The Seventh q-bio Summer School: San Diego Program

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Contents

Tracks offered at the San Diego campus

Project descriptions

QB5
TBA
QB6
TBA

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, Nikolai Rulkov, Map-based models
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

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.

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