6th q-bio Summer School: Santa Fe Program

Tracks offered at the Santa Fe campus

Project descriptions

QB1
A variety of group projects will be proposed and discussed in the first few days of class. Projects are expected to last beyond the dates of the school and may result in a scientific publications. Projects will consider open problems in the integration of experimental and computational investigations of stochastic gene regulation. General research projects will include: single cell image processing, computational analysis of single cell and single molecule measurements, computer aided experiment selection, among others.
QB2
Individual students or teams of students will develop computational models for Ras/RAF/MEK/ERK signaling. All students participating in this track are expected to read two modeling papers before arriving in Santa Fe: PMID:17947584 and PMID:19167334. Additional reading about Ras/RAF/MEK/ERK signaling is encouraged. Journal club discussions will be led by a student selected by the organizers; this student will receive a special scholarship.
QB3
Projects will be conducted by individual students or groups. Areas of interests varies as protein structure/dynamics, biomolecular aggregations, ligand binding interactions, membrane proteins, carbohydrate characterization, and includes methodologies such as molecular dynamics, Monte-Carlo, enhanced sampling methods, quantum mechanics, polymer models, etc. Students are also encouraged to bring their own questions to solve as projects during the school time and beyond.
QB4
A variety of group projects will be proposed and discussed in the first few days of class. Students are also encouraged to bring their own project ideas. More details are available at Projects QB4.

Detailed schedule

The following schedule is tentative and subject to change at any time. A Google calendar is posted here

Welcome

July 22, 2012 - Sunday
Arrive at St. John's College, Santa Fe, NM
Opening Reception and Orientation, 5-9 PM

Week 1

This week features three lectures per day that will be attended by all students. Each lecture consists of two 45-minute periods with a short break between. There may be a track-specific talk and/or hands-on lab in the afternoon.

July 23, 2012 - Monday
08:00 - 08:30 Welcome and Introductions
08:30 - 10:10 Lecture 1, Bill Hlavacek, Introduction to rule-based modeling
10:30 - 12:10 Lecture 2, Brian Munsky, Introduction to stochastic gene regulation
12:10 - 14:00 Lunch
14:00 - 15:40 Lecture 3, Tony Redondo, Introduction to biomolecular simulations
Track-specific hands-on lab and/or talk
15:40 - 17:30 QB1.1, Student Introductions and discussion of course projects.
15:40 - 17:30 QB2.1 Computer Lab, Bill Hlavacek, BioNetGen, RuleBender and the BioNetGen language (BNGL)
15:40 - 17:30 QB3.1 Talk/Lab, Protein Data Bank Tutorial
15:40 - 17:30 QB4.1, Student introductions and discussion of course projects.
17:30 Dinner
20:00 - 21:00 QB1 Journal Club 1, Discussion of Cagatay, T., et al. (2009) Cell, 1396:512–522.
20:00 - 21:00 QB2 Journal Club 1, Discussion of Dushek O et al. (2011) Biophys J 100, 1189-1197.
20:00 - 21:00 QB3 Journal Club 1, Discussion of Tuckerman et al. (2000) J Phys Chem B 104, 159-178
20:00 - 21:00 QB4 Journal Club 1, Discussion / comparison of Neumann et al (1998) Science 282: 103 HCV dynamics and Perelson et al (1997) Nature 387:188 HIV dynamics
July 24, 2012 - Tuesday
08:30 - 10:10 Lecture 4, Walter Fontana, Fragmentation
10:30 - 11:15 Lecture 5a, Ruy Ribeiro, Introduction to Virus and Immune Response Dynamics
11:25 - 12:10 Lecture 5b, Bette Korber, HIV Evolution and Vaccines
12:10 - 14:00 Lunch
14:00 - 15:40 Lecture 6, Anton Zilman, Stochastic Models of Lymphocyte Proliferation and Death
Track-specific hands-on lab and/or talk
15:40 - 17:30 QB1.2 Computer Lab, Writing and Running the Stochastic Simulation Algorithm -- Matlab required
15:40 - 17:30 QB2.2 Lab, Walter Fontana, extended discussion of fragments and Q&A
15:40 - 17:30 QB3.2 Talk/Lab, Journal Club 2 & 3, Discussion of Tian et al. (2011) J Am Chem Soc 133, 15157-15164 and Liwo et al. (2008) Current Opinion in Structural Biology 18, 134–139.
15:40 - 17:30 QB4.2 Lab Project development
17:30 Dinner
20:00 - 21:00 QB1 Journal Club 2, Discussion of J. Raser, et al. (2004) Science, 304:1811-1814.
20:00 - 21:00 QB2 Journal Club 2, Discussion of Nag A et al. (2012) PLoS ONE 7: e28758.
20:00 - 21:00 QB3 Journal Club 4, Discussion of Venturoli et al. (2005) Biophys J 88, 1778-1798.
20:00 - 21:00 QB4 Journal Club 2, Discussion / comparison of Hellerstein et al (1999) Nat Med 5: 83 T cell dynamics and Ribeiro et al (2002) Proc Natl Acad Sci USA 99:15572 Modeling T cell dynamics
July 25, 2012 - Wednesday
08:30 - 10:10 Lecture 7, Eric Mjolsness, Multiscale simulation algorithms
10:30 - 12:10 Lecture 8, Alan Perelson, How to model a viral infection
12:10 - 14:00 Lunch
14:00 - 14:45 Lecture 9A, Michael Wall, Mechanisms of Gene Regulation
15:00 - 15:45 Lecture 9B, Brian Munsky, Using Single-Cell Mechanisms to Infer Mechanisms of Gene Regulation
Track-specific hands-on lab and/or talk
15:40 - 17:30 QB1.3 Computer Lab, Writing and Running a Finite State Projection Analysis -- Matlab required
15:40 - 17:30 QB2.3 Chalk Talk, Eric Mjolsness, Multiscale simulation algorithms: recitation and exercises
15:40 - 17:30 QB3.3 Talk/Lab, VMD Tutorial
15:40 - 17:30 QB4.3 Tutorial, Rob de Boer, Modeling immune responses
17:30 Dinner
20:00 - 21:00 QB1 Journal Club 3, Discussion of Raj, et al. (2006) PLoS Biology, 4:1707-1719.
20:00 - 21:00 QB2 Journal Club 3, Discussion of Kholodenko et al. (2012) Sci Signal 5:re1.
20:00 - 21:00 QB3 Journal Club 5, Discussion of Dror et al. (2011) Proc. Nat. Acad. Sci., 108:13118-13123.
July 26, 2012 - Thursday
08:30 - 10:10 Lecture 10, Jim Werner and Douglas Shepherd, Single cell and Single Molecule Experiments.
10:30 - 12:10 Lecture 11, Q-Bio Seminar - Regis Pomes, University of Toronto, Atomistic Computational Studies of Peptide-Lipid Interactions
12:10 - 14:00 Lunch
14:00 - 15:40 Lecture 12, Tanmoy Bhattacharya, Introduction to phylogenetics
Track-specific hands-on lab and/or talk
15:40 - 17:30 QB2.4 Talk/Lab, Bill Hlavacek, Extended contact maps and model guides (NB: please read Chylek et al. (2011) Mol BioSyst and Tiger et al. (2012) Mol Syst Biol)
15:40 - 17:30 QB3.4 Talk/Lab, Journal Club 6 & 7, Discussion of Sethi et al. (2011) PLoS Computational Biology, 7:e1002192, Tozzini et al. (2010) Acc. Chem. Res., 43:220-230 and Bellesia et al. (2010) Protein Sci., 19: 141-154.
15:40 - 17:30 QB1.4/QB4.4 Chalk Talk Anton Zilman
17:30 Dinner
20:00 - 21:00 QB1 Journal Club 4, Discussion of Zenklusen, D. et al. Nature Struct. and Mol. Biol. 15, 1263–1271.
20:00 - 21:00 QB2 Journal Club 4, Discussion of Lander AD (2010) BMC Biol 8:40.
20:00 - 21:00 QB3 Journal Club 8, Discussion of Yang et al. (2009) Proc. Nat. Acad. Sci. 106:3776-3781.
July 27, 2012 - Friday
08:30 - 09:15 Lecture 13a, Ruy Ribeiro, Why model in biology?
09:25 - 10:10 Lecture 13b, Brian Munsky, When is a biological model too simple or too complex.
10:30 - 12:10 Lecture 14, Mike Crowley (NREL) - Biomolecular Simulations using molecular dynamics packages CHARMM and AMBER
12:10 - 14:00 Lunch
14:00 - 15:40 Lecture 15, Gregg Beckham (NREL) - Statistical mechanics methods/Biopolymer material properties/Catalyst Design
Track-specific hands-on lab and/or talk
15:40 - 17:30 QB2.5 Talk/Lab, Bill Hlavacek, Q&A, discussion about potential projects, brainstorming, team building
15:40 - 17:30 QB3.5 Talk/Lab, Monte Carlo methods in structural biology
15:40 - 17:30 QB4.5/QB1.5 Tutorial, Mario Castro, Stochastic modelling in viral and immunological systems
17:30 Dinner

Weekend 1

July 28 and 29, 2012 (Saturday and Sunday)
Ideas for weekend activities TBA

Week 2

This week features time for faculty-guided track-specific project work as well as track-specific talks and/or hands-on labs. Note that some talks are intended for students of multiple tracks. This week will also feature several 20-minute student talks per day. The actual schedule will change from day to day depending upon the theme activities.

July 30, 2012 - Monday
8:30 - 11:00 QB1 - Chalk Talk, Derivation of moments for bursting gene expression and other simple biochemical models.
8:30 - 12:00 QB3 - Lectures, Anurag Sethi, Introduction to molecular dynamics simulation and Applications to signaling proteins and quick introduction to free energy calculation methods.
9:00 - 11:00 QB4 - Chalk Talk and Discussion, Frederik Graw, Spatial models of the immune response
14:00-16:00 Tutorial, Anurag Sethi, NAMD & Free energy calculation with NAMD
16:30 - 17:30 Student Talks 1-4
16:30 - 16:50 Sarah E. Kolitz, Measuring Kinase Activities in Single Cells
16:50 - 17:10 Bill Edelman, Dynamic changes in protein abundance and phosphorylation in yeast stress response
17:10 - 17:30 Ziya Kalay, Kinetics of reversible reactions in a structured space, at low reactant densities
17:30 - 17:50 Marek Kochanczyk, SpatKin: Rule-based modeling of spatially extended systems on the membrane
20:00 - 21:00 QB1 Journal Club 5, Discussion of So L-H. et al. (2011) Nature Genetics 6, 554–560.
20:00 - 21:00 QB3 Project, Student project discussion
July 31, 2012 - Tuesday
8:30 am - 10:00am QB3 Lectures, Christoph Junghans, General introduction to Gromacs and its algorithms
10:30 am - 12:00ap QB3 Tutorials, Roland Schulz, "From PDB to MD" - a short Hands-on tutorials
2:00pm - 3:00 pm QB3 Lectures Roland Schulz, Advanced MD simulation techniques and Simulation on HPC machines
3:00pm - 5:00pm QB3 Tutorials Christoph Junghans, Hands-on with Benchmarks and Tests in Gromacs 4.5 and 4.6
8:30 - 11:30 QB1 - Computer Lab, Image processing for single molecule experiments
8:30 - 11:30 QB2 - Experimental Workshop, Kevin Seale, Vanderbilt University, Microfluidic devices to measure single cell dynamics: from design to fabrication to experiment.
9:00 - 12:00 QB4 - Lab, Project development
13:30 - 16:00 QB2 - Experimental Workshop, Kevin Seale, Vanderbilt University, Microfluidic devices to measure single cell dynamics: from design to fabrication to experiment.
20:00 - 21:00 QB1 Journal Club 6, Discussion of Gandhi, S. et al. (2011) Nature Struct. and Mol. Biol. 18, 27–34.
20:00 - 21:00 QB3 Project, Student project discussion
August 1, 2012 - Wednesday
9:00 - 11:30 QB1 - Chalk talk, Nicolai Sinitsyn, Los Alamos National Laboratory, Using moment generating functions to analyze stochastic biochemical kinetics.
8:30 - 12:00 QB3 - Lectures, Giovanni Bellesia, Coarse-grained models for biomacromolecules and Examples of coarse grained models (proteins + lipids + nucleic acids + carbohydrates).
09:00 - 09:50 QB2 - Short lecture, Nathan Lemons, TBA
10:00 - 10:50 QB2 - Talk, Dipak Barua, TBA
09:00 - 10:45 QB4 - Talk, Thomas Leitner, Applying phylogenetics to understanding virus epidemics
13:30 - 16:00 QB1 - Experimental Workshop, Kevin Seale, Vanderbilt University, Microfluidic devices to measure single cell dynamics: from design to fabrication to experiment.
14:00 - 16:00 QB3 - Tutorial, Giovanni Bellesia, Metropolis Monte Carlo and the 2D ising model - code writing from scratch (Java or Fortran 90 or C) and A simple polymer model for proteins - implementation in NAMD (writing topology and parameter files - starting simulations).
16:30 - 17:30 Student Talks 5-8
16:30 - 16:50 Justine Dattani, Analytical solutions of separable Master Equations and applications to gene regulatory networks
16:50 - 17:10 Jonathan Friedman, Stochastic models of the Human Microbiome
17:10 - 17:30 Lily Chylek, Modeling phosphorylation dynamics of the T-cell receptor signaling network
17:30 - 17:50 Pawel Kocieniewski, TBA
20:00 - 21:00 QB1 Journal Club 7, Discussion of Dunlop, M. et al. (2008) Nature Genetics 40, 1493.
20:00 - 21:00 QB3 Project, Student project discussion
August 2, 2012 - Thursday
8:30 - 11:30 QB1 - Experimental Workshop, Kevin Seale, Vanderbilt University, Microfluidic devices to measure single cell dynamics: from design to fabrication to experiment.
8:30 - 9:30 am, QB3 - Lectures, Jianhui Tian, Enhanced sampling methods in classical molecular simulations and Calculation of macroscropic observables and comparison with experiments.
9:45 -10:45 am, QB3 - Lectures, Chang-Shung Tung, A homology-based approach for modeling protein and nucleoprotein complexes.
09:00 - 10:45 QB4 - Talk, Will Fischer, Visualization of sequence diversity and evolution
11:00 - 12:20 QB4/QB3/QB2 - Talk, Zoe Fisher, Los Alamos National Lab Structure determination of biomolecules
14:00 - 16:00 QB3 - Tutorial, Jianhui Tian, Membrane proteins (VMD + Gromacs)
13:30 - 16:00 QB4/??? - Experimental Workshop, Kevin Seale, Vanderbilt University, Microfluidic devices to measure single cell dynamics: from design to fabrication to experiment.
13:30 - 16:00 QB1 - Project Development
16:30 - 17:30 Student Talks 9-12
16:30 - 16:50 Yao Xu, Molecular Dynamics Simulation Studies of Dielectric Response in Photoactive Yellow Protein and Green Fluorescent Protein
16:50 - 17:10 Byoung Koo Lee, Three Dimensional Mathematical Model of Extracellular Matrix in Breast Cancer
17:10 - 17:30 Jonathan Reichel
17:30 - 17:50 Shayani Pieris
20:00 - 21:00 QB1 Journal Club 8, Discussion of Taniguchi, et al. (2008) Science 329, 553.
20:00 - 21:00 QB3 Project, Student project discussion
August 3, 2012 - Friday
8:30 - 12:00, QB3 - Lecture,TBA
9:00 - 10:40 QB1/QB2 Lecture, Jim Faeder, Network-free stochastic simulation of large rule-based models
11:00 - 12:00 QB1/QB2/QB3/QB4, Angel Garcia, Mechanism of Enhanced Mechanical Stability of a Minimal RNA Kissing Complex Elucidated by Non-Equilibrium Molecular Dynamics Simulations. W206
11:00 - 12:00 QB1 - Project Development
14:00 - 17:30 QB1 - Project Development
14:00 - 17:30 QB2 - Lab, Jim Faeder, A general-purpose network-free simulator: NFsim
9:00 - 17:30 QB4 - Project Development

Weekend 2

August 4 and 5, 2012 (Saturday and Sunday)
Ideas for weekend activities TBA

The q-bio Student Symposium

The Sixth Annual q-bio Conference

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

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