MASS Toolbox Bootcamp
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1_Mathematica_101.nb
2_Toolbox_Quick_introduction.nb
3_Toolbox_Notation.nb
4_Model_building.nb
5_Chapter_9_SB2.nb
6_RBC.nb
7_COBRA.nb
README.md
Tutorial.nb
config.m

README.md

MASS Toolbox Bootcamp

Material covered

  • Mathematica essentials (functional programming, equations solving and manipulation, rule-based programming, ...)
  • Toolbox design principles + model construction and manipulation
  • Simulation & Visualization, IO (SBML, ...), COBRA capabilities
  • Advanced topics: enzyme module construction, symbolic capabilities, thermodynamics, ...

Date and location

The course will take place June 10, 1pm–5pm in the Zweifach library in PFBH.

Prerequisites

You'll have to bring your own laptop. If you don't have Mathematica you will have to install the 30 day trial version before the course. Trial versions for multiple operating systems (Windows, Linux, OS X) are available here.

Download and install the MASS Toolbox

  1. Download the latest MASS Toolbox here
  2. Unpack the ZIP file (the installation will not work otherwise!)
  3. Open the Installer.nb
  4. Evaluate the first code block
  5. Open a new Mathematica notebook and run <<Toolbox` to see if the installation worked (don't forget the backtick)

The installation procedure will put the package into platform dependent location. You can figure out this location by evaluating $UserBaseDirectory.

Download the bootcamp course material

Go to the top of the repository page and press the ZIP button to download a a ZIP file of the course content. Unpack it. ZIP

You can also clone it to your favorite location

git clone https://github.com/SBRG/Bootcamp.git

if you are familiar with git.