The Ninth q-bio Summer School - Albuquerque: Schedule

Back to The Ninth q-bio Summer School - Albuquerque

Arrival

Sunday, July 12

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); Pizza and cash bar

Week 1

Monday, July 13

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Orientation: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); 08:30-08:55 Welcome, Bill Hlavacek; 08:55-09:15 Overview and Description of Project(s) - Biomolecular Simulations, Giovanni Bellesia; 09:15-09:35 Overview and Description of Project(s) - Cell Signaling, Bill Hlavacek; 09:35-09:55 Overview and Description of Experimental Labs - Membrane Biology, Mara Steinkamp; 09:55-10:15 Overview and Description of Project(s) - Viral Dynamics, Ruy Ribeiro
10:15-10:30 Coffee Break: Please sign up for a Student Talk and Experimental Labs during this time or as soon as possible (see an organizer)
10:30-12:15 Lecture 1: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Ruy M. Ribeiro; Title and Abstract: Introduction to modeling the immune response to virus
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-15:00 Lecture 2: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); Lecturer: James R. Faeder and William S. Hlavacek; Title and Abstract: Introduction to rule-based modeling: principles and algorithms
15:00-15:15 Break
15:15-16:15 Labs: 15:15-16:15 Computer Lab 1; Student Union Building, Room 3037 (Lobo); Instructor: Ruy M. Ribeiro; Title and Abstract: R for statistical computing
16:15-17:00 Kick-off Project Team Meetings with Mentors: Biomolecular Simulations Team(s); Student Union Building, Room 3037 (Lobo A); Cell Signaling Team(s); Student Union Building, Room 3019 (Sandia); Viral Dynamics Team(s); Student Union Building, Room 3018 (Scholars)
17:00-18:30 Dinner: La Posada Dining Hall
18:30-20:30 Project Team Work: Biomolecular Simulations Team(s); Meet at first floor common room/lounge and then move to a study/meeting room, Chama Building, Casas del Rio; Cell Signaling Team(s); Meet at first floor common room/lounge and then move to a study/meeting room, Chama Building, Casas del Rio; Viral Dynamics Team(s); Meet at first floor common room/lounge and then move to a study/meeting room, Chama Building, Casas del Rio

Tuesday, July 14

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 3: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Giovanni Bellesia; Title and Abstract: Introduction to molecular dynamics simulations
10:15-10:30 Coffee Break
10:30-12:15 Lecture 4: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Cesar Lopez Bautista; Title and Abstract: Coarse grained molecular dynamics simulations of biological systems
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 1 - Mathias Engel; 13:35-13:55 Student Talk 2 - Sanjana Gupta; 13:55-14:15 Student Talk 3
14:15-16:00 Labs: 14:15-16:00 Computer Lab 3; Student Union Building, Room 3019 (Lobo); Instructor: James R. Faeder and William S. Hlavacek; Title and Abstract: Software for compartmental rule-based modeling: RuleBender, BioNetGen and NFsim
16:00-16:15 Break
16:15-17:00 Recitation: Recitation 2; Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Discussant/Tutor: Mara Steinkamp and Cédric Cleyrat; Title and Abstract: Current Trends in Single Particle Tracking and Superresolution Microscopy
17:00-18:30 Dinner: La Posada Dining Hall
17:00-19:00: Laboratory session 1 5-7 PM (single particle tracking or localization microscopy): [students participating in this session will miss dinner; the dining hall closes at 7]
18:30-20:30 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Wednesday, July 15

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 5: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Sergei Tretiak; Title and Abstract: Introduction to Quantum Mechanics Simulations
10:15-10:30 Coffee Break
10:30-12:15 Lecture 6: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Judy Cannon; Title and Abstract: Quantitative analysis of T cell movement in lymph nodes
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 4 - Nazanin Mosavian; 13:35-13:55 Student Talk 5; 13:55-14:15 Student Talk 6
14:15-16:00 Labs: 14:15-16:00 Computer Lab 5; Student Union Building, Room 3019 (Sandia); Instructor: James R. Faeder; Title and Abstract: Software for spatial modeling of cellular processes: MCell and CellBlender
16:00-16:15 Break
16:15-17:30 Recitation: Recitation 3; Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Discussant/Tutor: Nikolai A. Sinitsyn; Topic: Mesoscopic fluctuations in biological systems (a chalk talk)
17:30-18:30 Dinner: La Posada Dining Hall
18:30-20:30 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Thursday, July 16

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 7: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Bridget Wilson; Title and Abstract: The Fundamentals of Signal Transduction
10:15-10:30 Coffee Break
10:30-12:15 Lecture 8: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Mario Castro; Title and Abstract: Stochastic modelling of viral and immunological systems
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 7 - Tess Shideler; 13:35-13:55 Student Talk 8 - Emil Markland; 13:55-14:15 Student Talk 9 - Claudia Hernandez
14:15-16:00 Labs: 14:15-16:00 Computer Lab 7; Student Union Building, Room 3019 (Sandia); Instructor: TBA; Title and Abstract: TBA; 14:15-16:00 Computer Lab 8; Student Union Building, Room 3018 (Scholars); Instructor: Mario Castro; Title and Abstract: Using TinkerCell for modelling dynamical systems
16:00-16:15 Break
16:15-17:00 Free time for project team meetings
17:00-18:30 Dinner: La Posada Dining Hall
17:00-19:00: Laboratory session 1 5-7 PM (single particle tracking or localization microscopy): [students participating in this session will miss dinner]
18:30-20:30 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Friday, July 17

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 9: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Aaron K. Neumann; Title and Abstract: Biophysics of T cell Activation
10:15-10:30 Coffee Break
10:30-12:15 Lecture 10: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Danny Perez; Title and Abstract: Kinetic Monte Carlo
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 10 - Yi Bao; 13:35-13:55 Student Talk 11; 13:55-14:15 Student Talk 12
14:15-16:00 Labs: 14:15-16:00 Computer Lab 10; Student Union Building, Room 3018 (Scholars); Instructor: Danny Perez; Title and Abstract: KMC tutorial
16:00-16:15 Break
16:15-17:30 Lab: Computer Lab 9; Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Instructor: Youfang Cao; Title and Abstract: Using the the multi-buffer method for stochastic modeling; '16:15-17:30 Computer Lab 10
17:30-19:00 Dinner: La Posada Dining Hall
19:00-21:00 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Weekend 1

Saturday, July 18

Free time

Sunday, July 19

Free time

Week 2

Monday, July 20

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 11: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Diane Lidke; Title and Abstract: Fluorescence microscopy to quantify protein behavior in living cells
10:15-10:30 Coffee Break
10:30-12:15 Lecture 12: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Maciek Swat; Title and Abstract: Introduction to Virtual Tissues. Implementing Virtual Tissues in CompuCell3D
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 13; 13:35-13:55 Student Talk 14 - Gulio Prevedello; 13:55-14:15 Student Talk 15 - Afroza Shirin
14:15-17:00 Lab: 14:15-17:00 Computer Lab 11; Student Union Building, Lobo conference room (3rd floor); Instructor: Maciek Swat; Title and Abstract: Simulations using CompuCell3D
17:00-19:00 Dinner: La Posada Dining Hall
19:00-21:00 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Tuesday, July 21

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 13: Student Union Building, Acoma conference room (3rd floor); Lecturer: Gerard Ostheimer; Title and Abstract: Data-driven modeling of cell signaling networks
10:15-10:30 Coffee Break
10:30-12:15 Lecture 14: Student Union Building, Acoma conference room (3rd floor); Lecturer: Alan S. Perelson; 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: Student Union Building, Acoma conference room (3rd floor); 13:15-13:35 Student Talk 16 - Mahboobeh Ghorbani; 13:35-13:55 Student Talk 17 - Nicola Coker Gordon; 13:55-14:15 Student Talk 18
14:15-16:00 Lab: 14:15-16:00 Computer Lab 14; Student Union Building, Acoma conference room (3rd floor); Instructor: Maciek Swat; Title and Abstract: CompuCell3D lab (part 2)
16:00-16:15 Break
16:15-17:30 Recitation: Recitation 7; Student Union Building, Acoma conference room (3rd floor); Discussant/Tutor: Ruy M. Ribeiro; Topic: Why model in biology?; Recitation 10; Student Union Building, Acoma conference room (3rd floor); Discussant/Tutor: Gerard Ostheimer; Topic: The global bioeconomy: bioenergy and biomedicine (perspectives and discussion)
17:30-19:00 Dinner: La Posada Dining Hall
19:00-21:00 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Wednesday, July 22

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 15: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Lydia Tapia; Title and Abstract: Geometric and physics-based simulation of macromolecular complex assembly
10:15-10:30 Coffee Break
10:30-12:15 Lecture 16: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Ludmil B. Alexandrov; Title and Abstract: Discovering signatures of mutational processes
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 19 - Elena Aruffo; 13:35-13:55 Student Talk 20 - Luis de la Higuera; 13:55-14:15 Student Talk 21
14:15-17:30 Labs: 14:15-16:00 Computer Lab 15; Student Union Building, Lobo conference room (3rd floor); Instructor: Mark Olah and Keith Lidke; Title and Abstract: Introduction to data analysis for single-particle tracking and super-resolution; 16:00-17:30 Computer Lab 16; Student Union Building, Lobo conference room (3rd floor); Instructor: Ludmil B. Alexandrov; Title and Abstract: Non-negative matrix factorization
17:30-18:00 Recitation: Recitation 8; Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Discussant/Tutor: Ludmil B. Alexandrov; Topic: Big data (Q&A)
18:00-19:00 Dinner: La Posada Dining Hall
18:30-20:30 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Thursday, July 23

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 17: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Adam Halasz, West Virginia University; Title and Abstract: Integration of spatial data in modeling
10:15-10:30 Coffee Break
10:30-12:15 Lecture 18: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Nick Hengartner; Title: Small n, Large p. A primer of modern model selection with application to function estimation
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 22 - Angie Raad; 13:35-13:55 Student Talk 23 - Harry Tideswell; 13:55-14:15 Student Talk 24
14:15-17:30 Labs: 14:15-16:00 Computer Lab 17; Student Union Building, Lobo conference room (3rd floor); Instructor: Keith Lidke and Mark Olah; Title and Abstract: Data analysis for single particle tracking and super-resolution 2; 16:00-17:30 Computer Lab 18; Student Union Building, Lobo conference room (3rd floor); Instructor: Gerard Ostheimer; Title and Abstract: Partial least squares regression
17:30-19:00 Dinner: La Posada Dining Hall
19:00-21:00 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Friday, July 24

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 19: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Brian Munsky; Title and Abstract: Listening to the noise: learning predictive models for single-cell gene regulation
10:15-10:30 Coffee Break
10:30-12:15 Lecture 20: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Rob de Boer; Title and Abstract: Modeling the immune response
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:15 Student Talks: Student Union Building, Rooms 3037 and 3039 (Lobo A & B); 13:15-13:35 Student Talk 25 - Allen Liu; 13:35-13:55 Student Talk 26 - Breanne Sparta; 13:55-14:15 Student Talk 27 - Daniel Hancock
14:15-17:30 Labs: 14:15-16:00 Computer Lab 19; Student Union Building, Lobo conference room (3rd floor); Instructor: Rob de Boer; Title and Abstract: Fitting deuterium labeling data of T-cell dynamics; 16:00-17:30 Computer Lab 20; Student Union Building, Lobo conference room (3rd floor); Instructor: Brian Munsky; Title and Abstract: Using finite state projection to solve the chemical master equation, Download Codes
17:30-19:00 Dinner: La Posada Dining Hall
19:00-21:00 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Weekend 2

Saturday, July 25

Free time

Sunday, July 26

Free time

Week 3

Monday, July 27

07:00-08:30 Breakfast: La Posada Dining Hall
08:30-10:15 Lecture 21: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Ryan N. Gutenkunst; Title and Abstract: Parameter estimation, sensitivity analysis, and sloppiness in systems biology
10:15-10:30 Coffee Break
10:30-12:15 Lecture 22: Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Lecturer: Tanmoy Bhattacharya; Title and Abstract: Introduction to phylogenetics
12:15-13:15 Lunch: Student Union Building, Dining Area, Level 2
13:15-14:45 Lecture: Lecturer: Giovanni Bellesia; Title and Abstract: Introduction to Markov chain Monte Carlo methods
14:45-16:30 Lab: 14:45-16:30 Computer Lab 22; Student Union Building, Room 3018 (Scholars); Instructor: Ryan N. Gutenkunst; Title and Abstract: Using and contributing to the BioModels database
16:30-17:00 Break
17:00-17:45 Recitation: Recitation 11; Student Union Building, Rooms 3037 & 3039 (Lobo A & B); Discussant/Tutor: Cesar Lopez; Topic: Coarse-grained molecular dynamics of biological systems
17:45-19:00 Dinner: La Posada Dining Hall
19:00-21:00 Project Team Work: Common rooms and study/meeting rooms in Building 1 (Chama), Casas del Rio

Tuesday, July 28

07:00-08:30 Breakfast

La Posada Dining Hall

08:30-12:15 Student Symposium

Student Union Building, Rooms 3037 & 3039 (Lobo A & B)

Project Presentations

08:30-09:20 Biomolecular Simulations Team Report(s)

09:20-10:10 Cell Signaling Team Report(s)

10:10-10:35 Break

10:35-11:25 Membrane Biology Team Report(s)

11:25-12:15 Viral Dynamics Team Report(s)

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-16:30 Student Symposium (continued)

Student Union Building, Rooms 3037 & 3039 (Lobo A & B)

13:15-15:15 Poster Session

15:15-16:00 Closing Talk

Lecturer: Mac Hyman

Title and Abstract: Good choices for a great career

16:00-16:30 Farewell

16:30-17:00 Group Picture

Please return completed exit survey!

17:00-18:30 Dinner