The Eighth q-bio Summer School: San Diego Program

Tracks offered at the San Diego campus

• QB5, Computational Synthetic Biology
• QB6, Experimental Synthetic Biology

Venues

The school program will feature three 1-hour lectures per day in the morning that will be attended by all students. There will be a coffee break between he second and third lecture. In the afternoon there will be track-specific hands-on tutorial sessions (for QB5), lab work (QB6), and independent project work.

All lectures and tutorial sessions will be held at Bonner Hall, room 2130

Detailed schedule

Welcome

July 27, 2014 - Sunday

Arrival at UCSD campus, La Jolla, CA

Registration and check-in

Dinner 5-6pm

Opening Reception and Orientation, Bonner Hall, 2130, 6-9 PM

Jeff Hasty. Introduction to Synthetic Biology Program

Week 1

July 28, 2014 - Monday

09:00 - 9:55 Lecture 1, Jeff Hasty, Phenomenological modeling of regulatory and signaling networks

10:00 - 10:55 Lecture 2, Jeff Hasty, Mass-action kinetics: Transport, enzymes and Michaelis-Menten

11:05 - 12:00 Research lecture 1 Stephen Mayfield, Programming Algae for Advanced Photosynthetic Bio-Manufacturing

12:00 - 14:00 Lunch

14:00 - 17:00 Introduction to group projects; Software installation

17:30 Dinner

18:30 - 20:30 Student presentations

July 29, 2014 - Tuesday

09:00 - 9:55 Lecture 3, Jeff Hasty, Gene Regulation: Positive feedback

10:00 - 10:55 Lecture 4, Jeff Hasty, Vectors fields and bifurcations in 1D

11:05 - 12:00 Research lecture 2 Nan Hao, Dynamic signal processing by transcription factors

12:00 - 14:00 Lunch

14:00 - 17:00 Tutorial session (Intro to COPASI; Mass action kinetics)/Lab work

17:30 Dinner

18:30 - 20:30 Student presentations

July 30, 2014 - Wednesday

09:00 - 9:55 Lecture 5, Jeff Hasty, Oscillations and synchronization on a circle

10:00 - 10:55 Lecture 6, Jeff Hasty, The phase plane: Clocks and toggle switches

11:05 - 12:00 Research lecture 3 Eva-Maria Collins, "Induced oscillatory locomotion in flatworms"

12:00 - 14:00 Lunch

14:00 - 17:00 Tutorial session (Bifurcation analysis)/Lab work

17:30 Dinner

18:30 - 20:30 Student presentations

July 31, 2014 - Thursday

09:00 - 9:55 Lecture 1, Will Mather, Stochastic modeling of gene expression: basic concepts

10:00 - 10:55 Lecture 2, Will Mather, Stochastic modeling of gene circuits: Master equation

11:05 - 12:00 Research lecture 4 Hamilton Smith, Synthetic biology approaches to genetic engineering

12:00 - 14:00 Lunch

14:00 - 17:00 Tutorial session (Stochastic modeling - discrete simulations) /Lab work

17:30 Dinner

August 1, 2014 - Friday

09:00 - 9:55 Lecture 3, Will Mather, Stochastic simulation algorithms: Gillespie, Gibson-Bruck, Tau-leap

10:00 - 10:55 Lecture 4, Will Mather, Noise in gene circuits: Intrinsic vs Extrinsic

11:05 - 12:00 Research lecture 5 Kun Zhang, Single-cell transcriptional diversity of mammalian brains

12:00 - 14:00 Lunch

14:00 - 17:00 Tutorial session (Stochastic modeling - SDE framework/statistical analysis)/Lab work

17:30 Dinner

Weekend 1

August 2, 2014 (Saturday)

Group kayak & hike tour

Hike and Kayaktour. A chartered bus departs from UCSD campus at 8:30 am. Approximate time of return - 3:30pm.

Week 2

August 4, 2014 - Monday

09:00 - 9:55 Lecture 5, Will Mather, Transcriptional and translational bursting

10:00 - 10:55 Lecture 6, Will Mather, Stochastic switching and population diversity

11:05 - 12:00 Research lecture 6 Gurol Suel, Coping with stress: Lessons from single cells and collective dynamics

12:00 - 14:00 Lunch

14:00 – 16:00 Tutorial session (Parameter fitting/Parameter sensitivity)/Lab work

17:30 Dinner

August 5, 2014 - Tuesday

09:00 - 9:55 Lecture 1, Lev Tsimring, Advanced topics in synthetic gene circuit dynamics: Slow-Fast dynamics in gene regulation

10:00 - 10:55 Lecture 2, Lev Tsimring, Advanced topics in synthetic gene circuit dynamics: Slow-Fast dynamics in gene regulation

11:05 - 12:00 Research lecture 7 Roy Wollman, Reliability of signal transduction

12:00 - 14:00 Lunch

14:00 - 17:00 Tutorial session (Image analysis)/Synthetic Biology lab tour for CompSynBio track/Lab work

17:30 Dinner

August 6, 2014 - Wednesday

09:00 - 9:55 Lecture 3, Lev Tsimring, Advanced topics in synthetic gene circuit dynamics: Modeling delayed biochemical reactions with delay.

10:00 - 10:55 Lecture 4, Lev Tsimring, Advanced topics in synthetic gene circuit dynamics: Stochastic delay-induced oscillations

11:05 - 12:00 Research lecture 8 Ruth Williams, Enzymatic queueing

12:00 - 14:00 Lunch

14:00 - 17:00 Group project work

17:30 Dinner

August 7, 2014 - Thursday

09:00 - 9:55 Lecture 5, Lev Tsimring, Advanced topics in synthetic gene circuit dynamics: Robustness, Adaptation, and Sensitivity

10:00 - 10:55 Lecture 6, Lev Tsimring, Advanced topics in synthetic gene circuit dynamics: Robustness, Adaptation, and Sensitivity

11:05 - 12:00 Research lecture 9 Tim Gardner, Moving on up: the essential role of measurement quality and modeling in scaling to 200,000L fermentations

12:00 - 14:00 Lunch

14:00 - 17:00 Group project work

17:30 Dinner

August 8, 2014 – Friday

09:00 – 12:00 School project presentations

12:00 - 14:00 Lunch

14:00 – 17:00 School project presentations

17:30 Dinner

Weekend 2

August 9-10, 2014 (Saturday and Sunday)

Individual activities

Transfer from San Diego to Santa Fe (students arrange transfer on their own).

The possibilities include a short flight or a long but memorable drive with a possible stopover at Grand Canyon.

q-bio Student Symposium

• Student Symposium, Albuquerque, New Mexico, August 11 - August 12, 2014

The Eighth Annual q-bio Conference

All students are encouraged to attend the 2014 q-bio Conference, which takes place from August 13 to 16 in Santa Fe, NM.