Methodology article
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
-
* Corresponding author: Fabian J Theis fabian.theis@helmholtz-muenchen.de
1 Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
2 Department of Mathematical Science, Technische Universität München, 85747 Garching, Germany
3 Biological Engineering Department, M.I.T., Cambridge MA 02139, USA
4 Department of Systems Biology, Harvard Medical School, Boston MA 02115, USA
5 Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
6 Max Planck Institute for Dynamics and Self-Organisation, 37073 Göttingen, Germany
BMC Systems Biology 2009, 3:98 doi:10.1186/1752-0509-3-98
Published: 28 September 2009Additional files
Additional file 1:
Example for the hypergraph representation of a Boolean model. Supplementary text (.pdf) giving an example for the hypergraph representation of Boolean models.
Format: PDF Size: 42KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 2:
Hill functions. Figure (.pdf) showing Hill functions f(x) = xn/(xn + kn) with Hill coefficients n = 2, 4, 8, 16, 32 and threshold k = 0.5.
Format: PDF Size: 7KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
HillCubes. Figure (.png) showing HillCubes of all 16 two-variable Boolean gates. Hill parameters are n = 3 and k = 0.5 for both inputs.
Format: PNG Size: 108KB Download file
Additional file 4:
Regulatory domains. Figure (.pdf) showing the regulatory domains in a two-variable example.
Format: PDF Size: 9KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 5:
Steady-states in discrete and continuous models. Supplementary text (.pdf) discussing a toy example where the steady-states of a discrete model are not preserved in a continuous version of the model.
Format: PDF Size: 317KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 6:
Comparison of different best fit parameter sets with respect to model dynamics. Figure (.pdf) showing simulations of the continuous T-cell model for 5 different best fit parameter sets (without regularization, cf. section on parameter fitting). While not perfectly agreeing, the overall dynamic behavior is the same in all simulations.
Format: PDF Size: 43KB Download file
This file can be viewed with: Adobe Acrobat Reader