Gulf Coast Campus (Rice University - Houston, Texas)

(+) General Information

The 2018 qbSS will take place from June 11-25, 2018 at Rice University, Houston, Texas, USA. The daily schedule of the qbSS will be as follows:

  • 09:00 - 10:15 Lecture
  • 10:15 - 10:45 Coffee Break
  • 10:45 - 12:00 Lecture or panel discussion
  • 12:00 - 13:20 Lunch
  • 13:30 - 14:50 Student talks
  • 14:50-15:20 Coffee Break
  • 15:20-18:20 Breakout sessions
  • 18:20-20:00 Dinner
  • 20:20 -    Optional evening session / Project work
(+) Week 1

Please click here for a general outline of Week 1.

Please click here for a detailed schedule of Week 1.

(+) Week 2

Please click here for a general outline of Week 2.

Please click here for a detailed schedule of Week 2.

(+) Week 3

Please click here for a detailed schedule of Week 3.

(+) Student Talk Abstracts

Ankit Chandra (North Carolina State University)  abstract

Edward Williams (Cancer Research UK Cambridge Institute) abstract

Federico Bocci (Rice University) abstract

Gennady Gorin (Baylor College of Medicine) abstract

Jamie Dean (Dana-Farber Cancer Institute) abstract

John Vastola (Vanderbilt University) abstract

Justyna Mika (Silesian University of Technology) abstract

Karolina Tudelska (Institute of Fundamntal Technological Research) abstract

Keisha Cook  (The University of Alabama) abstract

Linh Huynh (Case Western Reserve University) abstract

Matthew Smart (University of Toronto) abstract

Maziyar Keshavarzian (The University of Texas at Dallas) abstract

Sahil Seth (MD Anderson Cancer Center) abstract

Shivam Gupta (Purdue University) abstract

Xingcheng Lin (Rice University) abstract

Xubin Li (MD Anderson Cancer Center) abstract

Yannis Zervantonakis (Harvard Medical School) abstract

Zikai Xu (University of Delaware) abstract

Coralie Dessauges (Institute of Cell Biology, University of Bern) abstract

Steven Dabelow (University of Notre Dame) abstract

Timothy Charles Stutz (University of California, Los Angeles) abstract

Seth Coleman (Rice University) abstract

Robert Mines (Duke University) abstract

Southwest Campus

(University of New Mexico - Albuquerque, New Mexico)

(+) General Information

The 2018 qbSS will take place from June 10-25, 2018 at the University of New Mexico, Albuquerque, New Mexico, USA. 

Reception

An evening reception is scheduled for 18:00-20:00 Sunday, June 10, 201y. Please try your best to attend this event, which will include orientation. The event will take place at the University of New Mexico University Club.

Weekdays

Unless otherwise noted in the detailed schedule below, the program each weekday will consist of two lectures in the morning, two student talks and two computer labs in the afternoon, and project team work in the evening. A typical schedule will be as follows:

  • 07:00-08:30 -- Breakfast
  • 08:30-10:15 -- Lecture 1 (organized into two 45-minute parts)
  • 10:15-10:30 -- Coffee Break
  • 10:30-12:15 -- Lecture 2 (organized into two 45-minute parts)
  • 12:15-13:15 -- Lunch
  • 13:15-14:15 -- Student Talks (up to three talks per day, 20 minutes each)
  • 14:15-15:30 -- Computer Lab 1
  • 15:30-15:45 -- Break
  • 15:45-17:00 -- Computer Lab 2
  • 17:00-18:30 -- Dinner
  • 18:30-20:30 -- Project Team Work

Weekends

  • June 16 and 17
  • June 23 and 24
(+) Week 1

Sunday, June 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)

Monday, June 11

07:00-08:30 Breakfast

La Posada Dining Hall

08:30-10:15 Lecture 1

Location: Student Union Building Acoma A and B
Title: School Introduction

10:15-10:30 Coffee Break

10:30-12:15 Lecture 2

Location: Student Union Building Acoma A and B
Lecturer: Bill Hlavacek
Title and Presentation Slides: Rule-based Modeling and Examples

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Student Talks

13:15-13:45 Student Talk 1: Antonio Herrera

13:45-14:15 Student Talk 2: Anastasiia Nemashkalo

Location: Student Union Building Acoma A and B

14:15-17:00 Labs

14:15-15:30 Computer Lab 1

Location: Student Union Building Acoma A and B
Lecturer: Bill Hlavacek
Title: Modeling in BioNetGen
**Please download BioNetGen in preparation for this presentation

15:30-15:45 Break

15:45-17:00 Computer Lab 2

Location: Student Union Building Acoma A and B
Lecturer: Bill Hlavacek
Title: Modeling in BioNetGen (continued)

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, June 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: Bridget Wilson
Title: TBA

10:15-10:30 Coffee Break

10:30-12:15 Lecture 4

Location: Student Union Building Acoma A and B
Lecturer: Yen-Ting Lin, Eshan Mitra
Title and Presentation Slides: Stochastic processes: Fundamentals and numerical methods
**Please download Python (Anaconda) in preparation for this presentation

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Student Talks

13:15-13:45 Student Talk 3: Kazi Tasneem

13:45-14:15 Student Talk: Nikita Tsyba

Location: Student Union Building Acoma A and B

14:15-17:00 Labs

14:15-15:30 Computer Lab 3

Location: Student Union Building Acoma A and B
Lecturer: Yen-Ting Lin
Title and Presentation Slides: Stochastic simulations for discrete-time Markov chain

15:30-15:45 Break

15:45-17:00 Computer Lab 4

Location: Student Union Building Acoma A and B
Lecturer: Yen-Ting Lin
Title and Presentation Slides: Stochastic simulations for continuous-time Markov chain

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, June 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: Judy Cannon, Matthew Fricke
Title and Slides: Quantitative analysis of T cell movement in tissues: Experimental considerations

10:15-10:30 Coffee Break

10:30-12:15 Lecture 6

Location: Student Union Building Acoma A and B
Lecturer: Song Feng
Title: Parameter Fitting for Biological Models

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Student Talks

13:15-13:45 Student Talk 5: Melanie Rivera

13:45-14:15 Student Talk 6: Jon Christian David

Location: Student Union Building Acoma A and B

14:15-17:00 Labs

14:15-15:30 Computer Lab 5

Location: Student Union Building Acoma A and B
Lecturer: Song Feng, Eshan Mitra
Title: Introduction to BioNetFit

15:30-15:45 Break

15:45-17:00 Computer Lab 6

Location: Student Union Building Acoma A and B
Lecturer: Song Feng, Eshan Mitra
Title: Introduction to BioNetFit (continued)

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, June 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: Adam Halasz
Title: Spatial stochastic models of membrane receptors

10:15-10:30 Coffee Break

10:30-12:15 Lecture 8

Location: Student Union Building Acoma A and B
Lecturer: Eshan Mitra, Yen-Ting Lin
Title: Spatial Modeling

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Student Talks

13:15-13:45 Student Talk 7: Lewis Baker

13:45-14:15 Student Talk 8: Jennifer Longo

Location: Student Union Building Acoma A and B

14:15-18:00 Labs

14:15-15:30 Computer Lab 7

Location: Student Union Building Acoma A and B
Lecturer: Eshan Mitra
Title: Spatial simulations with Smoldyn

15:30-15:45 Break

15:45-18:00 Computer Lab 8

Location: Cancer Research Facility
Lecturer: Mara Steinkamp
Single Particle Tracking of Quantum Dots: Lewis Baker, Sara Oehmke, Martina Prugger, Melanie Rivera, Kazi Tasneem
dSTORM Super-Resolution Imaging: Maria Ramos, Pawel Kocieniewski, Jennifer Longo, Nikita Tsyba, Jon David, Anastasiia Nemashkalo

18:00-19:00 Dinner

La Posada Dining Hall

19:00-20:30 Project Team Work

Common rooms and study/meeting rooms in Casas del Rio

Friday, June 15

07:00-08:30 Breakfast

La Posada Dining Hall

9:00-10:00 Student Talks

9:00-9:30 Student Talk 9: Maria Ramos Alamo

9:30-10:00 Student Talk 10: Pawel Kocieniewski

Location: Student Union Building Acoma A and B

10:15-10:30 Coffee Break

10:30-12:15 Lecture 10

Location: Student Union Building Acoma A and B
Lecturer: Eshan Mitra
Title: Machine Learning in Biology

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Student Talks

13:15-13:45 Student Talk 11: Sara Oehmke

13:45-14:15 Student Talk 12: Martina Prugger

Location: Student Union Building Acoma A and B

14:15-18:00 Labs

14:15-15:30 Computer Lab 9

Location: Student Union Building Acoma A and B
Lecturer: Eshan Mitra
Title: Neural network classifiers

15:30-15:45 Break

15:45-18:00 Computer Lab 10

Location: Cancer Research Facility
Lecturer: Mara Steinkamp
Single Particle Tracking of Quantum Dots: Maria Ramos, Pawel Kocieniewski, Jennifer Longo, Nikita Tsyba, Jon David, Anastasiia Nemashkalo
dSTORM Super-Resolution Imaging: Martina Prugger, Melanie Rivera, Kazi Tasneem, Antonio Herrera

18:00-19:00 Dinner

La Posada Dining Hall

19:00-20:30 Project Team Work

Common rooms and study/meeting rooms in Casas del Rio

Saturday, June 16

Free time

(+) Week 2

Sunday, June 17

Free time

Monday, June 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: Michael Blinov
Title: TBA

10:15-10:30 Coffee Break

10:30-12:15 Lecture 12

Location: Student Union Building Acoma A and B
Lecturer: Keesha Erickson
Title and Materials: Introduction to Cluster Analysis

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Panel Discussions

Location: Student Union Building Acoma A and B

14:15-17:00 Labs

14:15-15:30 Computer Lab 11

Location: Student Union Building Acoma A and B
Lecturer: Keesha Erickson
Title: Implementation and Interpretation
**Please download CobraPy in preparation for this presentation

15:30-15:45 Break

15:45-17:00 Computer Lab 12

Location: Student Union Building Acoma A and B
Lecturer: Michael Blinov
Title: TBA

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, June 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: Diane Lidke
Title: TBA

10:15-10:30 Coffee Break

10:30-12:15 Lecture 14

Location: Student Union Building Acoma A and B
Lecturer: Song Feng
Title: Compartmentalized Simulations

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Panel Discussions

Location: Student Union Building Acoma A and B

14:15-17:00 Labs

14:15-15:30 Computer Lab 13

Location: Student Union Building Acoma A and B
Lecturer: Song Feng
Title: Simulations in MLRules

15:30-15:45 Break

15:45-17:00 Computer Lab 14

Location: Student Union Building Acoma A and B
Lecturer: Keith Lidke
Title: Single Particle Tracking Analysis

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, June 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: TBA
Title: TBA

10:15-10:30 Coffee Break

10:30-12:15 Lecture 16

Location: Student Union Building Acoma A and B
Lecturer: Yen-Ting Lin
Title and Presentation Slides: Bayesian statistical inference and uncertainty quantification Part 1, Part 2

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Panel Discussions

Location: Student Union Building Acoma A and B

14:15-17:00 Labs

14:15-15:30 Computer Lab 15

Location: Student Union Building Acoma A and B
Lecturer: Yen-Ting Lin
Title and Materials: Markov chain Monte Carlo

15:30-15:45 Break

15:45-17:00 Computer Lab 16

Location: Student Union Building Acoma A and B
Lecturer: Keith Lidke
Title: Superresolution Analysis

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, June 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: TBA
Title: TBA

10:15-10:30 Coffee Break

10:30-12:15 Lecture 18

Location: Student Union Building Acoma A and B
Lecturer: Keesha Erickson
Title and Presentation Slides: Introduction to Flux Balance Analysis

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Panel Discussions

Location: Student Union Building Acoma A and B

14:15-17:00 Labs

14:15-15:30 Computer Lab 17

Location: Student Union Building Acoma A and B
Lecturer: Keesha Erickson
Title: Genome-scale metabolic network analysis with CobraPy
**Please download CobraPy in preparation for this presentation

15:30-15:45 Break

15:45-17:00 Computer Lab 18

Location: Student Union Building Acoma A and B
Lecturer: Keesha Erickson
Title: Genome-scale metabolic network analysis with CobraPy  (continued)

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, June 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: Aaron Neumann
Title: TBA

10:15-10:30 Coffee Break

10:30-12:15 Lecture 20

Location: Student Union Building Acoma A and B
Lecturer: Cesar Lopez
Title: MD Simulations

12:15-13:15 Lunch

Student Union Building, Dining Area, Level 2

13:15-14:15 Panel Discussions

Location: Student Union Building Acoma A and B

14:15-15:30 Lecture 21

Location: Student Union Building Acoma A and B
Lecturer: Mac Hyman
Title: Good Choices for Great Careers

15:30-15:45 Break

15:45-17:00 Project Team Work

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, June 23

Free time

(+) Week 3

Sunday, June 24

Free time

Monday, June 25

07:00-08:30 Breakfast

La Posada Dining Hall

08:30-12:15 Student Symposium

Location: Student Union Building Acoma A and B

10:15-10:30 Coffee Break

12:15-13:15 Lunch

Location: Student Union Building Acoma A and B

13:15-13:30 Farewell and Group Picture

Students

Pawel Kocieniewski, IPPT PAN



Kazi Tasneem, Vanderbilt University



Maria Ramos Alamo, University of Puerto Rico



Sara Oehmke, Colorado State University



Anastasiia Nemashkalo, Rice University



Martina Prugger, Vanderbilt University



Lewis Baker, University of Colorado - Boulder



Melanie Rivera, University of New Mexico



Nikita Tsyba, Vanderbilt University



Jennifer Longo, University of New Mexico



Antonio Herrera, Stony Brook University



Jon Christian David, University of New Mexico