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The Second q-bio Summer School on Cellular Information Processing
Back to The Second q-bio School. You may also want to view the program of the associated Conference.
This is an evolving document.
The Summer School is being sponsored by the New Mexico Consortium and the Center for Nonlinear Studies at Los Alamos National Laboratoty. Participants will attend daily lectures about theory and modeling of cellular networks. They will work in small teams on open-ended homework problems with mentors from Los Alamos National Laboratory. The Summer School is designed for graduate students, postdocs, or anyone with a quantitative background who is new to modeling cellular regulatory systems.
You may want to review the information about The First q-bio Summer School as a guidance about what the second one may look like.
The q-bio Summer School is not affiliated with arXiv.q-bio.
Contents
School Logistics
- School dates: Jul 21- Aug 5, 2008
- Hotel check in Jul 20, check out Aug 6
- School Participants
- Pictures
- Travel Information
- The school hotel
- Essential information about the Los Alamos area
- What to do in the vicinity of Los Alamos
- Lecture hall information
- Ride Sharing Board
- Safety and Security
Main School Themes
After the summer school, students will participate in the q-bio Conference in Santa Fe, NM, Aug 6-9, 2008; this facilitated the choice of the themes for the summer school. They are
- Signal Transduction Systems, organized by William Hlavacek
- Stochasticity in Biochemistry and Systems Biology, organized by Ilya Nemenman
- Genetic Regulatory Networks, organized by Michael Wall
- Other Topics in Biological Modeling, organized by Yi Jiang
School Schedule
Overview
Unless otherwise noted on specific dates, the school schedule will consist of 4 hours of lectures in the morning, separated by a short break. A typical schedule will look like
- 8:40-10:25 -- Lecture One
- 10:25-10:45 -- Break
- 10:45-12:30 -- Lecture Two
Catered lunch will be provided at 12:30.
Afternoons will be left for other activities, such as ad hoc lectures, student lectures, discussions, and study sessions, work on homework projects, continuation of the participants' regular academic work, and recreation. Classroom with internet access will be reserved for the school participants for all afternoons during the school program. Additionally, we expect the students to spend some of the afternoons with the school faculty, most of them staff members at LANL, familiarizing themselves with the workings of the research institution and potentially starting collaborative research with the faculty.
For the two school weekends, we are planning to organize outdoor activities, such as hiking in the Jemez or Sangre de Cristo mountains, white-water rafting at the Taos Box, etc.
Detailed schedule
- July 20
- Arrive in Los Alamos
- July 21
- Opening remarks
- Alan S. Perelson -- Other Topics in Biological Modeling, Lecture 1 (slides)
- Byron Goldstein -- Signal Transduction Systems, Lecture 1 (slides)
- July 22
- Ruy M. Ribeiro -- Other Topics in Biological Modeling, Lecture 2 (slides)
- William S. Hlavacek -- Signal Transduction Systems, Lecture 2 (slides), Homework: Rule-based modeling
- Krzysztof Puszynski -- student talk (30 minutes) (slides)
- July 23
- Brian Munsky -- Stochasticity in Biochemistry and Systems Biology, Lecture 1 (slides)
- Bridget S. Wilson -- Signal Transduction Systems, Lecture 3 (slides)
- Beata Hat -- student talk (30 minutes) (slides)
- Jose Teles -- student talk (30 minutes) (slides)
- July 24
- James P. Freyer -- Other Topics in Biological Modeling, Lecture 3 (slides)
- Brian Munsky -- Stochasticity in Biochemistry and Systems Biology, Lecture 2
- Kevin Y. Sanbonmatsu -- High performance computing and large molecular simulations: Ribosome dynamics (1:30 - 2:30) (slides)
- July 25
- Yi Jiang -- Other Topics in Biological Modelings, Lecture 4 (slides)
- Hans Frauenfelder -- Other Topics in Biological Modeling, Lecture 5
- July 26 and 27
- Ideas for weekend activities -- Spanish Market in Santa Fe, Santa Ana Day corn dance at Taos Pueblo, and kayaking (pictures)
- July 28
- Nikolai Sinitsyn -- Stochasticity in Biochemistry and Systems Biology, Lecture 3
- V. M. Kenkre -- Other Topics in Biological Modeling, Lecture 6, Homework: Strange behavior of the diffusion coefficient
- Gnana Gnanakaran -- Alzheimer's disease: protein misfolding (1:30 - 2:30)
- Bryan Daniels - student talk (30 minutes) (slides)
- Wiet de Ronde - talk on mathematical modeling of signal transduction (10/15 minutes)
- July 29
- Ilya Nemenman -- Stochasticity in Biochemistry and Systems Biology, Lecture 4
- Clifford J. Unkefer -- Other Topics in Biological Modeling, Lecture 7 (45 minutes)
- Pat J. Unkefer -- Other Topics in Biological Modeling, Lecture 8 (45 minutes)
- Andrew Mugler -- student talk (30 minutes)
- Michal Komorowski -- student talk (30 minutes)
- July 30
- John P. Pearson -- Signal Transduction Systems, Lecture 4 (canceled)
- Arthur F. Voter -- Other Topics in Biological Modeling, Lecture 9
- Qiong Yang - student talk (30 minutes)
- Elizabeth Jones - student talk (30 minutes)
- July 31
- Michael E. Wall -- Genetic Regulatory Networks, Lecture 1
- Ilya Nemenman -- Stochasticity in Biochemistry and Systems Biology, Lecture 5
- Steven Wang -- student talk (30 minutes)
- Margaritis Voliotis - student talk (30 minutes)
- Ilya Nemenman -- 3:00pm; an informal tutorial on information theory and molecular sensing
- August 1
- Cynthia J. Olson Reichhardt -- Genetic Regulatory Networks, Lecture 2, part 1 (45 minutes)
- Ilya Nemenman -- Genetic Regulatory Networks, Lecture 2, part 2 (45 minutes)
- Anton Zilman -- Stochasticity in Biochemistry and Systems Biology, Lecture 6
- Abhyudai Singh - student talk (45 min) Stochastic modeling of chemical reactions and gene networks
- Thomas Graham -- student talk (30 min) Measurement and Modeling of Transcriptional Regulation at a Simple Artificial Promoter in Drosophila
- August 2 and 3
- Ideas for weekend activities -- Hiking: volcanic hot springs (e.g., San Antonio Hot Springs) in the Jemez mountains and Bandelier National Monument
- August 4
- Andre Levchenko -- Genetic Regulatory Networks, Lecture 3
- Tomasz Lipniacki -- Genetic Regulatory Networks, Lecture 4 (slides)
- Philip Maini -- Dr. Maini will present a colloquium talk at CNLS (attendance requires LANL visitor badge)
- August 5
- 08:00-09:30 Martha Bulyk -- Genetic Regulatory Networks, Lecture 5 (Rm 203, Los Alamos Research Park)
- 10:00-11:00 Harley McAdams -- Reverse Engineering the Bacterial Cell's Control System (Rm 203, Los Alamos Research Park)
- 11:00-12:00 Lucy Shapiro -- Integration of Dynamic Protein Localization, Proteolysis, and Phospho-signaling Drives Transcriptional Cell Cycle Circuitry (Rm 203, Los Alamos Research Park)
- 12:30-14:00 Robert H. Austin -- Other Topics in Biological Modeling, Lecture 10 (Rm 203, Los Alamos Research Park)
- 14:00-16:00 25 years of GenBank -- (Jemez Room, Oppenheimer Study Center, attendance requires LANL visitor badge)
- August 6
- Depart to Santa Fe for the q-bio Conference
School homeworks
These are representative open-ended homework problems that the students will be asked to work on. New problems will be added soon.
- Homework: Basic problems in stochastic kinetics
- Homework: The toggle switch (Example FSP M-file)
- Homework: Rule-based modeling
- Homework: Generating functional techniques
- Homework: Strange behavior of the diffusion coefficient
- Project: Numerical simulation of a complex biochemical reaction
- Project: Exploring the (hidden) assumptions of signal transduction models
- Project: Designing a directed stochastic oscillator
- Project: Mathematical modeling of gene regulation
- Project: Finding cancer candidate genes
Before arriving to the school, please browse these projects/homework problems and select the ones you'd like to work on. We expect that some of the homeworks will continue well after the school is over, leading to collaborative publications between the school faculty and the students.
