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Newcastle University Drylab/13 June 2008
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Newcastle University
GOLD MEDAL WINNER 2008
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13 June 2008
Mark
Had to do some troubleshooting with the jsim program as it would not compile. Turned out a different version of Java was required and the import statements in a number of the class files were wrong and needed altering. There was also a major problem in one of the files with one of the getState() methods that had a problem due to different Java versions. This too needed to be fixed before the probelm would compile. Got the program to run.
Then found a newer version of Jsim - better GUI to work in and incorporated the Lac operon cellML model that I had produced. The language is slightly different in the cellML model to the jSim version and so several alterations neede to be made - I also had problems with the units that needed to be solved.
Plan for the weekend - Have a good go at a flyer and sort out some logo issues - start planning the incorpoation of the part models into the EA.#
Megan
Morgan
Tried to run JAXB on the Linuxbox. Got it to kind of working, except for big long scrolling errors. I had to download the MathML and XLink schema onto this machine (page.... by... page....) and so it doesn't complain that it can't find that anymore. I modified the CellML schema to reflect the location of those schema(s?). It does complain now about some kind of ambiguity error though:
$ jaxb-ri/bin/xjc.sh -p test.jaxb cellml_1_1.xsd -d test
parsing a schema... [ERROR] cos-nonambig: "http://www.w3.org/1998/Math/MathML":math and WC[##other:"http://www.cellml.org/cellml/1.1#"] (or elements from their substitution group) violate "Unique Particle Attribution". During validation against this schema, ambiguity would be created for those two particles.
line 100 of file:/home/mtaschuk/Desktop/Test/cellml_1_1.xsd
[ERROR] cos-nonambig: "http://www.cellml.org/cellml/1.1#":relationship_ref and "http://www.cellml.org/cellml/1.1#":relationship_ref (or elements from their substitution group) violate "Unique Particle Attribution". During validation against this schema, ambiguity would be created for those two particles.
line 112 of file:/home/mtaschuk/Desktop/Test/cellml_1_1.xsd
[ERROR] cos-nonambig: "http://www.cellml.org/cellml/1.1#":component_ref and "http://www.cellml.org/cellml/1.1#":component_ref (or elements from their substitution group) violate "Unique Particle Attribution". During validation against this schema, ambiguity would be created for those two particles.
line 145 of file:/home/mtaschuk/Desktop/Test/cellml_1_1.xsd
[ERROR] cos-nonambig: "http://www.w3.org/1998/Math/MathML":math and WC[##other:"http://www.cellml.org/cellml/1.1#"] (or elements from their substitution group) violate "Unique Particle Attribution". During validation against this schema, ambiguity would be created for those two particles.
line 278 of file:/home/mtaschuk/Desktop/Test/cellml_1_1.xsd
Failed to parse a schema.
I emailed Mike and James to see if it was something fixable or that they knew about. I found a forum where they discuss it (http://lists.w3.org/Archives/Public/www-math/2003May/0032.html), and it sounds kind of scary. It might also have to go on the cellml mailing list. I hope it's fixable though. I've given up on that for now.
Lunch now!
Nina
Attended a safety and ethics discussion with Prof. Colin Harwood. He showed us how and which forms we will have to fill in.
Wrote architecture of interface for constraints repository.
- Get interactionsID for partID (partID): Set <interactionID> - Get partners (interactionID): Set <partID>
- Get all interction typeIDs(): Set <interactionTypeID>
- Get interactionTypeID for interactionID (interactionID) <interactionTypeID> - Get interactionIDs for interactionTypeID (interactionTypeID): Set <interactionID>
- Get model for interactionID (interactionID): <model>
- Get interactionTypeName for interactionTypeID (interactionTypeID): Set <interactionTypeName>
