/biosimulations-rulehub

Repository of rule-based models implemented with the BioNetGen model language (BNGL) and command-line program for publishing RuleHub to BioSimulations

Primary LanguagePythonMIT LicenseMIT

All Contributors

Published models

Model name Description
Dolan2015 Stochastic model of DNA damage repair by non-homologous end joining and of gamma irradiation-induced cellular senescence.
Faeder2003 Model of early events in FcεRI signaling, including Lyn recruitment and Syk activation.
Mitra2019 Suite of benchmark parameter fitting problems for PyBioNetFit
Thomas2016 Parameter fitting problems published with BioNetFit v1.0
Salazar-Cavazos2019 Model of EGFR signaling fit to Single Molecule Pull-down (SiMPull) data

Contributed models

Model name Description
Hlavacek2018Egg Benchmark parameter fitting problem consisting of a simple egg-shaped curve.
Hlavacek2018Elephant Benchmark parameter fitting problem consisting of an elephant-shaped curve.
Mitra2019Likelihood Model of IgE-mediated degranulation configured to demonstrate performing Bayesian uncertainty quantification with qualitative data in PyBioNetFit.
Mitra2019Rab Model of Rab5 and Rab7 activation

For instructions on adding new models to the repo, see AddingModels.md.

Development team

This package was developed by the contributors listed here.