Mathematical Modeling in Systems Biology#
Course information#
👩🏫 Instructor: An-Chi Wei @ MD 521
🦜 Teaching assistant: Wen-Wei Tseng @ MD 705
📝 Announcements & homeworks: NTU Cool
📗 Textbook: Mathematical Modeling in Systems Biology(2013), by Brian P. Ingalls (pdf, MATLAB code)
📚 Additional materials
An Introduction to Stochastic Processes with Applications to Biology (Google the pdf file)
Course content#
Chapter 1-4 describes mathematical modelling in molecular systems biology.
Basic notions of mathematical modelling.
Dynamic mathematical models of chemical reaction networks. (ODE models)
Biochemical kinetics of enzyme-catalysed reactions and cooperative binding.
Model reductions.
Analyzing differential equation models: phase plane, stability, bifurcations, sensitivity analysis.
Chapter 5 and beyond are applications in specific biological domain(s).
Stoichiometric modelling for large-scale metabolic networks. e.g. COBRA
Signal transduction pathways.
Gene regulatory networks.
Electrophysiology and action potentials in exitable cells.
Other topics:
Agent-based modeling (ABM)
(Metabolic) flux balance analysis
Runtime information#
import Pkg
Pkg.status()
Status `~/work/mmsb-bebi-5009/mmsb-bebi-5009/Project.toml`
[336ed68f] CSV v0.10.14
[479239e8] Catalyst v13.5.1
[a93c6f00] DataFrames v1.6.1
[0c46a032] DifferentialEquations v7.13.0
[31c24e10] Distributions v0.25.108
[f6369f11] ForwardDiff v0.10.36
[a98d9a8b] Interpolations v0.15.1
⌅ [961ee093] ModelingToolkit v8.75.0
[91a5bcdd] Plots v1.40.4
[ce78b400] SimpleUnPack v1.1.0
[2913bbd2] StatsBase v0.34.3
[9a3f8284] Random
[10745b16] Statistics v1.10.0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated`
import InteractiveUtils
InteractiveUtils.versioninfo()
Julia Version 1.10.3
Commit 0b4590a5507 (2024-04-30 10:59 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 × AMD EPYC 7763 64-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
Environment:
JULIA_CI = true
LD_LIBRARY_PATH = /opt/hostedtoolcache/Python/3.12.3/x64/lib
JULIA_DEPOT_PATH = /home/runner/.julia:/opt/hostedtoolcache/julia/1.10.3/x64/local/share/julia:/opt/hostedtoolcache/julia/1.10.3/x64/share/julia
JULIA_CONDAPKG_BACKEND = Null
JULIA_LOAD_PATH = @:@v#.#:@stdlib
This notebook was generated using Literate.jl.