Monday, July 28, 2014

Weekly Log: July 21 - July 27

The flattening routine should in theory work for all SBML core constructs. I have been testing the flattening function this past week. I integrated the flattening routine in a tool called iBioSim, which is a tool being developed at the University of Utah that can be used for the modeling and analysis of SBML models. Within iBioSim, I was able to construct an arrayed model thanks to one of my lab colleagues, Scott Glass, who is responsible for the GUI support for the Arrays package.

Here is a model in iBioSim. In this model, there are two parameters of size n and one rule of size n, where n is a constant parameter of value 10. This parameter is not shown here, because constant parameters are kept in the constants tab. These objects are enclosed by a compartment Cell, but this is irrelevant to this model. iBioSim adds a compartment by default.

I give a initial assignment to Y as shown below.

Y is given a vector as initial assignment. This can be translated as
Y[0] = 0
Y[1] = 1 and so on

Finally, I specify the attributes for the rule:



rule0 is an assignment rule, where X is the LHS and Y is the RHS. This is actually saying that:
X[9-d0] = Y[d0] where d0 is the dimension id for a Dimension object of the assignment rule with array dimension 0. Since the dimension has size 10, d0 can take any value from 0 to 9. When this is simulated, I get the following:

Values of Y

Values of X

You can see that X has the values of Y in reverse order, just like we specified in the assignment rule.

One of the requirements for a package to be fully accepted to the standard is to have at least two tools implement the package. iBioSim has started the implementation, though it is not yet finalized. Hopefully, there will be other tools using the arrays package because I believe it can be very helpful from a modeling standpoint.

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