The Ninth q-bio Summer School - Albuquerque: Computer Lab 8

Using TinkerCell for modelling dynamical systems

Mario Castro

In this computer lab session, we will do a hands-on project using the freely available software TinkerCell. TinkerCell is a really simple software that allows to create mathematical versions of biochemical problems in minutes. Moreover, it allows to integrate deterministic or stochastic versions of the model straightforwardly, what makes it a powerful exploratory tool, suitable for a huge variety of problems. During the session, we will cover the following topics: (i) Download and installation of TinkerCell. (i) how to implement a biochemical model in TinkerCell graphically (iii) how to use the antimony module to write down a biochemical model in plain text (iv) how to integrate the ordinary differential equations corresponding to the biochemical model (v) how to integrate the stochastic dynamics of the biochemical model using the Gillespie and the tau-leap algorithms