Read more about the 8th q-Bio Summer School

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

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

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

August 2, 2014 – Saturday

Group kayak & hike tour

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

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, Measurement systems analysis and controlling noise in experimental systems

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

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 the 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.

Venues

The school program will feature three lectures per day that will be attended by all students. Each lecture consists of two 40-minute periods with a short break between. In the afternoon there will be track-specific talks, hands-on tutorial sessions, lab tours, and project work.

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

Detailed schedule

Welcome

July 21, 2013 – 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

Misha Rabinovich. Introduction to Computational Neuroscience Program

Week 1

July 22, 2013 – Monday

09:00 – 10:25 Lecture 1, Jeff Hasty, Deterministic modeling of gene circuits

10:30 – 11:55 Lecture 2, Jeff Hasty, Deterministic modeling of gene circuits

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 3, Misha Rabinovich, Nonlinear dynamics of human attention

15:00 – 17:00 COPASI Basics – Will Mather

17:30 Dinner

18:30 – 20:30 Student presentations

July 23, 2013 – Tuesday

09:00 – 10:25 Lecture 4, Ramon Huerta. Neurons as dynamical systems: from complex to reduced models

10:30 – 11:55 Lecture 5, Lev Tsimring. Stochastic modeling of gene circuits

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 6, Ruth Williams. Queueing effects in enzymatic processing

15:00 – 17:00 Projects selection session

17:30 Dinner

18:30 – 20:30 Student presentations

July 24, 2013 – Wednesday

09:00 – 10:25 Lecture 7, Lev Tsimring. Stochastic modeling of gene circuits

10:30 – 11:55 Lecture 8, Will Mather. Delays in gene regulation

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 9, Terry Sejnowski. Life at Low Particle Number

15:00 – 17:00 Image analysis tutorial (Schnitzcell/CellProfiler) – Mark Kittisopikul/Jangir Selimkhanov

17:30 Dinner

18:30 – 20:30 Student presentations

July 25, 2013 – Thursday

09:00 – 10:25 Lecture 10, Attila Szucs. Interfacing computational models and biological neurons with the dynamic clamp: Synaptic integration and firing – the role of intrinsic membrane properties

10:30 – 11:55 Lecture 11, Attila Szucs. Interfacing computational models and biological neurons with the dynamic clamp: Circuit interactions and spike dynamics in a compact neuronal network

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 12, Terry Hwa. Growth laws: origins and consequences

15:00 – 17:00 Bifurcation analysis tutorial (XPPAUT) – Irma Tristan /Jordi Fonnolosa

17:30 Dinner

July 26, 2013 – Friday

09:00 – 10:25 Lecture 13, Tal Danino. Experimental methods in Synthetic Biology

10:30 – 11:55 Lecture 14, Tal Danino. Experimental methods in Synthetic Biology

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 15, Gabriel Silva. Theoretical, computational, and experimental considerations for mapping dynamic neural network connectivity

15:00 – 17:00 Neurodynamics lab tour (Attila Szucs)

17:30 Dinner

Weekend 1

July 27, 2013 (Saturday)

Individual activities

July 28, 2013 (Sunday)

San Diego Zoo Safari Park tour. A chartered bus departs from UCSD campus on 8am. Approximate time of return – 4pm.

Week 2

July 29, 2013 – Monday

9:00 – 10:25 Lecture 16, Gurol Suel. Cellular decision-making

10:30 – 11:55 Lecture 17, Gurol Suel. Cellular decision-making

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 18, Roy Wollman. Spatio-temporal signaling control of biological self-organization

15:00 – 17:00 Synthetic Biology lab/Pond tour (Megan Dueck/Andriy Didovyk/Mike Ferry, Bonner 2130)

17:30 Dinner

July 30, 2013 – Tuesday

9:00 – 10:25 Lecture 19, Andrey Shilnikov, Voltage maps revealing dynamics transitions in individual neuron models.

10:30 – 11:55 Lecture 20, Andrey Shilnikov, Phase-lag maps for rhythmic activity patterns in central pattern generators

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 21, Mike Ferry. Synthetic biology for biofuels

15:00 – 17:00 Bifurcation analysis of neuronal models using XPPAUT (Andrey Shilnikov/Irma Tristan/Bart Borek)

17:30 Dinner

July 31, 2013 – Wednesday

9:00 – 10:25 Lecture 22, Gert Cauwenberghs, Neuromorphic engineering

10:30 – 11:55 Lecture 23, Gert Cauwenberghs, Neuromorphic engineering

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 24, Eva-Maria Schoetz-Collins. Embryonic pattern formation

15:00 – 17:00 Group projects work

17:30 Dinner

August 1, 2013 – Thursday

9:00 – 10:25 Lecture 25, Garrett Kenyon. Models of Retinal and Cortical Circuits

10:30 – 11:55 Lecture 26, Garrett Kenyon. Models of Retinal and Cortical Circuits

12:00 – 14:00 Lunch

14:00 – 15:00 Lecture 27 Roberto Galan, The phase oscillator approximation in neuroscience

15:00 – 17:00 Tutorial on phase approximation analysis (Roberto Galan)/ Project work

17:30 Dinner

August 2, 2013 – Friday

9:00 – 10:25 Lecture 27, Nan Hao, Dynamic analysis of signaling and gene regulation

10:30 – 11:55 Lecture 28, Mark Adams, TBA

12:00 – 14:00 Lunch

14:00 – 17:00 School project presentations

17:30 Dinner

Weekend 2

August 3-4, 2013 (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, Santa Fe, New Mexico, August 5 – August 6, 2013

The Seventh Annual q-bio Conference

All students are encouraged to attend the 2013 q-bio Conference, which takes place from August 7 to 10 in Santa Fe. There are optional satellite workshops on August 11.