Simulations 2019 Team Page

Application of mathematical modeling and computer simulations to synthetic biology

Spring Class: Thursdays 7-8pm, SAV 157

Ed van Bruggen

Simulations Team Lead

Office Hours: Tuesdays 3:30-5pm Life Sciences Lobby

Email GitHub

Joshua Ip

Simulations Liaison

Email GitHub

Yoshi Goto


Email GitHub

Weekly Assignments

May 2

  • Install Rosetta

April 11

  • Finish in class GitHub activity, push 1 file and 1 folder with a file inside to a GitHub repo
  • (Recommend) Work on installing Linux

April 4

  • Add profile picture to Zulip
  • Create a GitHub account if you don't have one already
  • Install git, either git bash if you're on Windows or regular git on Mac
  • (Recommend) Start installing Linux, if on Windows will be useful later for Rosetta as well as for git
  • (Optional) Read through Monte Carlo circle code and try to extend it in some way (eg calculate area of oval)


Topic Presenter Date Notes
Intro to Programming and Linux Ed April 4
Commandline and Git Ed April 11
Tellurium Zach and Kateka April 18
Tellurium pt II Kateka April 25
Rosetta Ed May 2
Rosetta pt II Ed May 9
Rosetta Tips and Tricks Ed May 16 Vim
Final Project Ed May 23