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

Advisor

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)

Schedule

Topic Presenter Date Notes
Intro to Programming and Linux Ed April 4 circle.py
Commandline and Git Ed April 11
Tellurium Zach and Kateka April 18
Tellurium pt II Kateka April 25 nanobody.py tellurium-p2.py
Rosetta Ed May 2
Rosetta pt II Ed May 9
Rosetta Tips and Tricks Ed May 16 Vim
Final Project Ed May 23