Thomas2016

Name

Thomas2016

Reference

Thomas BR, Chylek LA, Colvin J, Sirimulla S, Clayton AHA, Hlavacek WS, Posner RG (2016) BioNetFit: A Fitting Tool Compatible with BioNetGen, NFsim and Distributed Computing Environments. Bioinformatics 32:798–800.

Description

Benchmark fitting problems published in conjunction with BioNetFit v1.0

Files

• example1_fit.bngl - A model of EGFR signaling, adapted from Kozer et al. (2013), simulated with ODEs.
• example1_BNFfiles - Files needed to fit example1 in BioNetFit v1.0.1
• example2_fit.bngl - A model of EGFR signaling, adapted from Kozer et al. (2013), simulated with NFsim.
• example2_BNFfiles - Files needed to fit example2 in BioNetFit v1.0.1
• example3_fit.bngl - A model of trivalent ligand, bivalent receptor, adapted from Monine et al. (2010).
• example3_BNFfiles - Files needed to fit example3 in BioNetFit v1.0.1
• example4_fit.bngl - A model of TCR signaling
• example4_BNFfiles - Files needed to fit example4 in BioNetFit v1.0.1
• example5_fit.bngl - A small, synthetic receptor model, simulated with ODEs
• example5_groundtruth.bngl - The ground truth parameter values used to generate synthetic data for this example.
• example5_BNFfiles - Files needed to fit example5 in BioNetFit v1.0.1
• example6_fit.bngl - A small, synthetic receptor model, simulated with NFsim (missing file)
• example6_groundtruth.bngl - The ground truth parameter values used to generate synthetic data for this example.
• example6_BNFfiles - Files needed to fit example6 in BioNetFit v1.0.1

Notes

These benchmark fitting problems can be run with BioNetFit v1.0.1. BioNetFit files are provided as they appear in the BioNetFit download; to run on your computer, it may be necessary to edit the file paths and settings. For more information, refer to the BioNetFit documentation.