From 2008.igem.org
Newcastle University
GOLD MEDAL WINNER 2008
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| May
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| [http://2008.igem.org/Newcastle_University_Drylab/1_May_2008 1]
| [http://2008.igem.org/Newcastle_University_Drylab/2_May_2008 2]
| [http://2008.igem.org/Newcastle_University_Drylab/3_May_2008 3]
| [http://2008.igem.org/Newcastle_University_Drylab/4_May_2008 4]
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| [http://2008.igem.org/Newcastle_University_Drylab/5_May_2008 5]
| [http://2008.igem.org/Newcastle_University_Drylab/6_May_2008 6]
| [http://2008.igem.org/Newcastle_University_Drylab/7_May_2008 7]
| [http://2008.igem.org/Newcastle_University_Drylab/8_May_2008 8]
| [http://2008.igem.org/Newcastle_University_Drylab/9_May_2008 9]
| [http://2008.igem.org/Newcastle_University_Drylab/10_May_2008 10]
| [http://2008.igem.org/Newcastle_University_Drylab/11_May_2008 11]
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| [http://2008.igem.org/Newcastle_University_Drylab/12_May_2008 12]
| [http://2008.igem.org/Newcastle_University_Drylab/13_May_2008 13]
| [http://2008.igem.org/Newcastle_University_Drylab/14_May_2008 14]
| [http://2008.igem.org/Newcastle_University_Drylab/15_May_2008 15]
| [http://2008.igem.org/Newcastle_University_Drylab/16_May_2008 16]
| [http://2008.igem.org/Newcastle_University_Drylab/17_May_2008 17]
| [http://2008.igem.org/Newcastle_University_Drylab/18_May_2008 18]
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| [http://2008.igem.org/Newcastle_University_Drylab/19_May_2008 19]
| [http://2008.igem.org/Newcastle_University_Drylab/20_May_2008 20]
| [http://2008.igem.org/Newcastle_University_Drylab/21_May_2008 21]
| [http://2008.igem.org/Newcastle_University_Drylab/22_May_2008 22]
| [http://2008.igem.org/Newcastle_University_Drylab/23_May_2008 23]
| [http://2008.igem.org/Newcastle_University_Drylab/24_May_2008 24]
| [http://2008.igem.org/Newcastle_University_Drylab/25_May_2008 25]
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| [http://2008.igem.org/Newcastle_University_Drylab/26_May_2008 26]
| [http://2008.igem.org/Newcastle_University_Drylab/27_May_2008 27]
| [http://2008.igem.org/Newcastle_University_Drylab/28_May_2008 28]
| [http://2008.igem.org/Newcastle_University_Drylab/29_May_2008 29]
| [http://2008.igem.org/Newcastle_University_Drylab/30_May_2008 30]
| [http://2008.igem.org/Newcastle_University_Drylab/31_May_2008 31]
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| June
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| [http://2008.igem.org/Newcastle_University_Drylab/1_June_2008 1]
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| [http://2008.igem.org/Newcastle_University_Drylab/2_June_2008 2]
| [http://2008.igem.org/Newcastle_University_Drylab/3_June_2008 3]
| [http://2008.igem.org/Newcastle_University_Drylab/4_June_2008 4]
| [http://2008.igem.org/Newcastle_University_Drylab/5_June_2008 5]
| [http://2008.igem.org/Newcastle_University_Drylab/6_June_2008 6]
| [http://2008.igem.org/Newcastle_University_Drylab/7_June_2008 7]
| [http://2008.igem.org/Newcastle_University_Drylab/8_June_2008 8]
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| [http://2008.igem.org/Newcastle_University_Drylab/9_June_2008 9]
| [http://2008.igem.org/Newcastle_University_Drylab/10_June_2008 10]
| [http://2008.igem.org/Newcastle_University_Drylab/11_June_2008 11]
| [http://2008.igem.org/Newcastle_University_Drylab/12_June_2008 12]
| [http://2008.igem.org/Newcastle_University_Drylab/13_June_2008 13]
| [http://2008.igem.org/Newcastle_University_Drylab/14_June_2008 14]
| [http://2008.igem.org/Newcastle_University_Drylab/15_June_2008 15]
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| [http://2008.igem.org/Newcastle_University_Drylab/16_June_2008 16]
| [http://2008.igem.org/Newcastle_University_Drylab/17_June_2008 17]
| [http://2008.igem.org/Newcastle_University_Drylab/18_June_2008 18]
| [http://2008.igem.org/Newcastle_University_Drylab/19_June_2008 19]
| [http://2008.igem.org/Newcastle_University_Drylab/20_June_2008 20]
| [http://2008.igem.org/Newcastle_University_Drylab/21_June_2008 21]
| [http://2008.igem.org/Newcastle_University_Drylab/22_June_2008 22]
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| [http://2008.igem.org/Newcastle_University_Drylab/23_June_2008 23]
| [http://2008.igem.org/Newcastle_University_Drylab/24_June_2008 24]
| [http://2008.igem.org/Newcastle_University_Drylab/25_June_2008 25]
| [http://2008.igem.org/Newcastle_University_Drylab/26_June_2008 26]
| [http://2008.igem.org/Newcastle_University_Drylab/27_June_2008 27]
| [http://2008.igem.org/Newcastle_University_Drylab/28_June_2008 28]
| [http://2008.igem.org/Newcastle_University_Drylab/29_June_2008 29]
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| [http://2008.igem.org/Newcastle_University_Drylab/30_June_2008 30]
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| July
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| [http://2008.igem.org/Newcastle_University_Drylab/1_July_2008 1]
| [http://2008.igem.org/Newcastle_University_Drylab/2_July_2008 2]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/3_July_2008&action=edit 3]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/4_July_2008&action=edit 4]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/5_July_2008&action=edit 5]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/6_July_2008&action=edit 6]
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| [http://2008.igem.org/Newcastle_University_Drylab/7_July_2008 7]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/8_July_2008&action=edit 8]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/9_July_2008&action=edit 9]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/10_July_2008&action=edit 10]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/11_July_2008&action=edit 11]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/12_July_2008&action=edit 12]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/13_July_2008&action=edit 13]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/14_July_2008&action=edit 14]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/15_July_2008&action=edit 15]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/16_July_2008&action=edit 16]
| [http://2008.igem.org/Newcastle_University_Drylab/17_July_2008 17]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/18_July_2008&action=edit 18]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/19_July_2008&action=edit 19]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/20_July_2008&action=edit 20]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/21_July_2008&action=edit 21]
| [http://2008.igem.org/Newcastle_University_Drylab/22_July_2008 22]
| [http://2008.igem.org/Newcastle_University_Drylab/23_July_2008 23]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/24_July_2008&action=edit 24]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/25_July_2008&action=edit 25]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/26_July_2008&action=edit 26]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/27_July_2008&action=edit 27]
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| [http://2008.igem.org/Newcastle_University_Drylab/28_July_2008 28]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/29_July_2008&action=edit 29]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/30_July_2008&action=edit 30]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/31_July_2008&action=edit 31]
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| August
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/1_August_2008&action=edit 1]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/2_August_2008&action=edit 2]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/3_August_2008&action=edit 3]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/4_August_2008&action=edit 4]
| [http://2008.igem.org/Newcastle_University_Drylab/5_August_2008 5]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/6_August_2008&action=edit 6]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/7_August_2008&action=edit 7]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/8_August_2008&action=edit 8]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/9_August_2008&action=edit 9]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/10_August_2008&action=edit 10]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/11_August_2008&action=edit 11]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/12_August_2008&action=edit 12]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/13_August_2008&action=edit 13]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/14_August_2008&action=edit 14]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/15_August_2008&action=edit 15]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/16_August_2008&action=edit 16]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/17_August_2008&action=edit 17]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/18_August_2008&action=edit 18]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/19_August_2008&action=edit 19]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/20_August_2008&action=edit 20]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/21_August_2008&action=edit 21]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/22_August_2008&action=edit 22]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/23_August_2008&action=edit 23]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/24_August_2008&action=edit 24]
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| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/25_August_2008&action=edit 25]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/26_August_2008&action=edit 26]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/27_August_2008&action=edit 27]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/28_August_2008&action=edit 28]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/29_August_2008&action=edit 29]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/30_August_2008&action=edit 30]
| [http://2008.igem.org/wiki/index.php?title=Newcastle_University_Drylab/31_August_2008&action=edit 31]
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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>
"
