DigiLab - The Digital Cellular Laboratory in MATLAB
=========
The Digital Cellular Laboratory in MATLAB is a MATLAB package that is designed to easily model large biochemical networks with complex rate equations. It achieves this by allowing modularisation of biochemical networks and abstracting away any modelling component that is more complex that designing the network connections and state of the network (i.e. parameter and initial condition selection). However, the deeper mathematics can be edited by changing the underlying default rate equations used by the package.
To use this package, either download the package, unzip the contents into any folder. Then add all contents of the folder into the MATLAB search path. Alternately you can create a fork of the repository (following this guide ), and then adding the path of your local fork to the MATLAB search path. The functions within the package should then work.
The basic usage steps are:
- modelName = mkModel('filename') - this creates a barebones sigMat model to build from.
- [t,Y] = findTC(modelName,t) - this simulates the model name.
- posterior = MCMC(objFun,pt0,bnd) - this performs parameter fitting on the objective function objFun.
Type '>> help [function]' for more information about usage of these functions.
You can find a more comprehensive walkthrough of this package in the documentation for this package in documentation.pdf
This work is copyright. Apart from any use permitted under the Copyright Act 1968, no part may be reproduced by any process, nor may any other exclusive right be exercised, without the permission of Martin Wong, Sydney University, 2016.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at our option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.