality.

This project aims at providing a user-friendly web application, tentatively named EasyModel, which is connected to the powerful Mathematica calculus environment, thus encouraging non-expert users to use this powerful language through an easy-to-use User Interface. With this web application, inexpert users are able to design, simulate, analyze, and graphically represent the dynamic behavior of their own biological network models in easy steps.

Furthermore, expert users can download the generated Mathematica code with their models, which they can further tinker with to perform additional individually-taylored analysis, taking advantage of the vast array of mathematical functionality that Mathematica provides.