.BioChem

Information

About the BioChem Library

BioChem is a package for biochemical modeling and simulation with Modelica.

Basic idea of the library

The design idea behind the BioChem library is to create a general purpose Modelica library for modeling, simulation and visualization of biological and biochemical systems. The classes implemented in the BioChem library describe substances and reactions that can take place in-between these substances in a diverse number of biochemical pathways.

Library Structure

Since the design objective for BioChem was to provide properties and attributes that are common in biological and biochemical systems the library contains several packages holding classes and partial models. The classes can be used as they are in sub libraries to BioChem, while the partial models must be further extended to fully functional models.

Users Guide

Users Guide discusses some aspects of the BioChem Library, including a Getting Started chapter.

References

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

A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase
Albert Goldbeter. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 9107-9111, October 1991 Cell Biology

Hierarchical modeling of diabetes
Elin Nyman. ISRN:LiU-IKE-EX-09/14. Linköping University 2009.

A Minimal Generic Model of Bacteria-Induced Intracellular Ca²⁺ Oscillations in Epithelial Cells
Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemo. Biophysical Journal Volume 88 April 2005 2976-2981.

A mathematical model of metabolic insulin signaling.
A. Sedaghat, R, A. Sherman, and J. Quon, Michael. American Journal of Physiology - Endocrinology and Metabolism, 283:1048-1101, Jul 2002.

Modeling the cell division cycle: cdc2 and cyclin interactions
John J. Tyson. Proc. Nati. Acad. Sci. USA Vol. 88, pp. 7328-7332, August 1991 Cell Biology

Modeling Feedback Loops of the Mammalian Circadian Oscillator
Becker-Weimann S, Wolf J, Herzel H, Kramer A. Biophysical Journal Volume 87 November 2004 3023-3034

Contents

Name	Description
Math
Units	Units used in BioChem
Substances	Reaction nodes
Reactions	Reaction edges
Interfaces	Connection points and icons used in the BioChem package
Constants	Mathematical constants and constants of nature
Compartments	Different types of compartments used in the package
Icons	Icons
Examples	Some examples of BioChem models

Revisions

History

The first version of the library was created by Emma Larsdotter Nilsson at Linköping University. The current version of the library has been further developed by Erik Ulfhielm at Linköping University, and by MathCore Engineering AB.

• Main Author 2007-2009: MathCore Engineering AB
• Main Author 2006: Erik Ulfhielm
• Main Author 2004-2005: Emma Larsdotter Nilsson

Copyright © 2005-2015 MathCore Engineering AB, Linköpings universitet and Modelica Association

The BioChem library is free software released under the terms of the Mozilla Public License, version 2.0.

Versions

• Version 1.0.2 (2020-06-02)
  • All major components are separated into *.mo files
  • MSL 3.2.3 
• Version 1.0.1 (2013-04-18)
  • Applied patch to latest version provided by MathCore Engineering AB.
  • Changed uses-annotation to MSL 3.2, encoding to ASCII+HTML entities, and started using modelica:// URLs for image sources (Martin Sjölund).
• Version 1.0 (2009-08-31)
• Version 0.96 (2008-12-19)