Overview

The Mass-Action Stoichiometric Simulation (MASS) toolbox is a modeling software package that focuses on the construction and analysis of kinetic and constraint-based models of biochemical reactions systems. It has been developed in the systems biology group of Bernhard Palsson at the University of California, San Diego.

Installation

You can download the toolbox here. Download the binary package (MASS-Toolbox-vX.X.X, not the source distribution) and unzip the archive. Open the included installer notebook (Installer.nb) and execute the installation code.

If you don't have access to Mathematica, but still would like to try out the toolbox, you can obtain a 30 day unlimited trial version here.

First steps

The downloaded package contains a tutorial notebook that gives a broad overview over the most important functionality. Furthermore, the Mathematica documentation center provides access to documentation of most of the functions (which is accessible via the mouse context menu).

License

All code is licensed under the 3-clause BSD license (see statement below). The only exception is the AutomaticUnits folder that contains a slightly modified version of the Automatic Units package developed by Jon McLoone. Written permission to include and modify the package has been obtained from Jon (see correspondence).

License statement

Copyright (c) 2013, The Regents of the University of California All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• Neither the name of the University of California, San Diego (UCSD) nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.