CGSera

CGSera is a modular software framework used in computational genetics and serology research. It combines gene circuit design tools, dynamic simulation engines, and serology assay models to enable in silico experiments. The platform targets researchers, educators, and developers who need to prototype synthetic biology constructs, evaluate diagnostic workflows, and visualize complex interactions between genetic circuits and serum-based readouts.

The project originated from work at the CGSera Institute and later expanded through community contributions. It emphasizes reproducibility and interoperability, adopting standard data formats and a scriptable API. The framework has been used in academic courses and by industry collaborators for rapid prototyping and method validation.

Core components include a gene circuit designer with qualitative and quantitative modeling, library management for promoters and repressors, stochastic and deterministic simulators, and a serology module that models antigen-antibody interactions, ELISA-like readouts, and cross-reactivity. It provides data visualization dashboards and an API for Python and R.

CGSera supports reproducible research and educational use, enabling shared notebooks and workflows. Users should be aware that simulations are abstractions and depend on parameter estimates; real-world validation remains necessary. The project is distributed under an open-source license and maintained by a community of contributors. It's compatible with common bioinformatics formats and can interoperate with other simulation tools.