Team:INSA-UPS France/Model/SBGN

Croc'n Cholera
iGEM UPS-INSA Toulouse 2017

SBGN representation

SBGN: a standard representation of models in systems biology

“Systems biology is based on the understanding that the whole is greater than the sum of the parts.”(1) 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 system is composed of microorganisms interacting by responding to stimulations (inputs) and producing a molecular response (outputs). This is a perfect example of a systematic use of biological material, at the scale of both a unique microorganism and a microbial consortium.

Our SBGN representation

Abbreviations:

  • cqsA: cqsA gene
  • CqsS*: engineered CqsS receptor protein
  • als/ALS: acetolactate synthase
  • S: substrate for diacetyl production
  • dac: diacetyl
  • Odr10: Odr10 receptor protein
  • AMP: antimicrobial peptide
  • V: velocity
  • deg: degradation
  • diff: diffusion

Our SBGN representation is a way to present our system to different interlocutors (biologist, bioinformatician, mathematician), and to make it reusable and adaptable.

This SBGN representation is also an easy way to visualize and inventory all the elements we had to consider to model our synthetic system with Ordinary Differential Equations (ODEs).

References