MesoRD User's Guide
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MesoRD User's Guide

Johan Hattne

David Fange

Johan Elf

$Revision: 1.7 $

Copyright (c) 2004, 2005, 2006 Johan Elf, David Fange, Johan Hattne. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License".

This product includes software developed by Agner Fog ( http://www.agner.org).

This product includes software developed by the Apache Software Foundation (http://www.apache.org).

This product includes software developed by Ben Bornstein ( http://www.sbml.org/libsbml.html).

This product includes software developed by Roldan Pozo, Karin Remington, and Andrew Lumsdaine. ( http://math.nist.gov/sparselib++/).

Table of Contents

Welcome to the Wonderful World of MesoRD

1. Introduction

What is MesoRD?

An introductory Example
Where we go From Here

System Requirements

Design Goals

Project Status

What is new in MesoRD 0.2.0
Known Bugs
Todo

Citing use of MesoRD

Funding

2. Installation

MesoRD Dependencies

Installing a Binary Distribution

Building MesoRD from Source on Unix

Working the GNU AutoTools

Building MesoRD from Source on Windows™

How to use Intel's icc compiler with Microsoft Visual C++

Building a Distribution

Generating the Documentation

A Note on C++ Compilers

Source from CVS

3. Writing SBML for MesoRD

Systems Biology Markup Language

General SBML Structure
Departures from Standard SBML Level 2
Unit
Compartment
Species
Parameter
Reaction
Event
Function
Rule

4. Constructive Solid Geometry

Introduction to Constructive Solid Geometry

CSG Tree Nodes in MesoRD

Geometric Primitives in MesoRD
Set Operations in MesoRD
Transformations in MesoRD

Periodic Boundary Conditions

Issues with MesoRD CSG

5. The User Interface

Available Options

Sub Volume Geometry
Simulation Duration
Checkpointing
Sparse Output
Visual Appearance
Deterministic mode
Starting from an old checkpoint

Making Sense of MesoRD Output

The OpenGL Visualiser

6. Theory:How MesoRD does Stochastic and Deterministic Simulation of Reaction-Diffusion Kinetics

Introduction

State changes

Rates and probabilities
Mean-field time evolution

7. Tutorial

Units
Geometry
Species
Parameters
Reactions
Result

8. Hacking

Coding Standards

Bibliography

A. GNU Free Documentation License

PREAMBLE
APPLICABILITY AND DEFINITIONS
VERBATIM COPYING
COPYING IN QUANTITY
MODIFICATIONS
COMBINING DOCUMENTS
COLLECTIONS OF DOCUMENTS
AGGREGATION WITH INDEPENDENT WORKS
TRANSLATION
TERMINATION
FUTURE REVISIONS OF THIS LICENSE
ADDENDUM: How to use this License for your documents

List of Figures

1.1. Example of a three compartment geometry.
3.1. The SBML definition of UnitDefinition
3.2. The SBML definition of Unit
3.3. The SBML definition of Compartment
3.4. The SBML definition of Species
3.5. The SBML definition of Parameter
3.6. The SBML definition of Reaction
3.7. The SBML definition of SpeciesReference
3.8. The SBML definition of ModifierSpeciesReference
3.9. The SBML definition of KineticLaw
4.1. A Simple Object
4.2. Constructive Solid Geometry Set Operations in Two Dimensions
5.1. The GUI on Windows XP™
5.2. The available deterministic methods
5.3. The OpenGL Visualiser
7.1. Snapshot of simulation at 1 second simulation time.
7.2. Snapshot of simulation at 80 seconds simulation time.

List of Tables

2.1. MesoRD Dependencies

List of Examples

3.1. The basic structure of an SBML file.
3.2. Unit Definition.
3.3. Compartment Defintion.
3.4. Species Definition.
3.5. Reaction Defintion.
4.1. Box Geometry.
4.2. Compartment Primitive.
4.3. Cone Geometry.
4.4. Cylinder Geometry.
4.5. Sphere Geometry.
4.6. Difference Operation.
4.7. Intersection Operation.
4.8. Union Operation.
4.9. Rotation Transformation.
4.10. Scale Tansformation.
4.11. Translation Transformation.
4.12. Box Periodic Boundary Condition.
4.13. Cylinder Periodic Boundary Condition.

List of Equations

6.1. Average change
6.2. System of ordinary differential equation
6.3. Reaction diffusion equation