Hamner Course

Day 1: Monday 11th.

9.00 – 9.10: Welcome note (Jim Sluka, Indiana Univ.)
9.10 – 9.20: Welcome note (Sudin Bhattacharya, The Hamner Institute)

Location of the RoadRunner Configuration File on Windows:

c:\Python27\Lib\site-packages\roadrunner\roadrunner.conf

Load the file into compucell3d and change the first line to False, save and restart compucell3d.

Downloads

0. Template Script

1. Cheat Sheet 

2. Introductory Video to Tellurium and libRoadRunner

3. Download Windows and Mac versions here. 

4. PATCH to fix reset() bug (run patch inside Python, eg run telfix,py))

4. List of Rate laws

5. Sphinx (2.7 !)

6. Install Pip

7. Intro Slides

8. Sliders for Day 1

Slides 1
Slides 2
Slides 3 (Networks)

9. Slides for Day 2

10. Zip File containing most of the examples we worked on in the workshop

11. Additional models:

Various wave forms:  a) Generating a square wave; b) Generating a sawtooth wave; c) Generating a triangle wave

12. Listing for the final project contributed by Eric and Salil

9.20 – 10.00: Lecture and Exercises:

  1. Introduction to Modeling with Python
  2. Tellurium: An Integrated Environment
  3. Building Simple Models
  4. Basic libRoadRunner and Antimony Exercises

10.00 – 10.30: Basic Kinetic Principles for Modeling Building:

  1. Stoichiometry
  2. Rate Laws
  3. Boundary Species
  4. Steady States and Transients

10.30 – 11.00: Break

11.00-.12.30: Hands on exercises

  1. Getting Help: Documentation and tutorials
  2. Simple Closed Systems
  3. Simple Open Systems
  4. Applying Perturbations
  5. Plotting Simulations

12.30 – 1.30: Lunch

1.30 – 3.30: Lecture and Exercises:

  1. Exporting Models (SBML, Antimony, Matlab)
  2. Sensitivity Analysis
  3. Parameter Scans
  4. Events
  5. Mini Project

3.30 – 4.00: Break

4:00 – 5:40: Building Simple Models

Day 2: Tuesday 12th

9.00 – 10.30: Perturbations
9.35 – 10.30: Steady State Analysis
10.30 – 11.00: Break
11:00 – 11.45: Cascades
11.45 – 12.30: Gene regulation

12.30 – 1.30: Lunch
1.30 – 5.30: Project: Build a Signaling Pathway, combining gene an metabolic components, and Q&A session on Reaction Kinetics Modeling