Difference between revisions of "Optimization examples"
From BioUML platform
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For details about creation your oun optimization document in BioUML, see the chapter [[Optimization document]]. Some information about the optimization methods implemented in BioUML is done in the chapter [[Optimization problem]]. | For details about creation your oun optimization document in BioUML, see the chapter [[Optimization document]]. Some information about the optimization methods implemented in BioUML is done in the chapter [[Optimization problem]]. | ||
| − | + | ==Test case for the model of caspase-8 activation== | |
| + | |||
| + | <ul> | ||
| + | <li>'''Optimization document''': ''data''/''Examples''/''Optimization''/''Data''/''Documents''/''test_case_1A''</li> | ||
| + | <li>'''Model''': ''data''/''Examples''/''Optimization''/''Data''/''Diagrams''/''diagram_1A''</li> | ||
| + | <li>'''Experimental data''': ''data''/''Examples''/''Optimization''/''Data''/''Experiments''/''exp_data_1''</li> | ||
| + | </ul> | ||
| + | |||
| + | For the first test case, we considered a reaction chain extracted from the model by Neumann et al. [1] and representing activation of caspase-8 triggered by the receptor | ||
CD95 (APO-1/Fas). | CD95 (APO-1/Fas). | ||
Revision as of 16:56, 14 March 2019
Here we give some examples of BioUML using for solving the problem of parameter estimation applied to the models of biochemical pathways. For details about creation your oun optimization document in BioUML, see the chapter Optimization document. Some information about the optimization methods implemented in BioUML is done in the chapter Optimization problem.
Test case for the model of caspase-8 activation
- Optimization document: data/Examples/Optimization/Data/Documents/test_case_1A
- Model: data/Examples/Optimization/Data/Diagrams/diagram_1A
- Experimental data: data/Examples/Optimization/Data/Experiments/exp_data_1
For the first test case, we considered a reaction chain extracted from the model by Neumann et al. [1] and representing activation of caspase-8 triggered by the receptor CD95 (APO-1/Fas).
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References
- Neumann L., Pforr C., Beaudouin J., Pappa A., Fricker N., Krammer P.H., Lavrik I.N., Eils R. Dynamics within the CD95 death-inducing signaling complex decide life and death of cells. Molecular Systems Biology. 2010. 6:352.
