Welcome to the q-bio Summer School and Conference!

The Ninth q-bio Summer School: San Diego Program

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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 morning lectures will be held at Pacific Hall, room 3500. Computational track afternoon sessions will be held at Bonner Hall, room 2130. Experimental track afternoon sessions will be held at York Hall, room 3306

Detailed schedule

Welcome

July 12, 2015 - Sunday
Arrival at UCSD campus, La Jolla, CA
Registration and check-in
Dinner 5-6pm
Opening Reception and Orientation, Pacific Hall, 3500, 6-9 PM
Lev Tsimring. Introduction to Synthetic Biology Program

Week 1

July 13, 2015 - 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 Eva-Maria Collins, Induced oscillatory locomotion in flatworms
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 14, 2015 - 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 Justin Meyer, A case of synergism between synthetic and evolutionary biology
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 15, 2015 - 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 Stephen Mayfield, Programming Algae for Advanced Photosynthetic Bio-Manufacturing
12:00 - 14:00 Lunch
14:00 - 15:00 Seminar, Andrea Weisse, Mechanistic links between cellular trade-offs, gene expression, and growth
14:00 - 17:00 Tutorial session (Bifurcation analysis)/Lab work
17:30 Dinner
18:30 - 20:30 Student presentations
July 16, 2015 - 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 Nan Hao, Dynamic signal processing by transcription factors
12:00 - 14:00 Lunch
14:00 - 17:00 Tutorial session (Stochastic modeling - discrete simulations) /Lab work
17:30 Dinner


July 17, 2015 - 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 Suckjoon Jun, Single-cell physiology
12:00 - 14:00 Lunch
14:00 - 17:00 Tutorial session (Stochastic modeling - SDE framework/statistical analysis)/Lab work
17:30 Dinner

Weekend 1

July 18, 2015 - Saturday

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

July 19, 2015 - Sunday
Individual activities

Week 2

July 20, 2015 - 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 – 17:00 Tutorial session (Parameter fitting/Parameter sensitivity)/Lab work
17:30 Dinner
July 21, 2015 - 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 Gurol Suel, TBD
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
July 22, 2015 - 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 Roy Wollman, Reliability of signal transduction
12:00 - 14:00 Lunch
14:00 - 15:00 Brian Munsky seminar "Using the Finite State Projection to solve the Chemical Master Equation"
15:00 - 17:00 Group project work.
17:30 Dinner


July 23, 2015 - 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 Brian Munsky, Listening to the Noise - Learning Predictive Models for Single-Cell Gene Regulation
12:00 - 14:00 Lunch
14:00 - 17:00 Group project work
17:30 Dinner
July 24, 2015 – Friday
09:00 - 9:55 Research Lecture 10, Jeff Hasty. Synchronization of synthetic gene oscillators
10:00 - 10:55 Research Lecture 11, Ruth Williams, Enzymatic queueing
11:05 - 12:00 Research lecture 12 Elizabeth Winzeler. Systems Biology and the search for next generation antimalarial drugs
12:00 - 14:00 Lunch
14:00 - 17:00 Group project work
17:30 Dinner

Weekend 2

July 25-26, 2015 - Saturday and Sunday
Individual activities

Week 3: q-bio Student Symposium

July 27, 2015 – Monday
09:00 – 12:00 School project presentations
12:00 - 14:00 Lunch
14:00 – 17:00 School project presentations
17:30 Dinner
July 28, 2015 – Tuesday
09:00 – 12:00 Student research talks
12:00 - 14:00 Lunch
14:00 – 17:00 Student research talks
17:30 Dinner

The Ninth Annual q-bio Conference

All students are encouraged to attend the 2014 q-bio Conference, which takes place on August 5-8, 2015 in Blacksburg, Virginia, USA

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