Software

ChemChains: Simulation and Analysis Suite for Boolean models

ChemChains is a logical network simulation and analysis suite. The driving force behind the development of this tool was to be able to study and visualize the complex dynamics of biological signal transduction networks. While many research groups tend to focus on continuous models, our group took a different approach by using Boolean modeling technique as an alternative. Utilizing this approach allows us to focus on the dynamics of the network without having to deal with a sheer number parameters that are necessary when working with continuous models. The most prominent feature of ChemChains is that it allows users to interact with the model in a continuous manner, as they do in the laboratory experiments (e.g., users have the ability to set inputs to a percentage ON, as opposed to only 0 or 1). This allows bench biologiest to utilize ChemChains as a complimantary tool to for their wet lab experiments.

To download ChemChains, visit the project website.

Interview Truth Table Generator for Boolean models

Interview Truth Table Generator is a web-based tools aimed for laboratory biologists to create Boolean models of various biological structures (e.g., signal transduction networks, gene regulatory networks, etc.) in a USER- and MATH-FRIENDLY manner.

Interview Truth Table Generator is freely available here.