Installing the Pathway Logic Assistant (PLA)

Preliminaries

The Pathway Logic Assistant (PLA) relies on several programs that must be installed to use it. Below are instructions for obtaining those programs that you don't already have. Followed by the very simple instructions for installing and running PLA. Hopefully you won't be discouraged. As PLA matures, installation will get simpler, and once you have all the auxilliaries, updates will be easy!

PLA requires Maude and the IOP Platform along with the dot graph layout utilities to be installed.

We support Linux and Mac OS X platforms (not tested on Mac Intel!) as the required programs run on these.

Maude

Documentation and papers are available at http://maude.cs.uiuc.edu

Currently you need an Alpha release as some of the features needed are not yet in the official release on the Maude website. You can get Maude Alpha releases from the alpha release site http://www.csl.sri.com/~eker/Maude/ using the following authentication:

User Name: maudeabuser
Password: bughunter

Select the Alpha86a release directories.

Download

and put them in one directory (for example ~/Maude/bin/). Make sure that maude.<platform> is executable, e.g. by using this command 
  $> chmod a+x maude.<platform>

Set the MAUDE_LIB environment variable to include the directory where you put Maude and associated files. For example, users running a csh or tcsh might add 

  setenv MAUDE_LIB ${HOME}/Maude/bin
to their .cshrc file. Users running sh or bash would use 
  export MAUDE_LIB=$HOME/Maude/bin
in their .profile or .bashrc file.

Caveat: Your maude binary needs to retain the name maude.<platform> for iop to find it. If you want to call it maude, you can define an alias, or make a symbolic link from maude to the actual binary.

The IOP Platform

You can find more information and a small collection of examples about the IOP platform on its home page.

1.) Download

Download and install the latest binary for your platform from the IOP Binaries page.

2.) Install

You can either follow the instructions to manually unzip the downloaded file or use an installer script "installer.pl" that you save to the same location.

Before you run the installer you must set your IOBINDIR environment variable to the path where you would like the binaries to go. ~/bin/IOP is a good choice. Furthermore, IOPBINDIR must be in your PATH environment variable.

Make sure that the installer script is executable. To ensure this, you may run from the command line in the directory where you downloaded items from step 1.) 

  $> chmod a+x installer.pl

Run the installer script from the command line (in the directory where you downloaded items) using this command 

  $> ./installer.pl
and follow the instructions of the installer.

To test the installation (if you use tcsh, do "rehash" first), do from the command line 

  $> which iop
which should print the location of the IOP installation.

3.) Install "dot"

For IOP to support PLA you need to have the GraphViz program dot installed. If you do not have dot already you can get dot only by downloading one of these .zip files:

Unzip and follow instructions in README.txt. You need to have X11 installed as dot relies on some X11 libraries. You can also install a proper GraphViz. For Mac OS X, see install-dot-mac.txt. Or see the GraphViz website: http://www.graphviz.org

Pathway Logic Assistant

1.) Installation of PLA

Download the file IPLA-v<number>.zip from the resources directory. In this file name, <number> denotes a version number. Create a directory ~/Maude/Lib if you don't already have one. Unzip the file in this directory, which creates a new subdirectory called "IPLA".

2.) Obtaining a model

One or models will be available in the resources directory. They can be recognized as zip files with names beginning with PL. Download a file PL-<model-id>.zip, unzip this file anywhere you like.

3.) Running PLA

To run PLA, change into one of your model folders and execute the shell command "iop". To suppress the InterOperability Platform console window called "GUI.Editor" use the following command: 

  $> iop -n

The file PL-05Aug30-guide.txt in the resources directory contains a guide for getting started with PLA in connection with the model contained in PL-05Aug30.zip in that same directory.

4.) Customizing or writing your own model

Download a model .zip file from the web page or create your own set of .maude files that constitute a valid Pathway Logic model. As a minimum, you need the following 4 files:

Crucially, with the module QQ defined in qq.maude and including the modules defined in the other files.

Make sure that you copy 2 files from the example model into your other model directories if they are not already included in the directory:

Finally, a file called "input.txt" in the model directory is used when starting PLA with a console. This file is intended for expert users and can be omitted.