Biochemical reactions that take place inside cells can be modeled and approximated in a practical way through differential equations. In silico, it is possible to study biological process behaviors such as the difference in gene expression levels of a protein throughout a homogenous cell population. Computational methods are used to model, simulate, and infer such behavior. The implementation of this kind of methods requires having good knowledge of the biology involved and the algorithms to approximate its behavior. In this paper, we propose a tool for modeling gene expression of cell populations. Firstly, fundamental aspects of the biological system paradigm are gathered to present a graphical user interface that integrates some algorithms relevant to introduce beginners to the field. The interface could help students to obtain insights about basic topics on biological system definition, simulating from several variability sources and parameter identification. Free open-source software is used to ensure accessibility to the tool and its potential modification, enhancement, or usage of the implemented algorithms.