Newcastle University Drylab/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.#

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:

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  - Get partners (interactionID): Set 

- Get all interction typeIDs: Set 

- Get interactionTypeID for interactionID (interactionID)  - Get interactionIDs for interactionTypeID (interactionTypeID): Set 

- Get model for interactionID (interactionID):

- Get interactionTypeName for interactionTypeID (interactionTypeID): Set 