QBioS Hands-On Modeling Workshop Program

Georgia Institute of Technology

May 22-23, 2017

Instructors:

Prof. Joshua Weitz & members of the QBioS 1st year Ph.D. cohort, including Shlomi Cohen, Nolan English, Elma Kajtaz, Bo Lee, Joy Putney, Hector Velasco, Pedro Marquez Zacarias and Ali Zamani

Sponsors:

Georgia Tech Innovation in Graduate Education and the Burroughs Wellcome Fund

May 22 Program -  8:45am – 4:30pm

• Check in, 8am-8:45am
• Welcome by Joshua Weitz

• Introduction to Theory in Gene Expression 9:00am-12:00pm

• Transcription and Translation
• Uncertainty in gene expression
• Paper Discussion: Real-Time Kinetics of Gene Activity in Individual Bacteria

• Coffee Break, 10:15am-10:35am
• Lunch, 12pm
• Introduction to Computing 1:00pm-4:30p

• MATLAB or Python
• Variables and data types
• Loops
• Conditional statements
• Functions
• Data visualization

• Coffee Break, 2:15pm-2:35pm

May 23 Program -  9:00am – 12:00pm 

• Stochastic Gene Expression Modeling Exercise

• MATLAB or Python
• Generate random numbers
• Implementing the Gillespie algorithm
• Sampling from stochastic trajectories

• Coffee Break, 10:15am-10:35am
• Lunch, 12pm

May 23 Program – 1:00pm – 5:00pm (Optional) 

• Projects Presentations:

• Modeling the Spread of an Invasive Species in a Stream Network, Joy Putney
• The effect of population size on stochastic individual-based dynamics, Ashley Coenen

• Breakout Exercises

Planned Labs: (i) Core coding practice; (ii) Molecular, gene expression [continuation from the morning] (iii) Consultation on incorporating probability models in individual projects.