https://staging.physiomeproject.org/workspace/19f en-us This is the parent workspace containing the library of all models used in the GET project. https://staging.physiomeproject.org/workspace/19f/@@file/c59ca8c72ff6a2b57632cc270cafc33ac1e80865 Testing OpenCOR's new PMR Workspaces widget with a trivial change to the CellML model. Test Author 2017-02-02 https://staging.physiomeproject.org/workspace/19f/@@file/670ed6bde78fbcf74be57624df0eade260469cd4 adding SGLT1 David Nickerson 2015-02-26 https://staging.physiomeproject.org/workspace/19f/@@file/e960970a8520354e0383ec663d95a25dadf8f34e hacking in some annotations for the Weinstein 1995 NHE3 model David Nickerson 2015-02-26 https://staging.physiomeproject.org/workspace/19f/@@file/a7f04db437e7e9944cea9151517a4c6a2c3261ac adding a few more transporters and their annotations David Nickerson 2015-02-25 https://staging.physiomeproject.org/workspace/19f/@@file/071ff4a9c04579981d0ae2c221d5fd5f0335f5b3 adding a few more transporters and their annotations David Nickerson 2015-02-25 https://staging.physiomeproject.org/workspace/19f/@@file/c25157d28ba1bffaf1505743fe402891aff60ac1 adding a few more transporters and their annotations David Nickerson 2015-02-25 https://staging.physiomeproject.org/workspace/19f/@@file/309753d40db90ffca864921da8c528222b0dfc1b more annotations David Nickerson 2015-02-23 https://staging.physiomeproject.org/workspace/19f/@@file/74656ec7f062c851cd60f0c20481591fc1fd28a0 adding annotation for membrane location David Nickerson 2015-02-20 https://staging.physiomeproject.org/workspace/19f/@@file/8d4464a29be3cd9e3ebcd816ad195f29d2022246 adding preliminary annotations for the H/K ATPase from Weinstein 1998 model David Nickerson 2015-02-20 https://staging.physiomeproject.org/workspace/19f/@@file/b6ee456100c3f0e68d9c59d4935f9a62f1b55f9a adding a second dummy uniprot annotation for testing; now using the located_in property from the OBO Relationship Ontology to annotate a components cellular location (idea from Mikes document) rather than abusing the encapsulation grouping in the CellML model David Nickerson 2015-02-16 https://staging.physiomeproject.org/workspace/19f/@@file/e81a3d8099300cece6c998ea8cdd767e84cb8d6f need to update annotations to specify the source document now that they are separate David Nickerson 2015-02-16 https://staging.physiomeproject.org/workspace/19f/@@file/aba8e0e1a355f9e7d929c0eeab061db0564f8f5a extract annotations to separate document David Nickerson 2015-02-15 https://staging.physiomeproject.org/workspace/19f/@@file/ce9d2edc7bf724ecdd4ee9917967adf49163f613 adding an initial attempt at starting to create a comprehensive renal epithelial cell showing all the possible transporters and annotating them with UniProt terms. Currently this is just a basic start, but will gradually refine and add details. Using encapsulation to indicate location of the transporter on the apical or basolateral membrane, but this probably isn't the best way and should annotate containment, but not sure how to do this in OpenCOR. Also, OpenCOR doesn't provide direct access to UniProt terms for creating the annotations as it is not currently supported via PMR2, so I am manually adding the UniProt annotations. They are correctly displayed in OpenCOR. David Nickerson 2015-02-03 https://staging.physiomeproject.org/workspace/19f/@@file/9d3cd60502f25d046b1950c32bf331026380966f stupid little bug that has been bothering me for a long time. Found the bug thanks to the new model compactor code (https://github.com/nickerso/flattenCellML) David Nickerson 2014-09-04 https://staging.physiomeproject.org/workspace/19f/@@file/7debee4743dc6fe6687989e61ecee442e0abfd4a fixing error in definition of cubic centimetre units David Nickerson 2014-08-13 https://staging.physiomeproject.org/workspace/19f/@@file/0dc33eddd8f8211a26959ac4f71d68f713784048 updating with some fixes David Nickerson 2014-08-13 https://staging.physiomeproject.org/workspace/19f/@@file/8debc0659ae15f65ac671bafd09e5df7d065c74f adding a model which defines the base water flux equation, designed to be imported for each membrane and have the sum of each solute's contribution passed in David Nickerson 2014-07-22 https://staging.physiomeproject.org/workspace/19f/@@file/5bfa485ea33ff22db7798092b2f5ba2c34783920 update interface components to use the name 'interface' to make a consistent set of library modules for use in get-creator David Nickerson 2014-07-16 https://staging.physiomeproject.org/workspace/19f/@@file/7b0c95dada7e3fd8adb7990833c74f6e9e478f46 adding a copy of my standard chloride ion model to test out some ideas on generating cell models David Nickerson 2014-07-08 https://staging.physiomeproject.org/workspace/19f/@@file/c7f2cc6dd2e5ba9a438bbc6934d0a39f016a1708 adding an initial README, mainly for use in the bitucket clone of this workspace David Nickerson 2014-04-28 https://staging.physiomeproject.org/workspace/19f/@@file/43e847d7ed617f6130838688644379ebe1cc5318 fixing up 'typo' in the passive flux equation picked up now that I'm starting to try and create code from models generated by get-creator David Nickerson 2014-04-27 https://staging.physiomeproject.org/workspace/19f/@@file/18e1ccf30d6775a41c25e3ed0fc1ff5a0fad657d adding a copy of the passive flux model from the default passive cell mock-up model to use as the generic reusable passive flux model David Nickerson 2014-04-03 https://staging.physiomeproject.org/workspace/19f/@@file/b9433691a55c367f1aa648aac7369558fb150644 can remove the valence since we are after just the generic rate equation for a solute in a given compartment David Nickerson 2014-04-03 https://staging.physiomeproject.org/workspace/19f/@@file/1fe43a73b496607593beabd7f80bb21c20f537b9 adding a copy of the calcium ion model to start making a generic solute rate equation model David Nickerson 2014-04-03 https://staging.physiomeproject.org/workspace/19f/@@file/f1a22a563f98af4c3b81ec6c4ed0a7f26c754ec6 adding the total membrane and paracellular currents as variables in the model and the associated unit for current David Nickerson 2013-11-13 https://staging.physiomeproject.org/workspace/19f/@@file/c3f5050e0da2e135d2a9a5a81c0e426454c36970 tidy up the potential units David Nickerson 2013-10-07 https://staging.physiomeproject.org/workspace/19f/@@file/1efa664910786269c8ea26391e689f789f542850 defining a common units map which maps the actual units we define to common names for use in all our models, this allows single changes to trickle through to all the models easily; updating all the small-molecule models to use these units; couple more correction in the default passive cell model picked up in the process David Nickerson 2013-10-07 https://staging.physiomeproject.org/workspace/19f/@@file/5c883596de517036ad0d9b8b535f00aa9e5488b4 adding more units that are needed for the passive cell template model; starting to add connections in the passive cell model through to the underlying intracellular dynamics models David Nickerson 2013-10-07 https://staging.physiomeproject.org/workspace/19f/@@file/cacf12982a99d1e9ae3ec1cba59ed7bf4bd9c17e initial CellML model for the passive cell with a basic outline of the model and all the parameters; needed to add some more 'standard' units to cover all needs of this one. David Nickerson 2013-10-07 https://staging.physiomeproject.org/workspace/19f/@@file/10e7162557835982b27ab450ba7085180b4eca0a adding my default units collection as a independent workspace David Nickerson 2013-10-07