Systems Biology, SBML and Systems Biology Workbench

Systems biology is an interdisciplinary field that focuses on the systematic study of complex interactions within biological systems using a holistic approach, integrating computational modeling, experimental data, and network analysis to understand the behavior of entire biological systems. SBML (Systems Biology Markup Language) is an open, XML-based standard format used for representing computational models in systems biology, enabling researchers to share, reuse, and simulate models across various software tools. SBML provides a structured way to describe biochemical reaction networks, including species, reactions, compartments, and mathematical expressions. The Systems Biology Workbench (SBW) is a software framework that facilitates the integration of diverse modeling and analysis tools used in systems biology. SBW allows for seamless communication between different applications by providing a standardized interface and data exchange protocol, thereby promoting modular and interoperable software development. Together, SBML and SBW support the collaborative and reproducible modeling of biological systems, enabling researchers to simulate dynamic processes such as gene regulation, metabolic pathways, and signal transduction. These tools are pivotal for advancing predictive modeling and hypothesis generation in modern biological research.