Installation Instructions for PMR2

If you are only interested in interacting with an instance of PMR2, such as the CellML Model Repository, all you need is Mercurial. The download page has a large selection of binary packages, please download the one suitable for your operating system. Windows users may be more interested in TortoiseHg, a Windows shell extension that provides a graphical frontend to Mercurial (download page).

While it is possible to install the actual PMR2 software onto your system, please note that the instructions below are for reference only, as PMR2 is still under development (currently at v0.5). At this moment only Linux systems are supported, however the following should work on other *nix based systems (untested). Also, some knowledge of Plone administration is assumed. In future versions we hope to greatly simplify the installation process.

If all you are interested in is just the installation process, just download this zip file and extract it to a directory.

Alternatively, if you are interested in the latest development version, you can use git to clone the repository like so:

$ git clone git://github.com/PMR2/pmr2.buildout.git

Your system will need to provide the following dependencies (package names are from Ubuntu 10.04 LTS; your distribution may use different names):

• build-essential (i.e. C, C++ compiler, make)
• libxml2-dev
• libxslt1-dev
• python2.6
• python2.6-dev
• python-setuptools
• omniidl4 (needed to generate CellML API headers; might be in package omniORB on some systems)

If you are building the latest development packages, you will also need:

• cmake (needed to generate CellML API build scripts; must be version 2.8 and above)
• libgsl0-dev (needed by the CellML API simulation which is enabled in the development buildout; more info to come later as to how to make this requirement optional).

After have acquired the PMR2 buildout, you may now:

$ cd pmr2.buildout                  # this is the $INSTANCE_HOME directory
$ python2.6 bootstrap.py            # yes, Python 2.6 is required.
$ bin/buildout                      # optional: add -vvv for verbose output.

If you had used git to clone the development repository, buildout will use git to clone the PMR2 development packages into $INSTANCE_HOME/src.

Buildout will now download and build the Zope/Plone system and related dependencies, including PMR2 and all related modules (such as support for CellML) which is specified in the buildout.cfg file. This will take about fifteen to thirty minutes depending on the performance of the machine it is running on.

If the process completed without errors, you may use paster to start the Plone instance:

$ bin/zeoserver-testing start
$ bin/paster-testing serve paster_testing.ini

If paster successfully started, you will see something like:

Starting server in PID ....
serving on 0.0.0.0:8380 view at http://127.0.0.1:8380

You may now point your browser to http://localhost:8380/ and follow the on screen instruction to set up an initial Plone site. When the browser shows an authentication prompt, you may try admin/admin if the user/password combination in the instance-settings section of buildout.cfg had not been changed.

Once the default Plone site is added, you can continue the process by selecting the 'Site Setup' option by selecting the current user name (admin).

In the Site Setup page, select Add-on Products.

On the Add-on Products page, you will see a list of products available for install. Check 'Physiome Model Repository 2', and select 'Install'.

Once PMR2 is installed, you may select PMR2 Core Configuration under Add-on Product Configuration on the menu on the left side.

You may review the settings within there, but for now leave them unchanged.

Select 'Apply and Create Objects'.  The workspace and exposure containers will be created at their respective locations.

Go back to the home page.  You should see two new tabs, 'workspace' and 'exposure' respectively. You can now go into 'workspace' and select 'Add new...' then 'PMR2 Workspace'.  From that screen you can create a new workspace.

Once you create a new workspace, you can view the sharing tab.  If you have other users created you can grant them permissions to push to the workspace. As admin you should be able to push changes in without issues from an existing Mercurial repository.