Abstract
The dynamics of a synthetic gene circuit is obtained by solving a system of ordinary differential equations. However, even simple ODE systems can be too difficult to be tackled analytically. Hence, you shall recur to numerical methods. In this Chapter we will show how to use the software COPASI to write a model for a biological system and compute the dynamics of it. In particular, we will consider some of the models we derived in Chap. 2. You will learn how to build and simulate a model based on mass action kinetics and Hill functions. Moreover, useful features provided by COPASI – such as the definition of a report and the “parameter scan” function – are here described. We have chosen COPASI because it is open-source and easy to use thanks to an intuitive graphical user interface.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsNotes
- 1.
Here we use COPASI 4.16 (Build 104) on a Mac computer – OS X Yosemite.
- 2.
By default COPASI uses millimoles (mmol) to express the species amount and ml to quantify a volume. These units can be changed by clicking on the branch “Model”. In the corresponding panel, on the right, you can set “Volume Unit” to “l” and “Quantity Unit” to “mol”.
- 3.
If you open this branch and click on “Result” you can see the numerical values of species concentrations over time. You can always switch from concentrations to particle numbers by clicking on the corresponding button in the toolbar.
- 4.
In order to see the ODEs associated with the model, open (in the navigation panel) the branches “Model” and “Mathematical” then click on “Differential Equations”.
- 5.
This formula can be re-used for other reactions, if necessary. In order to check its correctness, click the button with the symbol \(\sqrt {x}\) on the right of the panel.
References
S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, U. Kummer, COPASI – a COmplex PAthway SImulator. Bioinformatics 22(24), 3067–3074 (2006)
M.A. Marchisio, J. Stelling, Computational design of synthetic gene circuits with composable parts. Bioinformatics 24(17), 1903–1910 (2008)
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Marchisio, M.A. (2018). Modeling at Computer: Getting Started. In: Introduction to Synthetic Biology. Learning Materials in Biosciences. Springer, Singapore. https://doi.org/10.1007/978-981-10-8752-3_3
Download citation
DOI: https://doi.org/10.1007/978-981-10-8752-3_3
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-8751-6
Online ISBN: 978-981-10-8752-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)