The Sixth 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

All morning lectures will be held at the Natural Sciences Building, room 3211

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

Detailed schedule

Welcome

July 22, 2012 - 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

This week features three lectures per day that will be attended by all students. Each lecture consists of two 40-minute periods with a short break between. There may be a track-specific talk and/or hands-on session and project work in the afternoon.


July 23, 2012 - 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, Kurt Wiesenfeld, Stochastic Resonance
15:00 - 17:00 XPPAUT Basics - Will Mather/Irma Tristán
17:30 Dinner
July 24, 2012 - Tuesday
09:00 - 10:25 Lecture 4, Kurt Wiesenfeld, Noise in Theory and Practice
10:30 - 11:55 Lecture 5, Kurt Wiesenfeld, Stories From a Noisy World
12:00 - 14:00 Lunch
14:00 - 15:00 Lecture 6, Will Mather, Delays in gene regulation
15:00 - 17:00 Projects selection session
17:30 Dinner
July 25, 2012 - Wednesday
09:00 - 10:25 Lecture 7, Lev Tsimring, Stochastic modeling of gene circuits
10:30 - 11:55 Lecture 8, Lev Tsimring, Stochastic modeling in gene circuits
12:00 - 14:00 Lunch
14:00 - 15:00 Lecture 9, Misha Rabinovich, Low-Dimensional cognitive dynamics
15:00 - 17:00 Dizzy basics - Will Mather/Irma Tristán
17:30 Dinner
July 26, 2012 - Thursday
09:00 - 10:25 Lecture 10, Attila Szucs, Interfacing computational models and biological neurons with the dynamic clamp: Circuit interactions and spike dynamics in a compact neuronal network
10:30 - 11:55 Lecture 11, Attila Szucs, Interfacing computational models and biological neurons with the dynamic clamp: Synaptic integration and firing - the role of intrinsic membrane properties
12:00 - 14:00 Lunch
14:00 - 15:00 Lecture 12, Ron Weiss, Synthetic biology: from parts to modules to systems
15:00 - 17:00 Synthetic Biology Lab tour (Mike Ferry/Andriy Didovyk) - Meet at Bonner 2130
17:30 Dinner
July 27, 2012 - Friday
09:00 - 10:25 Lecture 13, Ron Weiss, Synthetic biology: from parts to modules to systems
10:30 - 11:55 Lecture 14, Ron Weiss, Synthetic biology: from parts to modules to systems
12:00 - 14:00 Lunch
14:00 - 15:00 Lecture 15, Roberto Galan, The phase oscillator approximation in neuroscience
15:00 - 17:00 Roberto Galan tutorial
17:30 Dinner

Weekend 1

July 28, 2012 (Saturday)
Individual activities
July 29, 2012 (Sunday)
San Diego Zoo Safari Park tour. A chartered bus departs from UCSD campus on 8am. Approximate time of return - 4pm.

Week 2

July 30, 2012 - Monday
9:00 - 10:25 Lecture 16, Gennady Cymbalyuk, Reduced neuron models
10:30 - 11:55 Lecture 17, Gennady Cymbalyuk, Reduced neuron models
12:00 - 14:00 Lunch
14:00 - 15:00 Lecture 18, Matt Bennett, Limitations of mathematical models of gene regulation
15:00 – 17:00 Bifurcation analysis of neuronal models using XPPAUT (leader - Gennady Cymbalyuk)
17:30 Dinner
July 31, 2012 - Tuesday
9:00 - 10:25 Lecture 19, Matt Bennett, Limitations of mathematical models of gene regulation
10:30 - 11:55 Lecture 20, Matt Bennett, Limitations of mathematical models of gene regulation
12:00 - 14:00 Lunch
14:00 - 15:00 Lecture 21, Nikolai Rulkov. Map-based models
15:00 – 17:00 Microfluidics lab tour (Megan Dueck/Mike Ferry, Bonner 2130). Group project work
17:30 Dinner
August 1, 2012 – 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, Maxim Bazhenov. Neuronal modeling: from single cell to network
15:00 – 17:00 CompNeuro Tutorial: Modeling oscillatory activity is small networks (Leaders - Maxim Bazhenov/Giri Krishnan)/ SynBio: Group project work (Jangir Selimkhanov)
17:30 Dinner
August 2, 2012 – Thursday
9:00 - 10:25 Lecture 24, Alexander Hoffmann. Temporal coding in cell signaling
10:30 - 11:55 Lecture 25, Henry Abarbanel, Building neuron networks from the bottom up
12:00 - 14:00 Lunch
14:00 – 15:00 Lecture 26 Ruth Williams. Queueing effects in enzymatic processing
15:00 – 17:00 Neurodynamics lab tour (Attila Szucs), Group project work (Jangir Selimkhanov)
17:30 Dinner
August 3, 2012 – Friday
9:00 - 10:25 Lecture 27, Gabe Silva, Theoretical, computational, and experimental considerations for mapping dynamic neural network connectivity
10:30 - 11:55 Lecture 28, Gabe Silva, Theoretical, computational, and experimental considerations for mapping dynamic neural network connectivity
12:00 - 14:00 Lunch
14:00 – 17:00 Student presentations
17:30 Dinner

Weekend 2

August 4 and 5, 2012 (Saturday and Sunday)
Individual activities
Transfer from San Diego to Santa Fe

q-bio Student Symposium

All students will travel to Santa Fe, New Mexico for the 2012 q-bio Student Symposium.

The Sixth Annual q-bio Conference

All students are encouraged to attend the 2012 q-bio Conference, which takes place from August 8 to 11 in Santa Fe. There are optional satellite workshops on August 12.

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