Installation

Below is a short guide on how to obtain and build the BioSim toolkit. Head over to the tutorial for a walkthrough of how to use BioSim to create a simulation.

Getting the source

git clone [email protected]:biotracking/biosim2.git

Prerequisites

Most of the prerequisites come from MASON itself, and we've bundled the bare essentials as jar files in the lib/ directory. You can either use these jar files, or download the most recent versions from their respective websites. See the MASON project webpage for a full list of dependencies and where to obtain them.

Building

BioSim2 is (for the most part) a pure java library, and it should work for your favorite build system - whatever that may be (eclipse, ant, etc.) We've also included a set of makefiles that should work if you have make and can build java programs from the command line. Here's an example of setting the classpath and building the entire library on a Mac from the terminal (requires Xcode command line tools "Xcode > Preference > Download > Command Line Tools")

Last login: Wed Jan  8 17:29:46 on ttys002
lawn-128-61-126-35:~ hroly$ cd repos/biosim2/
lawn-128-61-126-35:biosim2 hroly$ export CLASSPATH+=:`pwd`
lawn-128-61-126-35:biosim2 hroly$ make

If you follow the build messages you can see that as long as you have your classpath set correctly everything should "just work".

After you've got a working install, head on over to the tutorial for a quick example of how to write a simulation.