IQRsbml

Systems Pharmacology gains in interest in the Modeling and Simulation community. Thus does also the Systems Biology Markup Language (SBML), in which many systems pharmacology type of models are coded (see, e.g. Biomodels Database).

SBML, however, is very badly supported when using R. Some packages (such as SBMLR) are available and claim to be able to import and simulate SBML models. However, typically, not all features of SBML models are considered.

The IQRsbml software from IntiQuan allows to convert SBML models to a humanly readable ODE and/or biochemical reaction based format. This format is very close to Berkeley Madonna and can easily be post-processed to get it into NONMEM or MONOLIX.

The future R based IntiQuan tools will be able to import SBML models directly via the IQRsbml software, which needs to be installed separately.

Description

  • IQRsbml handles SBML Level 2 Version 1,2,3, and 4.
  • It is implemented as a command line interface, allowing for easy integration of existing R or MATLAB calls.

Availability

  • IQRsbml is provided free of charge.
  • IQRsbml can be downloaded from the link to the right.
  • It is only available as a Windows 64 bit executable.
  • Development for Linux/Unix is out of scope due to the tremendous difficulty to successfully compile the SBML Toolbox and all required dependencies.

Installation

  • Download IQRsbml
  • Unzip the file
  • Follow instructions in the contained readme.txt file

Downloads

IQRsbml can be downloaded from the following links:

By downloading IQRsbml you agree to have understood that the downloaded software comes without any warranty.