From 2008.igem.org
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| - | '''The matrix.'''
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| - | To populate the compatibility matrix I used three methods.
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| - | Literature searching (google the parts and look through journals for conformation that they can interact/control gene expression of the connecting part)
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| - | Look at homologous structures of parts that have been confirmed to interact. If the structure is the same, they may also be compatible.
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| - | Use blast of the DNA sequence two parts together to see the sequence exists at all. This would confirm compatibility.
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Revision as of 20:25, 21 September 2008
Newcastle University
GOLD MEDAL WINNER 2008
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20 May 2008
Mark
Began the day by reading my new neural networks paper. Now moving onto the CellML tutorials. Worked through the cellML tutorials printing out the xml, and working through the signal transduction examples.
I then went onto downloading the COR program and started to look at becoming familiar with the language and how it fits in with XML.
Have also begun writing a java doc that reads in perfect data from a text file that can be used on a neural network. The program reads in each double value and performs a gaussian distribution on it generating a population of 1,000 tht is noisy data. It will output this in a file that can be input into the neural network program.
I started off by constructing a file parser which scanns the file for doubles. I also constructed a method that can perform the gaussian distribution step. I am now working on how to generate the population of 1 000 and also how to integrate the method with the parser.
Plan for tomorrow is to finish off the java doc and to start looking at further data structures for my evolutionary algorithm
Came in again to uni this evening and managed to get my double array input to work. I have also now written a full method for performing th gaussian distribution step.
Megan
Continue exploring the CELLML language and try to understand how to go about creating models of the parts
- Followed the cellML tutorial
- Look at wikipedia for brief overview
- Try to understand example models in COR and the output of these
- Outline possible variables and units for the broad parts
Morgan
Back to working on deletion. Hooked up the listener for the interaction types. Added BuildCircuit as a listener of that, and now it removes the TransferHandler when the edge button is enabled, and the edge listener when the pointer is enabled. Disabled un-selection of buttons.
Was trying to show Matt the debugged workbench and the truth tables promptly went back to hating my guts. God****. I'm going to rip the Input listener out entirely, since I think that's what's causing my grief. The user will just have to add his own god****ed rows.
Finally, that looks pretty stable. I also tooltipped all the buttons on the build panel and the behaviour panel, linking back to strings in Constants so that they're pretty easily changeable. I should make a method in PanelFactory for MenuItems and TreeNodes. Later, when I have deletion functionality.
DELETION WORKS. And it wasn't that hard either, not even the truth table stuff. HA. TAKE THAT.
Nina
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