University of Tuebingen Lehrstuhl Kognitive Systeme, Prof Dr. Zell
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JCell Documentation

Table of Contents

Preface
1. Introduction
Motivation
Inference
Cell Simulation/ Morphogenesis
Limited Growth
Ability of Self-Repair
2. Biology
How it all began
The Genome - Book of Life
DNA
Proteins and Enzymes
From DNA to Proteins
Gene Regulation
3. Algorithms
Inference
Mathematical Models
Random Boolean networks (RBN)
Qualitative models
Weight matrices
Pseudolinear weight matrices
Bayesian Networks
H-Systems
S-Systems
Arbitrary differenatial equations
Inference Strategies
Standard Inference
Separated Inference
BitSet Inference
Island Strategy
Virtual Knockouts
Singleton Inference
Skeletalizing
Evolutionary Algorithms
Genetic Algorithms
Evolution Strategy
Genetic Programming
Memetic Algorithm
4. Menu description
The File menu
Open
Export
Quit
The Data menu
Create Artificial Data
The Topology menu
Edit Graph
Map Expression Data
Query Database
The Analysis menu
Inference
Exploration
The Preferences menu
Program Settings
Inference Settings
Get Token
The Help menu
About...
5. Command Line Options
General Syntax
Command Line options and parameter
-HELP
-NOGUI
-KEEPALIVE
-CPU n
-EMAIL
-EXPORT
-OUT file
-CONFIG file
-TOPOLOGY file
-REFERENCE file
-DATA files
-FORMAT format
Literature
Christian Spieth.
http://www.ra.cs.uni-tuebingen.de/software/JCell/tutorial/tutorial.html
© 2004 University of Tübingen, Germany