CompCell3D 2015 Workshop

Topics for this stage of the workshop:

1. Basic Kinetics
2. Basic Enzyme Kinetics
3. Networks
4. Building models in Python
5. How to share models with others
6. Simulating models in Python
7. Steady states and stability
8. Positive Feedback
9. Oscillators
10. Other motifs

Downloads:

Telluirum/Python for Windows and Mac OS

Cheat-Sheet

Tellurium/libRoadRunner Cheat-sheet

Slides and other Material

Welcome Slides
Quick Introduction
Biological Networks
Some basic theory on kinetics (Chapter 1 and 2 of Modeling Booklet)
Common Rate laws
Intro to networks (Chapter 4)
Entering models into Tellurium (Chapter 5)
Sharing models (Chapter 6)

Running simulations (Chapter 7)
Steady state (Chapter 8)
Parameter Scans (Chapter 9)

Perturbations
Homeostasis
Protein Cascades
Gene Regulatory Networks
Positive Feedback
Oscillators
Advanced Topic: Steady State Properties

Free Tutorial Booklet
Modeling Text Book: Special discount: 20 dollars at the workshop
Enzyme Kinetics: Special discount: 15 dollars at the workshop

Papers for exercises in Chapter 5

Edelstein, Biochemical Model with Multiple Steady States and Hysteresis

Heinrich, Rapoport and Rapoport 1977 Paper

GUI based SBML Simulator

Coyote SBML Simulator for Windows

coyote