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Beer_MolBioSyst2014
Max Schelker edited this page Aug 29, 2016
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Reference: Beer et al. Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange. Mol. Biosyst. 10: 1709–18
Folder: /Examples/Beer_MolBiosyst2014
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Facts: The model contains 27132 data points, 72 free parameters and 19 experimental conditions.
Figure: Only an exemplary data set for synT1 is shown.
- Installation and system requirements
- Setting up models
- First steps
- Advanced events and pre-equilibration
- Computation of integration-based prediction bands
- How is the architecture of the code and the most important commands?
- What are the most important fields of the global variable ar?
- What are the most important functions?
- Optimization algorithms available in the d2d-framework
- Objective function, likelhood and chi-square in the d2d framework
- How to set up priors?
- How to set up steady state constraints?
- How do I restart the solver upon a step input?
- How to deal with integrator tolerances?
- How to implement a bolus injection?
- How to implement washing and an injection?
- How to implement a moment ODE model?
- How to run PLE calculations on a Cluster?