Documentation

libRoadRunner 1.1.0

Changes from 1.0.1 to 1.1.0:

  • Config system. RoadRunner can now read and write most default configuration parameters from / to a config file
  • Fixed memory leak in moiety conservation converter
  • New colored logging
  • Upgraded to standard Poco 1.5 distribution. RoadRunner’s Poco is now linked directly to the official Poco git repository.
  • Lots of integrator tuning parameters are now accessible via the SimulateOptions object.
  • Can run the integrator in new MULTI_STEP mode where the integrator determines time step size.
  • New SBML events — users can register listeners for any sbml event. Whenever a SBML event is triggered or assigned, the user can be notified.
  • New integrator events — users can register listeners for integrator events such as when a time step completes or an event was detected. 
  • Significantly improved integrator error handling. Whenever CVODE encounters any error such as numeric instability, the error is written directly to the Roadrunner logging system with exact details about the error. Descriptive exceptions are now raised detailing the exact source of the error.
  • Cleanup of integrator code.
  • New distutils based python installation system. We now provide binaries for 32/64 bit Linux (intel), 64 bit Mac OSX and 32 bit Windows.
  • Documentation updated
  • Can read sbml files through http on all platforms. The RoadRunner constructor load methods are smart in that that accept a string which can be either:
  1. The contents of a sbml document
  2. A local file path, i.e. /home/andy/feedback.xml
  3. A full URI identifier that can be either a local file or a remote file,  this can even be a biomodels identifier, i.e.  r=roadrunner.RoadRunner(“http://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000275”)

Performance Assessment

Benchmark Suite Brusselator & Piecewise models.

Features

  • Time Dependent Simulation (with optional conservation law reduction) using CVODE (using the Adams-Moulton method with max order 12 for non-stiff problems and Backward Differentiation Formulas (BDF) with max order 5 for stiff problems)
  • Supports SBML Level 2 to 3 but currently excludes algebraic rules and delay differential equations
  • Uses latest libSBML distribution
  • LLVM code generation backend is the default, resulting is very fast simulation times
  • Optional generation of model C code and linking at run-time
  • Compute steady state
  • Metabolic Control Analysis
  • Frequency Domain Analysis
  • Access to:
    1. Eigenvalues and Eigenvectors
    2. Jacobian, full and reduced
    3. Structural Matrices of the stoichiometry matrix
  • Ability to add plugins to the core, distribution comes with Levenberg-Marquardt optimizer plugin

Future expansion (Version >1.0):

  • Bifurcation Analysis
  • Loading and saving of SED-ML