What is libRoadRunner

RoadRunner is a package for loading, simulating and analyzing SBML based systems biology models utilzing JIT compilation.

RoadRunner 1.4.3

Up to date documentation can be found on http://libroadrunner.org/.

Also documentation home page provides an introduction.

Fundamental Objects

The libRoadRunner package uses two fundametal objects e.g. rr of class RoadRunner and e.g. rr.model of class ExecutableModel.

  • Typically the top level object

  • Responsible for orchestrating all of the internal components, such as model loading, JIT compilation, integration and output.

  • Initialized with rr = roadrunner.RoadRunner()

  • Represents a compiled sbml model

  • Properties to get and set any state variables.

  • Initialized when SBML is loaded rr.load('mymodel.xml')

The Python API is a very clean simple interface that uses all native Python objects. All the returned types are structured Numpy arrays.

Example of libRoadRunner in Use

Transcript from an Python session to demonstrate libRoadRunner use on this interactive Python console.

Import roardrunner and numpy:

import roadrunner
import roadrunner.tests
import numpy as n
import numpy.linalg as lin

Load an SBML model:

>>>  rr = roadrunner.RoadRunner()
>>>  rr.load(roadrunner.tests.get_data('Test_1.xml'))

Get the model, the model object has all the accessors sbml elements, names, values:

>>>  m = rr.getModel()

Use the built in RR function to get the Jacobian, notice this is returned as a native numpy matrix, and display it:

>>>  jac = rr.getFullJacobian()
>>>  jac
array([[-0.2  ,  0.067,  0.   ],
       [ 0.15 , -0.467,  0.09 ],
       [ 0.   ,  0.4  , -0.64 ]])

Get a vector of floating species amounts, and display it:

>>>  amt = m.getFloatingSpeciesAmounts()
>>>  amt
array([ 0.1 ,  0.25,  0.1 ])

Look at the floating species ids:

>>>  m.getFloatingSpeciesIds()
['S1', 'S2', 'S3']

Numpy has a huge amount of numeric capability, here we calculate the eigensystem from the Jacobian.:

>>>  lin.eig(jac)
(array([-0.15726345, -0.38237134, -0.76736521]),
 array([[ 0.77009381, -0.19510707,  0.03580588],
        [ 0.49121122,  0.53107368, -0.30320915],
        [ 0.40702219,  0.82455683,  0.95225109]]))

Suppose we wanted to calculate the matrix vector product of the jacobian with the floating species amounts, its a single statement, since we use native types.:

>>>  n.dot(jac, amt)
array([-0.00325, -0.09275,  0.036  ])

Finally, you can of course simulate over time. The first column in result is time, the rest are whatever is selected. The easies way to plot is to use RoadRunner.plot():

>>>  results = rr.simulate()
>>>  rr.plot(results)

See also

Plotting Data

Using libRoadRunner in IPython you can get documentation easily using a ? after the object or method:

>>>  rr.plot?

Type:        instancemethod
String form: <bound method RoadRunner.plot of <roadrunner.RoadRunner() { this = 0x101c70a00 }>>
File:        /Users/andy/Library/Python/2.7/lib/python/site-packages/roadrunner/roadrunner.py
Definition:  rr.plot(self, show=True)

Plot the previously run simulation result using Matplotlib.

This takes the contents of the simulation result and builds a
legend from the selection list.

If the optional prameter 'show' [default is True] is given, the pylab
show() method is called.

Technical Footnotes

Numpy arrays

Most of the time, Numpy array holds a pointer to a block of data owned by RoadRunner. For example, the array returned by rr.simulate() has a pointer to the results matrix which is owned by the RoadRunner, therefore NO COPYING is involved. If you have no need for the result, simply ignore it, since it costs virtually nothing to return it.

Current State of the System Group

When using the LLVM back end, all model state calculation are automatically performed using a techinque called lazy evaluation. If one sets the concentration of a specie, the amount of of that specie is automatically available without having to perform any addition operations, similar to any other value in the model. If an SBML parameter is defined by an assigment rule or a function and its value depends on a number of other values, simply setting to other values automatically cause the value of the most dependent variable to be set. This is identical how one operates in a spredsheet such as Microsoft Excel. For example, if one has a cell with an equation that depends on other cell, and those other cell depend on other values, setting the value of any upstream cell automatically causes that value to cascade down to the terminal cells. The LLVM back end roadruner function identically.