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 lab in the afternoon.

July 21, 2012 - Sunday

12:00-17:00, Arrive at St. John's College, Santa Fe, NM

17:00-19:30, Opening Reception and Orientation, (SJC Coffee Shop)

July 22, 2013 - Monday

08:20 - 08:50 Welcome and Introductions, (Great Hall)

08:50 - 10:30 Lecture 1, Brian Munsky, Introduction to stochastic gene regulation, (Great Hall)

10:50 - 12:30 Lecture 2, Tony Redondo, Introduction to biomolecular simulations, (Great Hall)

12:30 - 14:00 Lunch

14:00 - 15:40 Lecture 3, Bill Hlavacek, Introduction to rule-based modeling, (Great Hall) (slides, LA-UR-08-7878)

Track-specific hands-on labs and/or talks

15:40 - 17:30 Special Session, Cleve Moler, Installation and introduction to MATLAB, (Great Hall)

15:40 - 17:30 QB5.1, Student Introductions, discussion of course projects, software installation, or Special Session (Win 101)

17:30 Dinner

19:00 - 21:00 QB3.1, Gnana - Student Introductions, Giovanni Bellesia Theoretical Basis of Molecular Dynamics, (Win 201)

July 23, 2013 - Tuesday

08:30 - 10:10 Lecture 4, Marek Kimmel, Stochastic models of proliferation of normal and leukemic cell clones, (Great Hall)

10:30 - 12:10 Lecture 5, Ruy Ribeiro, Introduction to Virus and Immune Response Dynamics, (Great Hall)

12:10 - 14:00 Lunch

14:00 - 15:40 Lecture 6, Wouter-Jan Rappel, Chemotaxis, (Great Hall)

Track-specific hands-on lab and/or talk

15:40 - 17:00 QB1.2, Kevin Seale, Microfluidics Lab, (ESL 123 Lab)

15:40 - 17:30 QB2.2, Wouter-Jan Rappel, Models for chemotactic signaling, (Great Hall)

15:40 - 17:30 QB3.2, Giovanni Bellesia, Coarse-grained Molecular models, (Win 101)

15:40 - 17:30 QB4.2, Introduction and discussion of school projects, see Projects QB4, (Win 206)

15:40 - 17:30 QB5.2, Core lecturers: Time to meet and discuss, (Win 201)

17:30 Dinner

19:00 - 22:00 QB3 Evening Microfluidics Lab, (ESL 123 Lab)

July 24, 2013 - Wednesday

08:30 - 10:10 Lecture 7, Seth J. Corey, Molecular circuitry of granulocyte differentiation and its alterations leading to leukemia, (Great Hall)

10:30 - 12:10 Lecture 8, Linda Petzold, Stochastic Simulation: Algorithms and Software, (Great Hall)

12:10 - 14:00 Lunch

14:00 - 15:40 Lecture 9, Ryan N. Gutenkunst, "Systems biology's dirty secret: Parameter estimation, sensitivity analysis, and sloppiness", (Great Hall)

Track-specific hands-on lab and/or talk

15:40 - 17:30 QB1.3 Discussion/Lab, Spatial Stochastic Analyses, Linda Petzold and Giovanni Bellesia -- Matlab and COMSOL required, (Great Hall)

15:40 - 17:30 QB2.3, Ryan N. Gutenkunst, "Network constraints on protein evolution", (Win 201)

15:40 - 17:30 QB3.3, Anurag Sethi VMD Tutorial, (Win 101)

15:40 - 17:30 QB4.3, Mario Castro Stochastic modelling in viral and immunological systems, (ESL 123 - Side Room)

15:40 - 17:30 QB5.3, Biao Li, SimuPop and rare variant generation (intro, to be followed by demonstrations), (Win 206)

15:40 - 17:30 Community Microfluidics Lab, Kevin Seale, (ESL 123 Lab)

17:30 Dinner

19:00 - 22:00 QB4, Evening Microfluidics Lab, (ESL 123 Lab)

July 25, 2013 - Thursday

08:30 - 10:10 Lecture 10, Cristian Tomasetti, Population genetics of driver and passenger mutations in leukemic stem cells, (Great Hall)

10:30 - 12:10 Lecture 11, Alan Perelson, How to model a viral infection, (Great Hall)

12:10 - 14:00 Lunch

14:00 - 15:40 Lecture 12, Tanmoy Bhattacharya, Introduction to phylogenetics, (Great Hall)

Track-specific hands-on lab and/or talk

15:40 - 17:30 QB1.4, Students Should attend QB5.4, (Win 201)

15:40 - 17:30 QB2.4, Kevin Seale, Microfluidics Lab, (ESL 123 Lab)

15:40 - 17:30 QB3.4, Giovanni Bellesia, A simple MD study of a Lennard Jones system, (Win 101)

15:40 - 17:30 QB4.4, Rob de Boer, Spatial modeling of immune responses, (Great Hall)

15:40 - 17:30 QB5.4, Marek Kimmel, Models of genetic and phenotypic heterogeneity in cancer growth and progression (Part 1), (Win 201)

17:30 Dinner

19:00 - 22:00 QB1, Evening Microfluidics Lab, (ESL 123 Lab)

July 26, 2013 - Friday

08:30 - 10:10 Lecture 13, Gnana Gnanakaran (LANL) - Spatial Temporal Aspects of Cell Signaling (Great Hall)

10:30 - 12:10 Lecture 14, Gnana Gnanakaran (LANL) - Spatial Temporal Aspects of Cell Signaling (Great Hall)

12:10 - 14:00 Lunch

14:00 - 15:40 Lecture 15, Jim Werner, Single cell and Single Molecule Experiments, (Great Hall)

Track-specific hands-on lab and/or talk

15:40 - 17:30 QB1.5, Students should join QB3.5 or QB4.5

15:40 - 17:30 QB2.5, Journal club, (Win 101)

15:40 - 17:30 QB3.5, Giovanni Bellesia, Hands-on Monte Carlo Tutorial, (Great Hall)

15:40 - 17:30 QB4.5, Timothy Reluga, Introduction to population game methods for evolution, (Win 201)

15:40 - 17:30 QB5.5, Biao Li, software presentation (or join QB4.5)

17:30 Dinner