Daphne
1.0
Site
About Daphne
Tutorial
The Graphical User Interface (GUI)
Tools for data analysis
Default simulation scenarios
Software Design
Modeling Biology
Calibration
Mathematical and Physical Foundations
Simulation Experiments in Daphne
Using Systems Biology Markup Langague (SBML) in Daphne for Model Sharing
Gallery
Downloads
Works Cited
Page
Daphne (Multiscale Systems Immunology Simulation)
Indices and tables
About Daphne »
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Daphne (Multiscale Systems Immunology Simulation)
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Contents:
About Daphne
Tutorial
Introduction
Installation
Overview of the Graphical User Interface (GUI)
Load the blank protocol
Get subcellular components from the User Store
Review the subcellular components in the Protocol Store
Create a custom cell – add molecules and genes
Create a custom cell – add reactions Cytosol
Create a custom cell – add reaction complexes
Create a custom cell – add cell differentiation
Create a custom cell – add cell division
Create a custom cell – add cell death
Create a custom cell – movement
New simulation protocol – extracellular medium
New simulation protocol – add the custom cell to the simulation protocol
New simulation protocol – simulation settings
New simulation protocol – customize report files
Start and pause the simulation
Post-simulation analyses
The Graphical User Interface (GUI)
Protocol
Sim Setup
Reports
Rendering
3D view
Protocol Stores
Toolbar
Main Menu
Status Bar
Tools for data analysis
Reaction Complex Workbench
Cell population dynamics
Cell lineage analysis
Cell tracks
Default simulation scenarios
Software Design
Design Principles
Hierarchies of Persistence
Workbenches
Modeling Biology
Subcellular Components
Cell
Calibration
Gene Transcription
Receptor Internalization
Chemokine-Receptor Affinity
Cell-cycle calibration
Stochastic Motion
Mathematical and Physical Foundations
Introduction
Moment expansion scalar fields
Discretized scalar fields
Helpful identities
Simulation Experiments in Daphne
Modeling the inter-zonal dynamics of germinal center response
Lymphocyte locomotion kinetics: Comparison of 2D ex vivo and 3D intravital preparations.
Using Systems Biology Markup Langague (SBML) in Daphne for Model Sharing
What is SBML?
Daphne model sharing
Package implementation in libSBML and JSBML
Development of MOCCASIN
How to use:
Current limitations:
Future directions:
Example:
Gallery
Downloads
Works Cited
Indices and tables
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Index
Module Index
Search Page