Biomedical Engineering Reference
In-Depth Information
a Recording or Signal can be requested by using a comma separated list of intervals
as the query component of the object's URI; an interval can be either in the form of
“start-end” or “start:duration”. Signal data returned in response will always span the
requested interval(s); data outside of the request may also be returned, depending on
the actual format requested.
8.11 PMR2
PMR2 (Physiome Model Repository 2) is the software project that provides the
model repository for CellML and FieldML models. Note that SBML models are
available from biomodels.net.
The key features of PMR2 are:
•
facilitated model exchange directly between modellers, without reliance on a cen-
tral repository;
•
a detailed revision history for each mode;
•
user access workflows to control privacy when required;
•
embedded workspaces to enable model reuse and promote modular model devel-
opment.
Workspaces & model revision history
All the files related to a particular model are stored together in PMR2 within a defined
workspace
, which can be regarded as a folder. The implementation of workspaces
uses the Mercurial Distributed Version Control System (DVCS). By providing ver-
sion tracking, this system ensures that users within a group cannot accidentally over-
write or purge changes of other users. Furthermore, each change made to a model,
or its associated files, is recorded as a single changeset: a time-stamped, informative
comment from an identifiable user, which describes the changes they have made. As
model files are progressively altered, the changesets preserve the history of model
development. Finally, even if two users simultaneously change the same model file,
distinct changesets allow their work to be later merged in a controlled manner. An-
other advantage associated with using a DVCS is that it allows users to collaborate
directly with each other, independent of a centralized online repository, as collabo-
rators of any particular model will have a complete clone of the workspace with the
model and related files they are working on. This allows each individual collabora-
tor to work and commit changes to their local copy, creating new changesets which
may then be shared between themselves, or pushed to a centralized repository when
their work is ready to be reviewed or released.
Embedded workspaces
The previous version of the model repository software could only handle CellML 1.0
models. By introducing the concept of workspaces, PMR2 has enabled the storage
of CellML 1.1 models: models that use the
import
feature can reference components
and units from other existing models. PMR2 v0.2 has developed this concept further
by including support for embedded workspaces, in which one or more workspaces
