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Team:Groningen/modeling cumulus2
From 2011.igem.org
Cumulus 2.0
No piece of software is ever truly finished. This of course hold double for one that was produced under the time constrainst posed by a competition such as iGEM. Below is a list of features that we would like implement in a new version of Cumulus.
More modelling components
There are currently 15 different modelling components implemented in the cumulus system. While this is certainly enough to simulate a whole range of genetic circuits, it is not nearly enough to simulate the whole of the parts library. We would like to add more modelling components in order to give users a headstart in modeling their systems.
Dynamic Modelling
Our generic modeling approach allows for the construction of a model in a matter of minutes(or hours if it is very complicated). Its main disadvantage it that they need to be programmed directly into the code. A little more programming here could allow the components to be completly dynamicaly generated. This would allow us to store them in a database and have users exchange them without recompiling their software.
Connection to the parts registry
Dynamic modelling components are only a begining. For better sharing of modelling components Cumulus needs to be connected to and extend the parts library. This would allow users to compare their models for a single part and inspire eachother with new desings. It would also allow Cumulus to run comparative analisys and find out how different models for the same biobrick part hold out in different experiments.
Cellular mechanics
Currently cellular mechanics such as growth rate, and ribosome or polymerase concentrations are not included in our models. Adding these would greatly improve our modeling acuracy.
Multy cellular models
Although we only use single cell models we explicitly made abstraction layer between the cell level and the level of the whole model in cumulus. This will make it simple for us to create support for multicellular models, including communication an heterogeneous population.
Stogastic models
Noise is currently not modeled in cumulus even though it is a big factor in genetic circuits. Our vision is that we could best model noise by having the model generate mutiple states from every single states and again fusing states that are similar. This would allow us to compute not only single states but complete state distributions.
