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Citating Data2Dynamics
Clemens Kreutz edited this page Jan 19, 2017
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Cite:
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Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Raue A., et al. Bioinformatics, 31(21), 3558-3560, 2015.
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Lessons Learned from Quantitative Dynamical Modeling in Systems Biology. Raue A., et al. PLOS ONE, 8(9), e74335, 2013.
- 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?