Running the Pathway Logic Assistant (PLA)

We offer two different ways of running PLA. One involves a launcher application that is available as a command line script and as an application with a graphical user interface. The other option is to customize specific launch files and run iop from the command line. We suggest the first option for novice users.

Pathway Logic models

PLA operates on a Pathway Logic model that has to be present before running the software. We provide sample models on the Download page but users can modify these or create their own.

A minimum Pathway Logic model contains the following 5 files:

Optionally, a file "input.txt" is used to store often used commands and will be displayed in the IOP command interface called the "GUI.Editor". Two startup files must be present when running PLA: "startup.txt" and "load-pl.maude". When using the command line launcher (i.e. the script called "pla"), these files get created on-the-fly. If you want to customize these files, you would run "iop" directly, as described in more detail below.

When you save a knowledge base from a model for future re-use (using, for example, options of the launcher programs) then two more files are created: "<name>-tkb.txt" and "<name>-graph.txt" denote the knowledge base with the given <name>.

The command line launcher

In the directory where PLA was installed, you find a Perl script "pla". We advise to put the installation location into your PATH environment variable for easier access to the launch script as described here.

To run PLA on a model, change into the model directory (created from the downloaded and extracted .zip file) and call "pla". The manual page for "pla" is available when calling "pla -h". For example, execute the following commands to run PLA with the IOP window. 

  $> cd <model directory>
  $> pla -i

Running a customized PLA from the command line

This option is intended for expert users that want to customize their PLA using the files "startup.txt", "load-pl.maude" and "input.txt".

Change into one of your Pathway Logic model directories. Make sure that the two files "startup.txt" and "load-pl.maude" exist in this directory and that the path information in these short text files matches the location where you installed PLA. If in doubt, you may use the launcher script above to generate these two files from scratch using the following command 

  $> pla -g

Execute the shell command "iop". To suppress the InterOperability Platform console window called "GUI.Editor" use the command "iop -n".