7/21/13-8/3/13 – q-bio Summer School: San Diego Program | San Diego Center for Systems Biology

Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, 12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall, Fung Auditorium
Complete schedule here

7/21/13-8/3/13 – q-bio Summer School: San Diego Program

http://q-bio.org/wiki/The_Seventh_q-bio_Summer_School:_San_Diego_Program

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

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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.