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Team:Groningen/Modeling/Modeling Blog
From 2011.igem.org
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Jaap Oosterbroek - Juli 2nd 2011
We got the complete model of our system working to day. Well it works in priciple anyway. Now all we have to do is find the parameters for which it works and adapt reallilety to fit those parameters. Our biological collegues keep telling is that unfortunaly realty has its own mind and won't just do as we tell it to. So very different from computer sience...
Jaap Oosterbroek - May 26th 2011
Today we reworked our moddeling library beginning to end. We cleaned up a lot of te programming making it more object oriented (as far as one can do this in a weakly typed language) while trying to preserve effeciecy where needed. It is almost good enough to release a first version but it is still very tailored to our type of problem. Also: parameters are now read from files and reports are written to them. This will make paralel parameter fitting easier later on.
Jaap Oosterbroek - May 24th 2011
Tested our bistabilety analiser today and it worked like a charm. What it basically does is take a promotor description, a protein decay function and an rna halflife and predicts where (if any) the stable states of the sytem are goin to be. Afterwards you can use a full model to check how robust these points really are. To us that meant that we saw how extremly important it is to model the delay in transcription and translation.
Jaap Oosterbroek - May 19th 2011
We decided to drop simbiolegy today. It does not offer us the functionalty we need and is simply to buggy for our purposes. Instead we will be continueing with the modelling library I build last week. Maybe we can release on the wiki some time soon so other teams won't have to face up against all the awefull quircks of simbiolegy. But before that we need to clean it up a bit, and we are still in some dissagreement about some parts of it. Especially the trade-off between neat programming and effecientcy.
