Page Index - Data2Dynamics/d2d GitHub Wiki

132 page(s) in this GitHub Wiki:

• Home
• Data2Dynamics Software
• General Information
• Basic Introduction
• Advanced Functionalities
• Statistical Methods
• Computational methods
• Other Advanced Functionalities
• Application Examples
• Copyright notice
• Adapting the PLE Settings
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• Advanced events and pre equilibration
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• Bachmann_MSB2011
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• Becker_Science2010
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• Beer_MolBioSyst2014
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• Boehm_JProteomeRes2014
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• Citating Data2Dynamics
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• CitingProjects
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• CodeArchitecture
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• Computation of integration based prediction bands
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• Copyright
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• CV_TOO_MUCH_WORK: Possible reasons and solutions
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• Debugging residuals
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• Discrete Sampling of True Prediction Bands
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• Distributed Computing
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• Estimating Prediction Uncertainty
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• Example models in D2D
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• Experimental Design
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• Features
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• First steps
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• How do I reset the solver upon a step input
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• How to change the horizontal plotting limits (xlim, time interval, time range)
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• How to check and improve optimization
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• How to implement a bolus injection
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• How to implement a moment ODE model
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• How to implement washing and bolus injection
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• How to run PLE calculations on a Cluster
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• How to set up steady state constraints
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• Input estimation
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• Installation
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• Integration tolerances and modification possibilities
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• Introduction Video
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• L1 regularization
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• Lucarelli_TGFb_2017
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• MCMC Methods and Functions
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• Meaning of ar.config.fiterrors
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• Merkle_PCB2016
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• Model selection with PEtab Select
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• Modeling time delays using the linear chain trick
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• Objective function, likelhood and chi square in the d2d framework
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• Optimization algorithms available in the d2d framework
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• Parallelization
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• Parallelization of multi start optimization
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• Partial differential equations
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• Plotting options and the meaning of ar.config.ploterrors
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• Priors in the d2d framework
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• Raia_CancerResearch2011
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• RTF
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• Setting up models
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• Setup, compilation, configuration and transfer between systems
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• Solving issues with Ceres
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• Spline Example: A Modulating Input Function
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• Structural Identifiability and Observability Analysis for Nonlinear Dynamic Models
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• Support for PEtab
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• Swameye_PNAS2003
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• Uncertainty analysis
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• Using an older version revision of D2D
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• Using the bwCluster
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• Utilizing Example Collection
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• What are the most important fields of the variable ar?
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• What are the most important functions in d2d?
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