Model code repository for the second generation prostate model
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ExperimentDesign
src
PCC_ExperimentDesignInfo.xls
README.md

README.md

Prostate Cancer Model Code

#####author: kvr28@cornell.edu (Katharine Rogers) #####location: Varnerlab, Cornell University #####version: 1.0

Background

The model equations describe the signal transduction in a prostate cell due to different inputs (i.e. DHT, EGF). Different cell types (LNCaP C33, C51, and C81) are modeled. The model was adapted from our previous prostate model:

Tasseff R, Nayak S, Salim S, Kaushik P, Rizvi N, Varner JD (2010) Analysis of the Molecular Networks in Androgen Dependent and Independent Prostate Cancer Revealed Fragile and Robust Subsystems. PLoS ONE 5(1): e8864. doi:10.1371/journal.pone.0008864

and newer literature. The updated model equations and findings are described in the publication:

Rogers K, Wayman J, Tasseff R, Gee C, DeLisa M and J. Varner (2016) Modeling and Analysis of Hormone and Mitogenic Signal Integration in Prostate Cancer. bioRxiv 058552; doi: http://dx.doi.org/10.1101/058552

Instructions

How do we download and use the model code? Click the download ZIP button on the lower right hand of this page. A zip archive containing the model code will automatically download to your computer.

You can execute the model code using Octave, an open source clone of MATLAB. Octave is free, and available for Windows, Linux and MaxOSX. Precompiled Octave binaries can also be downloaded from Octave Forge.

In addition, you also must download and build the SUNDIALS library to solve the model equations. SUNDIALS is available for Linux and Windows, and can easily be built on MacOSX from source or installed using the Homebrew package manager.

Before running the code for the first time: Go to the src directory and issue the following command in the terminal:

sh BuildModel.sh

This will build the mass balances (encoded in MassBalances.c) and link against the SUNDIALS library.

How do we execute the simulation code and what gets returned? The model code is executed from the octave command prompt using the RunExperiment.m script. RunExperiment takes your experiment and parameter number inputs and solves the model equations. RunExperiment will output a graph of concentraion of the species given as the input vs time. The experiments run from 1 to 14 and parameter member numbers from 1 to 5000. The experiment stimulus options can be found in PCC_ExperimentDesignInfo.xls. The model species are given in DataFile.m and run from 1 to 780.

The solution of the model equations also gets returned to the octave workspace. The simulation time vector is held in the variable TSIM. TSIM is a 1 x T row vector, where T is the number of time steps. The model concentrations are held in the variable XALL. XALL is a 780 x T array, where the rows are the model species and the columns are the time values. The model species are given in DataFile.m.

The model time scale is in hours while the concentrations are in arbitrary units.