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Niklas Neubrand edited this page Jan 17, 2025
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This section contains articles which facilitate getting started with D2D.
- Video illustrating fitting
- Installation and system requirements
- First steps
- Setting up models
- 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?
- Uncertainty analysis
This section contains a list of many advanced functionalities implemented in D2D.
- Estimating Prediction Uncertainty
- Computation of integration-based prediction bands
- Discrete Sampling of True Prediction Bands
- L1 regularization
- Input estimation
- MCMC methods and functions
- Retarded Transient Function
- Moment ODE model
- Priors
- Objective function, likelihood and chi-square in the D2D framework
- Time delay modelling using the linear chain trick
- Structural identifiability and observability analysis for nonlinear dynamic models
- Experimental Design
- Adapting the PLE Settings
- Resetting the solver upon step input
- Integrator Tolerances
- Meaning of ar.config.fiterrors?
- Optimization algorithms available in the D2D-framework
- PLE calculations on a Cluster?
- Parallelization
- Parallelization of multi start optimization
- bwCluster Calculations
- Optimization Guidelines
- Advanced events and pre-equilibration
- Distributed computing
- Steady state constraints
- Bolus injection
- Bolus injection and washing
- Partial differential equations
- PEtab support
- Model selection with PEtab Select
- I get the error "Error C2011 'timespec': 'struct' type redefinition" while compiling
- Solving issues with Ceres
- Setup, compilation, configuration and transfer between systems
- Spline Example: A Modulating Input Function
- Using an older release version of D2D
- Utilizing Example Collection
- What's the meaning of ar.config.ploterrors?
This section contains some examples of models for which D2D was or can be utilized.
- Overview of application examples
- Bachmann model in more detail
- Becker model in more detail
- Beer model in more detail
- Boehm model in more detail
- Merkle model in more detail
- Lucarelli model in more detail
- Raia model in more detail
- Swameye model in more detail
Copyright © 2016 D2D development team. All rights reserved. Copyright text and third party software license information.
- 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?