Features
The ShAPE-DALSP software package provides numerical methods for the simulation of division-, age- and label-structured Population models. Furthermore, it facilitates the inference of model parameters from CFSE time-series data. Its key features are
- automatic compilation of symbolically defined DALSP models for the assessment of competing model hypotheses;
- efficient numerical integration by exploiting a decomposition of the solutions;
- multi-start local optimization using forward sensitivity equations for gradient evaluation;
- identifiability and uncertainty analysis using profile likelihoods and Markov chain Monte Carlo methods; and
- parallelization using the MATLAB Parallel Computing Toolbox and Distributed Computing Server.
For the parameter estimation we exploit the Parameter EStimation Toolbox (PESTO) developed in the Institute of Computational Biology of the Helmholtz Zentrum München.
Requirements
ShAPE-DALSP is a software package for MATLAB. To exploit its functionality the Optimization Toolbox and the Symbolic Math Toolbox are required. For high-performance computing, the Parallel Computing Toolbox and Distributed Computing Server is required.
References
If you use this software in a publication, please cite one of the following manuscripts:
- J. Hasenauer, D. Schittler and F. Allgöwer. Analysis and simulation of division- and label-structured population models: A new tool to analyze proliferation assays. Bulletin of Mathematical Biology, 74(11):2692-2732, 2012.
- P. Metzger, J. Hasenauer and F. Allgöwer. Modeling and analysis of division-, age-, and label-structured cell populations. In Proceedings of 9th International Workshop on Computational Systems Biology, 55-58, 2012.
Support or Contact
Jan Hasenauer - jan.hasenauer@helmholtz-muenchen.de