Quasi Steady State Petri Net (QSSPN)

Getting started tutorial

MacOSX users may download self contained ZIP archive to quickly run QSSPN simulation of our model of bile acid homeostasis in human hepatocytes (Bioinformatics, accepted). To run simulation follow the steps:
  1. Download the ZIP file by clicking Download link.
  2. Click on the ZIP archive to uncompress it and enter uncompressed directory in Finder.
  3. Click RUN to start simulation, which will take about 10 minutes.
  4. Open output.xls file in Excel.
  5. Use "Line plots" to quickly plot columns of the output which contain simulation trajectories for Petri Net nodes.

Download

To modify our model and run your own simulation install Snoopy Petri Net editor. You can then open HepatocyteQSSPN.spept file and modify the network. The QSSPN specific parameters are in the Comment fields of places and transitions and can be modified with Snoopy. The control file can be opened by clicking on HepatocyteQSSPN.ctrl.txt and simulation parameters can be modified. When new simulation setup is ready, the user should delete previous results by clicking "clean". Subsequently, new simulation can be executed by pressing RUN. The RUN script will execute spept2qsspn and qsspn commands. The detailed description of these commands and file formats can be found in Manual.pdf file in software distribution.

Linux and other Unix-based system users may prefer to download software distribution and follow software manual. They may however quickly adapt this tutorial by replacing qsspn file with a binary compiled according to instructions in software distribution.