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