- Course overview
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- What is a mathematical model?
- Introduction to networks and graphs
- Introduction to three mathematical model formalisms
- Case study – Infectious diseases (SIR Models)
- Other modelling approaches
- Sustainable modelling and sharing
- Summary
- Check your learning
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- References
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Translating the lac operon into a graph
Here we describe step by step approach to translate the biological process knowledge on the lac operon into a graph.
The graph created (Fig 6) using the steps above represents the conceptual model — a qualitative description of the system’s structure. It helps clarify what components and interactions are important before any equations are written.
To ensure clarity and compatibility with future steps, this graph should ideally follow SBGN (Systems Biology Graphical Notation) conventions, an effort to standardise the graphical notation used in maps of biological processes. SBGN encodes the type of the biological entities (e.g. macromolecules, chemicals, complexes) and interaction (eg. consumption, production, stimulation, catalysis, etc) in the shape of nodes and edges in the graph. Using these conventions not only clarifies the roles and relationships of the components but also enables compatibility with modelling software that supports automatic equation generation from SBGN-compliant diagrams. For tips on creating SBGN maps refer to this published article – Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation (Touré V et al, 2018).
Before moving on to the next section about various types of mathematical modelling, try out a simple true and false quiz to check your learning so far.