1 | Introduction Flashcards
What is an “emerging property”?
(nongraded quiz)
A property arising through the complex interplay of many different system components
What does any useful mathematical model have to achieve?
(nongraded quiz)
A balance between accuracy and complexity
What is the purpose of SBML?
(nongraded quiz)
- Standardised exchange format between different researchers
- Standardised exchange format between different software tools
Which tasks can software tools working with SBML do?
(nongraded quiz)
- Visualization of SBML model structure
- Interactive SBML model editing
- Solving the mathematical equations corresponding to an SBML model
- Importing/exporting SBML
What is meant with Curation of a model in the BioModels database?
(nongraded quiz)
Some figures / tables shown in a reference publication are reproduced using the uploaded model.
Do deterministic ODE systems account for spatial differences?
(nongraded quiz)
No, only with partial DE systems or with stochastic systems
Mathematical modelling: typical abstraction steps
→ mental model
→ model scheme
→ process model
→ dynamic model
→ quantitative results
Mathematical formalisms to represent biological networks
Qualitative networks:
- Boolean network
- Petri net
Quantitative networks:
- Deterministic
- ODEs: don’t account for spatial differences - just one container; much easier to use in a standardised way
- Partial differential equations: different spatial arrangements / structures can be considered - eg depending how deep it is in a lung - much more challenging computationally
- Stochastic
- Stochastic process: inherent randomness, linked to probabilities of whether a reaction would occur
SBML ?
In course: mostly worked on „small“ systems (<10 ODEs), use MATLAB to encode and simulate
But many „real“ systems biology models consist of >100 ODEs
→ standarized language to specify such models is useful:
SBML = Systems Biology Markup Language
BioModels database ?
BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the models in the curated section of BioModels Database have been described in peer-reviewed scientific literature.
→ manual curation: comprehensive process of reviewing, validating, and enhancing submitted models to ensure their quality, accuracy, and reproducibility.
