November 2011
Intermediate to advanced
363 pages
11h 23m
English
Content preview from Stochastic Modelling for Systems Biology, Second Edition, 2nd Edition
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SBML-SHORTHAND 41
k4. This constant will always be used in the formula of the kinetic law, masking any
global parameter of the same name. To use a global parameter called k4, the entire
section
<listOfParameters>
<parameter name="k4" value="1"/>
</listOfParameters>
should be removed from the kine tic law. Kinetic laws can use a mixture of global
and local parameters. Any reference to a compartment will be replaced by the size
(volume) of the compartment. A list of reactions should be inclu ded in the SBML
file between <listOfReactions> and </listOfReactions> tags.
2.5.7 The full SBML model
The various model components are embedded into the basic model structure. For
completen ess, Appendix A .1 lists a full SBML model for the simple auto- regulatory
network ...