The First q-bio Summer School: Program

Back to The First q-bio School. You may also want to view the program of the associated Conference.

This is an evolving document.

The First q-bio Summer School on Cellular Information Processing is being sponsored by the New Mexico Consortium's Institute for Advanced Studies and the Center for Nonlinear Studies at Los Alamos National Laboratoty. Participants will attend daily lectures about theory and modeling of cellular information processing systems, including coverage of signal transduction mechanisms, stochastic biochemistry, and design principles of genetic regulatory systems. Participants will work in small teams on selected research projects 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.

The summer school participants have been selected following a rigorous application process. If you'd like to put your name on the wait list, please contact us as described here. Participants, please be aware that you are expected to bring a laptop with you to the Summer School or to inform us about your inability to do so.

The q-bio Summer School is not affiliated with arXiv.q-bio.

School Logistics

• Ride Sharing Board
• School Participants
• Essential information about the Los Alamos area
• All dates are in 2007
• Information about the school hotel
• Travel Information
• What to do in the vicinity of Los Alamos
• The classes will be held at the Los Alamos Research Park, except for 08/07/07, when they will be held at the Otowi room.
• Safety and Security
• We will attempt to arrange Los Alamos visitor badges for students starting Wed, Jul 25, 2007. These will allow visiting school faculty in unclassified areas of the main technical area of the lab (TA-3). Note that some badge requests may not be approved. However, having or not having a badge will not adversely affect one's ability to participate in the school activities.

Main School Themes

After the summer school, students will participate in the q-bio Conference in Santa Fe, NM, Aug 8-11, 2007; this facilitated the choice of the themes for the summer school. They are

• Signal Transduction Mechanisms, organized by William Hlavacek and Jim Faeder
• Stochasticity in Biochemistry and Systems Biology, organized by Ilya Nemenman
• Gene Regulation, organized by Michael Wall
• Other Topics in Biological Modeling, organized by Yi Jiang

School Schedule

Unless otherwise noted on specific dates, the school schedule will consist of 4 hours of lectures in the morning, separated by a short break:

• 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 is left for other activities, such as ad hoc lectures, discussions, and study sessions, work on school 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 members at the Lab premises, familiarizing themselves with the workings of the research institution and potentially starting collaborative research with the faculty.

Finally, the class admitted to this summer school is extrmeely strong, and the students have a great opprtunity to learn from each other. Therefore, we will have regular one hour long seminars almost every afternoon, during which the students will be able to present their q-bio work (done prior to the arrival to the school) to the rest of the students, to the faculty, and to the laboratory staff in general. These lectures are scheduled for

• 2:00-3:00 -- Student Lectures

Please email the conference organizers if you want to present a student lecture.

July 22

Arrival to the School Hotel.

July 23

Opening remarks

Lecture One -- Signal Transduction Mechanisms, Lecture 1

Lecture Two -- Gene Regulation, Lecture 1

Student Lecture: introduction to school projects

July 24

Lecture One -- Stochasticity in Biochemistry and Systems Biology, Lecture 1

Lecture Two -- Other Topics in Biological Modeling, Lecture 1

July 25

Lecture One -- Signal Transduction Mechanisms, Lecture 2

Lecture Two -- Gene Regulation, Lecture 2

Student Lecture: Jaewook Joo. Roles of two negative feedback loops on dynamic patterns of NF-kappaB signaling.

July 26

Lecture One -- Stochasticity in Biochemistry and Systems Biology, Lecture 2

Lecture Two -- Other Topics in Biological Modeling, Lecture 2

Student Lecture: Brian Munsky, UCSB. Finite State Projection based solutions to the Chemical Master Equation.

July 27

Lecture One -- Other Topics in Biological Modeling, Lecture 3

Lecture Two -- Signal Transduction Mechanisms, Lecture 3

Student Lecture (note that this lecture will happpen at 2pm): Genie Hsieh, UNM. Modeling Cell Signaling Pathways with Spatially Explicit Mobile Agents.

July 28, 29

Weekend -- outdoor activities

July 30

Lecture One -- Stochasticity in Biochemistry and Systems Biology, Lecture 3

Lecture Two -- Other Topics in Biological Modeling, Lecture 4

Student Lecture: Ah Ram Kim, SUNYSB. Systems biology analysis of the transcriptional regulation of stripe 2 and 3 expression of drosophila even skipped gene.

July 31

Lecture One -- Other Topics in Biological Modeling, Lecture 5

Lecture Two -- Signal Transduction Mechanisms, Lecture 4

Student Lecture: Edda Schultz and Luca Mariani, Humboldt. Modeling regulatory mechanisms in T helper lymphocytes: Activation, differentiation and memory. Abstract.

August 1

Lecture One -- Stochasticity in Biochemistry and Systems Biology, Lecture 4

Lecture Two -- Other Topics in Biological Modeling, Lecture 6

Student Lecture: Maciej Dobrzynski, CWI. Computational methods for diffusion-influenced biochemical reactions. Relevant paper.

August 2

Lecture One -- Gene Regulation, Lecture 3

Lecture Two -- Signal Transduction Mechanisms, Lecture 5

Student Lecture: Michelle Costa, UNM. Merging Spatial and Non-Spatial Algorithms

Second Student Lecture: (short lecture) Bobby Prill, JHU. Network Motif Dynamics.

August 3

Lecture One -- Stochasticity in Biochemistry and Systems Biology, Lecture 5

Lecture Two -- Other Topics in Biological Modeling, Lecture 7

Student Lecture: Bibhash Mukhopadhyay, Baylor. Cell polarity: Understanding through experimental biology and mathematical modeling. Abstract.

August 4, 5

Weekend -- outdoor activities

August 6

Lecture One -- Other Topics in Biological Modeling, Lecture 8

Lecture Two -- Gene Regulation, Lecture 4

Student Project Reports -- Heather Hardway, Bobby Prill, Jay Konieczka and Katja Wegner, Brian Munsky, Luca Mariani and Maciej Dobrzynski and Srividya Iyer Biswas, Yang Yang and Edda Schulz

August 7 - lectures this day will be in the Otowi room

Lecture One (8:30 AM to 10:00) -- Stochasticity in Biochemistry and Systems Biology, Lecture 6

Lecture Two (10:30 to noon) -- Signal Transduction Mechanisms, Lecture 6

August 8

Departure to Santa Fe for the q-bio Conference (organized bus)

A fun morning in Santa Fe, followed by the conference tutorials and banquet

School projects

• Project: Numerical simulation of a complex biochemical reaction
• Project: Biofilm formation
• Project: Exploring the (hidden) assumptions of signal transduction models
• Project: Designing a directed stochastic oscillator
• Project: Mathematical modeling of gene regulation
• Project: Coarse-graining biochemical reactions by RG approach

Before arriving to the school, please browse these projects and select the ones you'd like to work on. Somewhere inbetween a regular homework problem and a full-scale research project, these summer school projects will represent a good opprtunity to immerse onself in the cutting-edge research. We expect that some of the projects will continue well after the school is over, leading to collaborative publications between the school faculty and the students.