CompuCell3D - open-source, allows researchers to create detailed models of cells and tissues and simulate their behaviors in 2D or 3D environments.
BioNetGen - modeling and simulation of biochemical reaction networks
Virtual Cell - modeling and simulating biological systems at the cellular level. Visual interface for constructing and simulating computational models of cellular processes, such as signal transduction, gene regulation, and cell signaling
COPASI (Complex Pathway Simulator) - simulation and analysis of biochemical networks. GUI for building and simulating models of cellular processes and offers various analysis features, including parameter estimation, sensitivity analysis, and optimization.
NetLogo - agent-based modeling platform that allows for simulating and studying complex systems, including cellular processes. Simple programming language and a user-friendly interface
Amber, free to academis. Charges $25,000 for pharma companies.
Alphafold - can predict structure of protein from sequence from aminoacic sequence. There are 20 aminoacids. Determines shape of molecule. But, can be amended for
CellOS in matlab
Symbiology is add on to Matlab.
CellML (like XML) and SBML (Systems Biology Markup Language)