- email: james.lu@oeaw.ac.at
- office: HF 130
Times:
- Lectures, Tuesdays 13:45-15:15
- Computing Sessions
- Session 1: Wednesdays, 14:30-15:30
- Meeting days: 28 March, 2 May, 23 May (finish-up
of Exercise 1)
- Session 3: Thursdays, 12:30-13:30
- Meeting days: 29 March, 3 May, 24 May (finish-up of Exercise 1)
- Session 4: Thursdays, 17:00-18:00
- Meeting days: 29 March (join Session 3), 24 May (finish-up of Exercise 1)
Textbooks:
- Computational Cell Biology, C.
P. Fall, E. S. Maryland, J. M. Wagner, J. J. Tyson, editors. Springer,
2002.
- Mathematical Biology I: an Introduction, J. D. Murray, Springer 2002.
- Introduction to Systems Biology: Design Principles of Biological Circuits, U. Alon, CRC Press, 2006.
Supplementary Reading Resouces:
- Systems
biology readings and lecture
notes, available at the MIT
OpenCourseWare
Lecture Notes:
- Lecture 1 (.nb / .html / .pdf )
- Lecture 2 (.nb / .html / .pdf )
- useful supplementary reading on Michaelis-Menten kinetics
- Lecture 3 (.nb / .html / .pdf )
- readings:
- Cooperative Phenomenon (Murray, Math. Biol., p. 197-201)
- Transcription Networks (Alon, Intro. Sys. Biol., p. 5-9)
- Feed-Forward Loop: Network Motif (Alon, Intro. Sys. Biol., p. 41-49)
- supplementary reading: Dynamics of Gene Regulation (S. Widder, J. Schicho and P. Schuster)
- Lecture 4 (by Stefan Mueller)
- Lecture 5 (.nb / .pdf )
- Lecture 6 (.nb / .pdf )
- Lecture 7 (.nb / .pdf )
- Lecture 8 (.nb / .pdf )
- Lecture 9 (.nb / .pdf )
- Lecture 10 (.nb / .pdf )
Computer Sessions Material:
- Tutorial 1 (.nb)
- solution (.nb)
- Tutorial 2 (Exercise1_Empty.nb)
Note: if you do not have Mathematica, you can still read the Notebook files (*.nb) by downloading the freely available MathReader.
Software Resources
- MathSBML: Mathematica package for SBML model analysis.
- Cellerator:
Mathematica package for automatic equation generation from biochemical
reactions.
- MATCONT: MATLAB package for bifurcation analysis.
- SBML ODE Solver Library: C library and command-line application for numeric and symbolic analysis of SBML models, including time-integration and parameter identification.
- SBML Inverse Eigenvalue Analyzer: Add-On to MathSBML, for probing possible qualitative behaviors of SBML models.
Course Overview
SBML Models
Exercises
- Assignment: due 18 May (extended to 25 May), Exercise1_Empty.nb
- solution: Exercise1_Solution.nb
- Assignment: due 22 June (extended to 29 June), Exercise2_Empty (.nb/.pdf)
- Model solution (from Bolaji Adesokan), using feed-forward circuit:
- Model solution (from Kattrin Arning), using serial
circuit: