Team:INSA-UPS France/test
iGEM UPS-INSA Toulouse 2017
SBGN overview
Our system is constituted of microorganisms interacting by responding to stimulations (inputs) and producing a molecular response (outputs). We had a perfect example of a systematic use of biological material, at the scale of both a unique microorganisms and a microbial consortium.
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The SBGN representation is an easy way to visualize and inventory all the elements we had to consider to modelize our synthetic system with Ordinary Differential Equations (ODEs). It is also a way to present our system to different interlocutors (biologist, bioinformatician, mathematician), and to make it reusable and adaptable.
To simplify our system, some assumptions were made such as the one that the substrate does not interact with Vibrio cholerae and Pichia pastoris.
SBGN: a way to normalize the models of systems biology
“Systems biology is based on the understanding that the whole is greater than the sum of the parts.”
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Systems biology is a new approach to understand and to manipulate biological material. It proposes to represent biological systems such as networks transforming inputs into outputs that could be modeled mathematically, similarly to technological and electronical devices.(1) It requires communication between biochemists, mathematicians and computer scientists. The SBGN (Systems Biology Graphical Notation) project has been launched in 2005 to facilitate this communication. It proposes a standard notation to represent biochemical and cellular processes, and to easily share biological systems to the community.(2) The standard notation can be found there.Our SBGN representation
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