The BioChem library
"MathModelica will essentially improve the state of the arts of kinetic analysis, which will better fit the progress in experimental area of Systems Biology"
Dr. Vitaly Selivanov, Universitat de Barcelona
Modeling and simulation of pathways
There is currently a great interest in the development of novel analytical technologies for rapid screening of biological dysfunctions in pharmaceutical and clinical applications. In the drug industry the later a substance is discharged from the drug development pipeline, the higher the financial cost. Not only is it costly to test many substances, the price of the tests increase along the development pipeline. Minimizing the number of substances that are fully tested, i.e., those that become lead compounds, is therefore one of the most important aims of all pharmaceutical discovery programs.
Since metabolic pathways tend to be rather large systems with huge similarities between their components the reuse of software components would be of great benefit. The BioChem library is the first fully object-oriented approach in the area of metabolic pathway simulation. The library has the following major benefits:
- Libraries of components/templates, the reuse of code at both component and template levels.
- Incremental development, the addition of new system functions are facilitated by the modularity.
- Higher structure, easier to develop and maintain the system.
Design principle
Most substances and reactions, respectively, have some common basic features. For instance, all substances must have a concentration and all reactions must have at least one substrate and one product. The design objective behind the BioChem library is to collect these basic features of substances and reactions along with units, compartment properties, and other attributes that are commonly used in such systems in a general-purpose biological and biochemical Modelica library.
The icons and interfaces are designed to be easily changed and/or replaced, most of the classes in BioChem are designed in such a way that they can easily be extended, and some parameters can also be replaced.
Important Publications
BioChem - A Biological and Chemical Library for Modelica (Conference paper)
Emma Larsdotter Nilsson, Peter Fritzson.
Proceedings of the 3rd International Modelica Conference (November 3-4, Linköping, Sweden) 2003, pp. 215-220
Download: [ PDF ]
About the authors
Main Author 2007: MathCore Engineering AB
Main Author 2006: Erik Ulfhielm
Main Author 2004-2005: Emma Larsdotter Nilsson
License conditions
The BioChem package is free software and can be redistributed and/or modified under the terms of the Modelica License with the additional provision that changed parts of BioChem also must be made available under this License.
Copyright (c) 2005-2007 Linköpings universitet and Modelica Association.
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