Biomedical Engineering Reference
In-Depth Information
can be included, by reference, into another workspace. Embedded workspaces are
intended to manage the separation of the core model from its subcomponents, and
thereby facilitate the sharing and reuse of model components independently from
the source model. As this separation enables the development of the subcomponents
to proceed independently of the main model, the version of the workspaces embed-
ded is also tracked. Changes made to a workspace which has been embedded in an-
other workspace will not affect the embedding workspace until the author explicitly
chooses to update the version to use. This gives the author the opportunity to review
the changes to the embedded workspace, and ensure that they won't adversely affect
the models in the embedding workspace. Finally, embedded workspaces enable the
import of components via relative URIs, thus promoting modular model develop-
ment.
Model exposures
In addition to the concept of a workspace as a folder, the other main feature of PMR2
is the presentation view of the model and any associated data which may be within
the workspace. As the contents of the workspace at the revision corresponding to
any changeset are immutable, one can select a single changeset and create an
ex-
posure
from it. Presently, creating an exposure leads to both the generation of the
presentation view of the contents of a workspace as at the selected revision, and to
the exposure's URL being included in the main repository category listings. Cur-
rently, a curator may annotate their assessment of the quality of the coded version of
the model using
curation stars
. PMR2 has been designed to be extensible to enable
the support of the range of presentation styles required for the different file types.
This requires a system where plug-ins can be installed with ease onto an instance of
PMR2; this system has been implemented and built on the Zope Component Archi-
tecture (Baiju, 2007), which makes use of the adapter pattern (Gamma et al., 1995)
to register and activate plugins based on their names. This system allows software
developers to construct specific plugins, to generate the presentation styles required
for any particular model type, which can be installed and enabled on an instance of
PMR2. This enables modellers to use them to render pages to describe models, or
activate specific browser plug-ins to create a richer web interface for viewing mod-
els.
The access control and presentational layer of PMR2 is managed by Plone (As-
pell, 2007), a Content Management System. The access control features of Plone al-
low authorized users to manage permissions for other users, such as allowing a user
to view a private workspace, push changesets, create exposures and update workflow
states such as expiring exposures.
The 600 models currently listed in the CellML component of the PMR2 repository
are categorised under the following headings:
•
Calcium Dynamics
•
Circadian Rhythms
•
Cardiovascular Circulation
•
Electrophysiology
•
Cell Cycle
•
Endocrine
•
Cell Migration
•
Excitation-Contraction Coupling
