BioUML

BioUML is an open-source, modular software platform designed for modeling and simulation in systems biology and related fields. It supports the creation, analysis, and exchange of biological models using standardized formats like SBML (Systems Biology Markup Language) and CellML. The platform aims to provide a comprehensive environment for researchers to develop and share their models, perform simulations, and visualize results.

Key features of BioUML include:

• Model Editing and Construction: BioUML offers tools for visually constructing and editing biological models. It supports various modeling formalisms commonly used in systems biology, such as ordinary differential equations (ODEs), stochastic models, and Petri nets.

• Simulation and Analysis: The platform provides simulation engines for analyzing model behavior under different conditions. Users can perform simulations, parameter fitting, and sensitivity analysis to gain insights into the dynamics of biological systems.

• Model Management and Exchange: BioUML allows users to manage their models in a structured manner and exchange them with other researchers using standardized formats. It supports importing and exporting models in SBML and CellML, facilitating collaboration and model reuse.

• Visualization: BioUML offers a range of visualization tools for exploring model structure and simulation results. Users can create diagrams, plots, and animations to visualize complex biological processes.

• Modular Architecture: The platform's modular architecture allows for the integration of new tools and functionalities. This enables users to extend BioUML with custom algorithms, analysis methods, and visualization techniques.

BioUML is used by researchers in various areas of systems biology, including metabolic modeling, signaling pathway analysis, and gene regulatory network analysis. Its open-source nature and modular design make it a valuable tool for advancing research in these fields. The project is actively developed and maintained by a community of researchers and developers.