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Minnesota/19 June 2009
From 2009.igem.org
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Patrick
I decided to take a closer look at the design GUI being used in order to determine if one could fix some of the major flaws. There are two main issues with the designGUI so far identified. The first, as mentioned in previous entries, is the fact that non-linear parameter variation is impossible.
Today I focused on that issue. The main problem as it turned out was that the program could not recognize when two different variations were acting on the same species or kinetic constant. This was an issue since the program used quick arithmetic to produce the final matrix of initial condition.
Since it was easier to simply give the program the ability to take all the variations and combine them into a vector when the variations operated on the same species, I created a simple work around. Unfortunately, since the program was given in a package I am unable to use it yet.
The second issue manifests itself when you delete reactions from an established reaction network. Essentially, the problem is the program won't delete species that no long exist from the species list until the user checks the initial conditions again. This is a very quick fix which I will continue to work on over the weekend.
