Welcome to Atlas v1.0 documentation!

Atlas is a small software developed to use simple text files that encode biological networks and write Rule-Based Models (RBMs). Atlas writes rules and others model components for the PySB python package PySB, PMID 23423320. The RBMs could be simulated within PySB with NFsim, PMID 26556387 (within the BioNetGen2 software, PMID 27402907), KaSim (KaSim, PMID 29950016). Models could be exported to text files in BioNetGen (BioNetGenLanguage) or kappa language (Kappa) for further calibration (BioNetFit, PMID 26556387 or pleione, PMID 31641245) and analysis (sterope for parameter sensibility and alcyone for parameter uncertainty).

Indices and tables