Re: Using revision control software with SBML files?
01 Mar '12 18:56
On 02/03/12 15:23, Michael Hucka wrote:
>> PMR2 looks like a great tool. I wonder what would be required to
>> develop a similar platform for distributed development of SBML models?
> IIRC, PMR2 will store SBML models too. It's not specific to CellML (AFAIK).
As Mike implies, PMR2 is the software not the repository, and you can
use it to create a repository for any format.
One feature of PMR2 is the ability to make exposures which display
additional information about particular types of models (extracted by
parsing the model file and its metadata); PMR2 needs to be adapted to
support different types of exposures if exposures are to be useful with
different types of models (currently the focus is on CellML and FieldML
exposures). Most likely, extending PMR2 to support a new type of
exposure would be less work than creating entirely new repository software.
However, PMR2 is useful for more than just exposures - workspaces are
essentially user-maintained Mercurial repositories, with a front-end to
see changes that have been made (similar to the software than runs sites
like github and Bitbucket). Users can sign up and create workspaces, and
then commit any type of model to that.
The Auckland Bioengineering Institute runs a repository using PMR2, at
http://models.physiomeproject.org/ - this is open for anyone to sign up
to (I think accounts need to be approved, but they are available to any
member of the physiological modelling community), at which point a
workspace can be created, and mathematical models of any kind can be
pushed to the workspace. I believe there are already some workspaces
containing MATLAB based models (pending the creation of a declarative
model) - and so it would certainly be appropriate to push SBML models to
a workspace in that repository.
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