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Hi Tommy,

Great work! Howabout tomorrow Andre, you and I discuss what should now be done with the model curation flags. Maybe the COR and OpenCell ones could be replaced with a single OpenCOR one, and we need to decide what 'curation status' now means.

Cheers, Peter


On 9/03/2016 7:24 p.m., Tommy Yu wrote:

Hi,

The release 11 of the PMR2 software suite which powers Physiome Model Repository (PMR) is now fully staged at

https://release11.staging.physiomeproject.org

Please note that this is NOT the same instance as https://staging.physiomeproject.org - that has remained untouched for quite some time, although a wipe is on the horizon it cannot be done now due to request by multiple parties for the mean time.

Anyway, notable features of this release:
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Model comparison tool

- Enabled by the integration of BiVeS.
- The visualisation is powered by cytoscape.js.

Improved mathematics viewer for CellML models

- Accessible via a link from the standard mathematics view.
- The view presents an interactive diagram of the model grouped by its
components, and selecting the components will show the equations
and variables associated with them.
- Again, this is powered by BiVeS and cytoscape.js.

Launch integration with OpenCOR

- Ability to launch models or their associated SedML file directly from
the web browser to OpenCOR-0.5 and above (currently, this feature is
available via its snapshot).
- https://release11.staging.physiomeproject.org/e/293/noble_1962.cellml/view

SPARQL search end point

- While restricted due to security concerns, most basic queries should
be compatible with most JSON-based SPARQL clients.
- https://release11.staging.physiomeproject.org/pmr2_virtuoso_search

Other various bugfixes and internal changes

- rdflib is now bump to version 4.
- Various internal changes to pmr2.app to enable the implementations of
the above features.

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One thing of interest - this release was done purely using data from the standard backup procedure with the software done using the standard deployment methods. So while the data is very slightly out of sync from production, it does contain all data within the last 12 hours. Importantly, this proves that the live instance could be largely recovered from backups in case of catastrophic failures affecting just that.

Please have a go at the staging instance, and do let me know or reply to this thread on issues that you may have encountered, or with any other general questions.

Regards,
Tommy.

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• [cellml-discussion] Staging of release 11 of PMR, Tommy Yu, 03/09/2016
  • Re: [cellml-discussion] Staging of release 11 of PMR, Peter Hunter, 03/09/2016
  • [cellml-discussion] PMR2 Release 11, Tommy Yu, 03/24/2016
    • Re: [cellml-discussion] PMR2 Release 11, Peter Hunter, 03/24/2016
    • Re: [cellml-discussion] PMR2 Release 11, David Nickerson, 03/24/2016

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