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The Tenth q-bio Summer School - New Mexico: Schedule

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Back to The Tenth q-bio Summer School - New Mexico

Week 1

Sunday, July 10

14:00- Check-in
Casas del Rio (on the campus of University of New Mexico at 420 Redondo E Dr NE, Albuquerque)
24/7 front desk service on the first floor of Building 2 (Jemez)
18:00-20:00 Reception
Faculty and Staff Club (on the campus of University of New Mexico at 1923 Las Lomas Rd NE, Albuquerque)
Buffet and cash bar
Orientation

Monday, July 11

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 1
Location: Student Union Building Acoma A and B
Lecturer: James R. Faeder, University of Pittsburgh School of Medicine
Title and Abstract: Introduction to modeling signal transduction using rules
Slides: Powerpoint slides
10:15-10:30 Coffee Break
10:30-12:15 Lecture 2
Location: Student Union Building Acoma A and B
Lecturer: Ruy M. Ribeiro, Los Alamos National Laboratory
Title and Abstract: Introduction to viral dynamics and modeling
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 1 - cancelled (orientation instead)
13:45-14:15 Student Talk 2 - cancelled (orientation instead)
14:15-17:00 Labs
14:15-15:30 Computer Lab 1
Location: Student Union Building Acoma A and B
Instructor: James R. Faeder, University of Pittsburgh School of Medicine
Title and Abstract: Introduction to biochemical modeling with BioNetGen
15:30-15:45 Break
15:45-17:00 Computer Lab 2
Location: Student Union Building Acoma A and B
Instructor: Ruy M. Ribeiro, Los Alamos National Laboratory
Title and Abstract: Modeling with statistics
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Tuesday, July 12

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 3
Location: Student Union Building Acoma A and B
Lecturer: Brian J. Drawert, University of California, Santa Barbara
Title and Abstract: Stochastic modeling and simulation of biochemical systems
10:15-10:30 Coffee Break
10:30-12:15 Lecture 4
Location: Student Union Building Acoma A and B
Lecturer: Martin Meier-Schellersheim, National Institute of Allergy and Infectious Disease
Title and Abstract: Exploring signaling network behavior and performing spatial simulations
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 3 - William Gray
13:45-14:15 Student Talk 4 - Thibaut Lagny (abstract)
14:15-17:00 Labs
14:15-15:30 Computer Lab 3
Location: Student Union Building Acoma A and B
Instructor: Brian J. Drawert, University of California, Santa Barbara
Title and Abstract: StochSS
15:30-15:45 Break
15:45-17:00 Computer Lab 4
Location: Student Union Building Acoma A and B
Instructor: James R. Faeder, University of Pittsburgh School of Medicine
Title and Abstract: Introduction to modeling reaction-diffusion systems with MCell and CellBlender
Link for software download
17:00-19:00 Hands on Workshops on Single Particle Tracking and Superresolution Imaging
Pizza dinner will be provided.
Location: Cancer Research Facility CRF 207 and Physics
Instructor: Mara P. Steinkamp
Groups
Super-resolution Group
Single Particle Tracking Group
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Wednesday, July 13

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 5
Location: Student Union Building Acoma A and B
Lecturer: Diane Lidke, University of New Mexico
Title and Abstract: Fluorescence microscopy to quantify protein behavior in living cells
10:15-10:30 Coffee Break
10:30-12:15 Lecture 6
Location: Student Union Building Acoma A and B
Lecturer: Fabian Cardozo, Los Alamos National Laboratory
Title and Abstract: HIV latency: biology and models
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 5 - mini tutorial on Data2Dynamics (Kalina Slavkova)
13:45-14:15 Student Talk 6 - Paul Mlynarczyk
14:15-17:00 Labs
14:15-15:30 Computer Lab 5
Location: Student Union Building Acoma A and B
Instructor: Martin Meier-Schellersheim, National Institute of Allergy and Infectious Disease
Title and Abstract: Simmune (part 1 of 2)
*Please download Simmune Software before this session from: Simmune Registration and Download
15:30-15:45 Break
15:45-17:00 Computer Lab 6
Location: Student Union Building Acoma A and B
Instructor: Martin Meier-Schellersheim, National Institute of Allergy and Infectious Disease
Title and Abstract: Simmune (part 2 of 2)
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Thursday, July 14

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 7
Location: Student Union Building Acoma A and B
Lecturer: Judy Cannon and Melanie Moses, University of New Mexico
Title and Abstract: Quantitative analysis and modeling of T cell movement
10:15-10:30 Coffee Break
10:30-12:15 Lecture 8
Location: Student Union Building Acoma A and B
Lecturer: Danny Perez, Los Alamos National Laboratory
Title and Abstract: Introduction to kinetic Monte Carlo (KMC)
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 7 - Kalina Slavkova
13:45-14:15 Student Talk 8 - Janie Rae Byrum (abstract)
14:15-17:00 Labs
14:15-15:30 Computer Lab 7
Location: Student Union Building Acoma A and B
Instructor: Youfang Cao, Los Alamos National Laboratory
Title and Abstract: Using the accurate chemical master equation (ACME) modeling method to study stochastic viral dynamics
15:30-15:45 Break
15:45-17:00 Computer Lab 8
Location: Student Union Building Acoma A and B
Instructor: William S. Hlavacek
Title and Abstract: Exercises in using the RuleBender/BioNetGen/NFsim software stack
17:00-19:00 Hands on Workshops on Single Particle Tracking and Superresolution Imaging
Pizza dinner will be provided.
Location: Cancer Research Facility CRF 207 and Physics
Instructor: Mara P. Steinkamp
Groups
Super-resolution Group 2
Single Particle Tracking Group 2
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Friday, July 15

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 9
Location: Student Union Building Acoma A and B
Lecturer: Cédric Cleyrat and Tess Shideler
Title and Abstract: Quantitative Analysis of Membrane Dynamics During Endocytosis
10:15-10:30 Coffee Break
10:30-12:15 Lecture 10
Location: Student Union Building Acoma A and B
Lecturer: Alan S. Perelson, Los Alamos National Laboratory
Title and Abstract: How to model a viral infection
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 9 - Maulik Nariya
13:45-14:15 Student Talk 10 - Amy Prager
14:15-17:00 Labs
14:15-15:30 Computer Lab 9
Location: Student Union Building Acoma A and B
Instructor: Keith Lidke
Title and Abstract: Data analysis for single-particle tracking and super-resolution Part 1
15:30-15:45 Break
15:45-17:00 Computer Lab 10
Location: Student Union Building Acoma A and B
Instructor: Keith Lidke
Title and Abstract: Data analysis for single-particle tracking and super-resolution Part 2
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Saturday, July 16

Free time

Week 2

Sunday, July 17

Free time

Monday, July 18

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 11
Location: Student Union Building Acoma A and B
Lecturer: Ryan N. Gutenkunst, University of Arizona
Title and Abstract: Parameter sensitivity, sloppiness, and evolution of biomolecular networks
10:15-10:30 Coffee Break
10:30-12:15 Lecture 12
Location: Student Union Building Acoma A and B
Lecturer: Ryan N. Gutenkunst, University of Arizona
Title and Abstract: BioModels - reproducible and reusable modeling in systems biology
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 11 - Rory Brittain
13:45-14:15 Student Talk 12 - Sara Lumbreras
14:15-17:00 Labs
14:15-15:30 Computer Lab 11
Location: Student Union Building Acoma A and B
Instructor: Ryan N. Gutenkunst, University of Arizona
Title and Abstract: BioModels curation and annotation using COPASI
15:30-15:45 Break
15:45-17:00 Computer Lab 12
Location: Student Union Building Acoma A and B
Instructor: Ryan N. Gutenkunst, University of Arizona
Title and Abstract: BioModels work session (part 1 of 2)
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Tuesday, July 19

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 13
Location: Student Union Building Acoma A and B
Lecturer: Bridget Wilson
Title and Abstract: Part 1: Fundamentals of membranes and signal transduction. Part II: Integrating Experimentation and Mathematical Modeling
10:15-10:30 Coffee Break
10:30-12:15 Lecture 14
Location: Student Union Building Acoma A and B
Lecturer: Jeremie Guedj, INSERM (French National Institute of Health and Medical Research), Paris, France
Title and Abstract: Pharmacokinetics / pharmacodynamics for viral infections
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 13 - Dhananjay Bhaskar (abstract)
13:45-14:15 Student Talk 14 - Sean Aller (abstract)
14:15-17:00 Labs
14:15-15:30 Computer Lab 13
Location: Student Union Building Acoma A and B
Instructor: Nick Hengartner, Los Alamos National Laboratory
Title and Abstract: Small n, Large p: A primer on modern model selection with application to function estimation
15:30-15:45 Break
15:45-17:00 Computer Lab 14
Location: Student Union Building Acoma A and B
Instructor: Ryan N. Gutenkunst, University of Arizona
Title and Abstract: Biomodels work session (part 2 of 2)
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Wednesday, July 20

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 15
Location: Student Union Building Acoma A and B
Lecturer: Ryan Suderman, Los Alamos National Laboratory
Title and Abstract: BioNetFit - a tool for fitting compatible with rule-based models and parallel computing resources
10:15-10:30 Coffee Break
10:30-12:15 Lecture 16
Location: Student Union Building Acoma A and B
Lecturer: Whelton A. Miller III, Lincoln University
Title and Abstract: A Brief Introduction to Medicinal Chemistry
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 15 - Charuta Palsuledesai
13:45-14:15 Student Talk 16 - Bronson Weston
14:15-17:00 Labs
14:15-15:30 Computer Lab 15
Location: Student Union Building Acoma A and B
Instructor: Mario Castro, U. Comillas, Madrid, Spain
Title and Abstract: Stochastic models in viral dynamics: a case study
15:30-15:45 Break
15:45-17:00 Computer Lab 16
Location: Student Union Building Acoma A and B
Instructor: Ryan Suderman, Los Alamos National Laboratory
Title and Abstract: ML-Rules tutorial
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Thursday, July 21

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 17
Location: Student Union Building Acoma A and B
Lecturer: Whelton A. Miller III, Lincoln University
Title and Abstract: Molecular docking with AutoDock
10:15-10:30 Coffee Break
10:30-12:15 Lecture 18
Location: Student Union Building Acoma A and B
Lecturer: Michael Wester, University of New Mexico SpatioTemporal Modeling Center
Title and Abstract: Clustering Algorithms
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 17 - Lauren Shriver (abstract)
13:45-14:15 Student Talk 18 - Amy Prager
14:15-17:00 Labs
14:15-15:30 Computer Lab 17 (actually a lecture)
Location: Student Union Building
Instructor: Martin Lopez Garcia
Title and Abstract: A Markovian approach for modelling biochemical reactions: analysis of stochastic performance measures
15:30-15:45 Break
15:45-17:00 Computer Lab 18
Location: Student Union Building
Instructor: Anton Zilman, University of Toronto, Canada
Title and Abstract: Stochastic models: chalk talk
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Friday, July 22

07:00-08:30 Breakfast
La Posada Dining Hall
08:30-10:15 Lecture 19
Location: Student Union Building Acoma A and B
Lecturer: Ruian Ke, North Carolina State University, Raleigh
Title and Abstract: Multiscale viral evolutionary dynamics
10:15-10:30 Coffee Break
10:30-12:15 Lecture 20
Location: Student Union Building Acoma A and B
Lecturer: James (Mac) Hyman, Tulane University
Title and Abstract: Good choices for great Careers (slides)
12:15-13:15 Lunch
Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks
Location: Student Union Building Acoma A and B
13:15-13:45 Student Talk 19 - Jonty Carruthers
13:45-14:15 Student Talk 20 - TBA
14:15-17:00 Labs
14:15-15:30 Computer Lab 19
Location: Student Union Building Acoma A and B
Instructor: Martin Lopez Garcia
Title and Abstract: A computational approach for stochastic performance measures: exact analysis vs. Gillespie simulations
15:30-15:45 Break
15:45-17:00 Computer Lab 20
Location: Student Union Building Acoma A and B
Instructor: Ruian Ke, North Carolina State University, Raleigh
Title and Abstract: Modeling approaches to describe multiscale dynamics
17:00-18:30 Dinner
La Posada Dining Hall
18:30-20:30 Project Team Work
Common rooms and study/meeting rooms in Casas del Rio

Saturday, July 23

Project presentations and poster presentations, Acoma meeting room in the Student Union Building (9 AM to noon)
Farewell, Lunch will be served at noon in the Luminaria room

Week 3

Sunday, July 24

Travel to Nashville (on your own) for q-bio Student Symposium and q-bio Conference

July 25 and 26

q-bio Student Symposium, Nashville, Tennessee

July 27-30

The 10th Annual q-bio Conference, Nashville, Tennessee