mbytwo

mbytwo is a computational framework designed for analyzing and simulating biological systems. It is developed by researchers aiming to provide a flexible and extensible platform for molecular biology and systems biology applications. The framework allows for the modeling of complex interactions within biological networks, such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks.

The core of mbytwo is built around a modular design, enabling users to incorporate different modeling approaches and analytical tools. This flexibility supports various simulation methods, including ordinary differential equations (ODEs), stochastic simulation, and agent-based modeling, depending on the nature of the biological question being addressed. Users can define the components of their biological system, specify their interactions, and then run simulations to observe the system's behavior over time.

mbytwo also incorporates features for data integration and analysis. It facilitates the import of experimental data, such as transcriptomic or proteomic profiles, which can then be used to calibrate or validate models. The framework includes tools for parameter estimation, sensitivity analysis, and model comparison, aiding researchers in drawing meaningful conclusions from their simulations and experimental results. The project emphasizes open-source development, encouraging community contributions and fostering collaboration within the systems biology research field. Its aim is to democratize access to advanced computational tools for a wider range of biological investigations.