Tutorial about the SBPOP PACKAGE

Different SBPOP PACKAGE tutorials are available. At the moment the online version of the tutotrial is limited to functionality of SBTOOLBOX2 and SBPD. A complete SBPOP tutorial is only available as classroom version, since feedback is required to improve it to a level that is self explaining and acceptable for an online self-study version. The SBTOOLBOX2 and SBPD part of the tutorial has been given numerous times on different occasions, so that can be made available online.

The tutorial material can be obtained from here: DOWNLOAD ONLINE VERSION OF TUTORIAL MATERIAL

Contents of SBPOP PACKAGE online tutorial

General introduction to the SBPOP Package
Model definition and simulation
- ODE based models
- Biochemical reaction equation based models
- Import and export of models (SBML, etc.)
- High performance computation via MEX simulation functions
- Simple simulation and analysis of models
- Commenting of models
Systems Biology relevant topics
- Model analysis
  - Steady-state analysis and stability
  - Moiety conservations and reduction
  - Parameter sensitivity analysis (steady-state & oscillating systems, MCA, local & global)
  - Localization of complex behaviors
- Definition of experiments and measurement data
  - Excel and CSV measurement representation
  - Experiment descriptions and merging with models
  - Import and export measurements and experiments
- Projects, parameter estimation, model reduction
  - Projects
  - Parameter estimation / manual tuning / parameter fit analysis / parameter identifiability analysis
  - Model reduction
  - Simulation of projects
  - Commenting of projects

Additional contents in classroom version of the SBPOP Tutorial

Pharmacometrics / Systems Pharmacology relevant topics
- Model and dosing description
  - Needed changes in SBmodels to allow for simulation of dosing scenarios
  - Simulation of dosing scenarios
- Datasets
  - Import, export, conversion
  - Analysis (plotting capabilities)
- Interface to Monolix and NONMEM
  - Creation of MLXTRAN / NONMEM Models
  - Creation and execution of MLXTRAN / NONMEM Projects
  - Import of Monolix / NONMEM results
- PopPK/PD workflow
  - Standard dataset specification
  - Data Exploration
  - Data Cleaning
  - Model building (base model, covariance model, covariate model, robustness assessment, ...)
  - PopPK Example
- Clinical trial simulations
- More complex modeling
  - PBPK
  - Antibody modeling