MesoRD User's Guide - 1.1

Johan Hattne

David Fange

Anel Mahmutovic

Johan Elf

$Revision: 675 $

Copyright (c) 2004-2011 Johan Elf, David Fange, Johan Hattne, Anel Mahmutovic. 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".

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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
Mission Statement
Project Status
What is new in MesoRD 1.1
What is new in MesoRD 1.0
What is new in MesoRD 0.3
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 OS X
Building MesoRD from Source on Windows
Building MesoRD from Source using Visual Studio 2005
Building MesoRD from Source using Visual Studio 6.0™.
Building a Distribution
Generating the Documentation
A Note on C++ Compilers
Source from SVN
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
Tree Representation of CSG
CSG Trees in MesoRD
Geometric Primitives
Set Operations
Transformations
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. Rates and state changes in MesoRD
Introduction
State changes
Rates and probabilities
Scale dependent association rate constants
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 XML definition of SpeciesDiffusion
3.6. The XML definition of Diffusion
3.7. The SBML definition of Species
3.8. The SBML definition of Reaction
3.9. The SBML definition of SpeciesReference.
3.10. The SBML definition of ModifierSpeciesReference
3.11. The SBML definition of KineticLaw
3.12. The XML definition of MicroscopicParameters.
3.13. The XML definition of AssociationRateConst.
3.14. The XML definition of ReactionRadius.
3.15. The XML definition of DegreeOfDiffusionControl.
4.1. A Simple Two-Dimensional Object
4.2. Constructive Solid Geometry Set Operations in Two Dimensions
4.3. The Utah Teapot in MesoRD CSG
4.4. A CSG Tree with Transformations
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
2.2. To build the MesoRD documentation

List of Examples

3.1. The basic structure of an SBML file used in MesoRD is
3.2. Unit Definition.
3.3. Compartment Definition.
3.4. Species Definition.
3.5. Reaction Definition.
3.6. Reaction Definitions with scale dependent reaction rates.
4.1. Box Geometry
4.2. Cone Geometry
4.3. Cylinder Geometry
4.4. Mesh Geometry
4.5. Sphere Geometry
4.6. The compartment Primitive
4.7. The rectangle Primitive
4.8. The circle Primitive
4.9. Difference Operation
4.10. Intersection Operation
4.11. Union Operation
4.12. Rotation Transformation
4.13. Scale Transformation
4.14. Shear Transformation
4.15. Translation Transformation
4.16. Box Periodic Boundary Condition
4.17. Cylinder Periodic Boundary Condition, or toroidal boundary condition