Distributions XML File
XML Schema: distribution.xsd
This distribution XML consists of two main blocks: ListOfVariables and ListOfIterations.
ListOfVariables
Parameter: this tag contains the id of the parameter to be inferred;
Species: this tag indicates the error distribution of a species of interest. Almost always, all species present in the Experiments should have a specified distribution. At present CaliBayes only allows Gaussian errors. If a species is defined by a SBML assignment rule, then a prior distribution not required (so hasValue=False), however a distribution for the error structure should still be specified.
The order specified in the ListOfVariables set corresponds to the order in ListOfIterations.
ListOfIterations
Iteration: each iteration should contain a value for the parameters and species contained in the ListOfVariables;
Parameter:
species:
error: the error associated with the species;
R
See the functions:
createCalibayes for creating XML distribution data structures;
loadCalibayes for parsing XML distribution data structures.
Example XML Distributions File
1 <Distribution>
2 <ListOfVariables>
3 <sequence>
4 <Parameter id="mu"/>
5 <Parameter id="alpha"/>
6 <Species id="X" error="Gaussian" hasValue="True"/>
7 <Species id="Y" error="Gaussian" hasValue="True"/>
8 </sequence>
9 </ListOfVariables>
10 <ListOfIterations>
11 <Iteration number="1">
12 <sequence>
13 <Parameter value="0.09274193"/>
14 <Parameter value="0.87930011"/>
15 <Species value="50.59543">
16 <sequence>
17 <Error value="12.2358"/>
18 </sequence>
19 </Species>
20 <Species value="91.63527">
21 <sequence>
22 <Error value="9.358987"/>
23 </sequence>
24 </Species>
25 </sequence>
26 </Iteration>
27 <Iteration number="2">
28 <sequence>
29 <Parameter value="0.07964082"/>
30 <Parameter value="0.67143854"/>
31 <Species value="50.5435">
32 <sequence>
33 <Error value="9.82322"/>
34 </sequence>
35 </Species>
36 <Species value="76.10357">
37 <sequence>
38 <Error value="9.35671"/>
39 </sequence>
40 </Species>
41 </sequence>
42 </Iteration>
43 </ListOfIterations>
44 </Distribution>