2017qbSS

Please visit the new q-bio Summer School Website at:

This site is soon to be discontinued.

Welcome to the wiki page for the 2017 q-bio Summer School! The 2017 qbSS will take place from June 4-20, 2017 at the Colorado State University in Fort Collins, Colorado, USA.

Information about the school can be found below. If you have questions about the q-bio Summer School, please email: qbio_summer_school@colostate.edu

Overview

The q-bio Summer School is an annual event intended to advance predictive modeling of cellular regulatory systems by exposing participants to a survey of work in quantitative biology and by providing in-depth instruction in selected techniques, with an emphasis on techniques useful for modeling cellular regulatory networks, although data analysis techniques and experimental methods will also be covered. Students will each work on mentored projects. Participants will attend daily core lectures, project-specific lectures, journal clubs, and computer and (in some cases) experimental labs. The summer school is designed for graduate students, postdocs, or anyone with a quantitative background who is new to modeling cellular regulatory systems/networks.

The origin of the term q-bio is explained here. A brief history of the q-bio events can be found here.

Dates and venue

The q-bio Summer School (qbSS17) will take place from Sunday evening June 4, 2017 through Tuesday morning June 20, 2017. The majority of lectures, tutorials and project sessions will take place in the Suzanne and Walter Scott, Jr. Bioengineering Building at the Colorado State University in Fort Collins Colorado. More information about the CSU venue can be found here.

Course Topics and Lectures

The qbSS17 will involve instruction in four overlapping courses ranging from inference of stochastic models from single-cell measurements to analysis of complexity in synthetic biological systems and to the modeling of dynamics in cancer. Information about specific course topics can be found via the following links:

Each course will include:

10 shared 1-hour general lectures from invited speakers
10 shared 1.5-hour chalk talks from invited speakers
30 hours of in-depth instruction during breakout discussions including expert panel discussions, chalk talks, computer/experimental lab demonstrations;
20+ hours of mentored project work and project presentations;
2 catered poster sessions
20-24 student talks
8 career oriented discussion panels on topics ranging from forming interdisciplinary collaborations to finding postdoctoral opportunities

Course Projects

The 2017 qbSS will include a strong emphasis on course projects. A list of possible mentors and project themes will made be available at the time of application selection. Students are encouraged to request specific project mentor from the list of organizers in their application statement. Some mentors may be willing to accommodate visiting students prior to, or following, the summer school in order to engage in more detailed computational, theoretical or experimental work. Such arrangements are on a one-by-one basis and should be requested well in advance of the summer school. Please contact individual organizers, lecturers, or mentors to discuss these possibilities.

Course Organizers

Rosemary Braun, Northwestern University
William S. Hlavacek, Los Alamos National Laboratory
Marek Kimmel, Rice University
Brian Munsky,Colorado State University
Ashok Prasad, Colorado State University
Patrick Shipman, Colorado State University
Douglas Shepherd, University of Colorado Denver
Sabrina Spencer, University of Colorado at Boulder
Lev Tsimring, University of California, San Diego

Lecturers

We expect to have approximately 30 lecturers at the 2017 qbSS program. Below is a list of confirmed lecturers for the 2017 q-bio Summer School. Please check back frequently for updates.

Matthew Bennet, Rice University
Meredith Betterton, University of Colorado Boulder
Rosemary Braun, Northwestern University
Moumita Das, Rochester Institute of Technology
James R. Faeder, University of Pittsburgh School of Medicine
Ryan N. Gutenkunst, University of Arizona
Steve Haase, Program in Cell and Molecular Biology, Duke University
William S. Hlavacek, Los Alamos National Laboratory
Srividya Iyer-Biswas, Purdue University
Marek Kimmel, Rice University
Katherine King, Baylor College of Medicine
Natalia Komarova, University of California, Irvine
Diego Krapf, Colorado State University
Herbert Levine, Rice University
Francis Motta, Duke University
Gerry Ostheimer, Global Lead for Sustainable Bioenergy - UN Sustainable Energy For All Initiative
Ashok Prasad, Colorado State University
Steve Presse, Indiana University and Purdue University
Michael Savageau, University of California, Davis
Brian Munsky, Colorado State University
Patrick Shipman, Colorado State University
Douglas Shephard, University of Colorado, Denver
Sabrina Spencer, University of Colorado, Boulder.
Tim Stasevich, Colorado State University
Lev Tsimring, University of California, San Diego
More TBA.

Examples of Past Lectures

Below are links to a handful of the lectures held and recorded during the 2015 q-bio Summer School in Fort Collins.

Douglas Shepherd, University of Colorado at Denver, "Single-Molecule approaches in Quantitative Biology", Stream video
Brian Munsky, Colorado State University, "The Finite State Projection Algorithm, Part 1", Stream video
Patrick Shipman, Colorado State University, "Phase-Locking in Discrete Dynamical Systems, Stream video
Abhyudai Singh, University of Delaware, "Using Moment Generating Functions", Stream video

Panel Discussion Leaders

Asa Ben-Hur, Associate Professor, Computer Science, Colorado State University
Dan Bush, Professor, Biology; Vice Provost for Faculty Affairs; Colorado State University
David Dandy, Head, Chemical and Biological Engineering; Colorado State University
Melissa Emerson, Director, Student Resolution Center; Colorado State University
Steve Haase, Associate Professor, Biology; Director, Duke University Program in Genetics and Genomics; Lead Scientist and co-Founder, Mimetics
Matthew Hickey, Professor, Health and Exercise Science; Director, Human Performance Clinical Research Lab; Colorado State University
Shing Ho, Professor, Biochemistry and Molecular Biology; Colorado State University
Sonia Kreidenweis, Professor, Atmospheric Science; Associate Dean of Research, Scott College of Engineering; Colorado State University
Herbert Levine, Hasselmann Professor of Bioengineering; Director, Center for Theoretical Biological Physics; Member, National Academy of Science; Rice University
Brian Munsky, Assistant Professor, Chemical and Biological Engineering; Director, q-bio Summer School, Colorado State University
Erin Nishimura, Assistant Professor, Biochemistry and Molecular Biology; Colorado State University
Gerry Ostheimer, Global Lead for Sustainable Bioenergy; Sustainable Energy for All
Mario G Oyola, President of the CSU Postdoc Association
Jean Peccoud, Professor, Chemical and Biological Engineering; Colorado State University
Jessica Prenni, Associate Professor, Biochemistry and Molecular Biology; Director, Research Core Facilities; Director, Proteomics and Metabolomics Facility; Colorado State University
Melissa Reynolds, Associate Professor, Chemistry; Colorado State University
Michael Savageau, Distinguished Professor, Biomedical Engineering; Member, National Academy of Science Institute of Medicine; University of California, Davis
Stuart Tobet, Professor, Department of Biomedical Sciences; Director, School of Biomedical Engineering; Colorado State University
Mark Wdowik, Assistant Vice President for Research & Industry Partnerships, Colorado State University
Carol Wilusz, Professor, Microbiology, Immunology, & Pathology; Colorado State University
More TBA.

Campus Schedule

The 2017 qbSS will take place from June 4-20, 2017 at the Colorado State University in Fort Collins, Colorado, USA. The daily schedule of the qbSS will be as follows:

08:30-09:30 General Seminar
09:30-10:45 Coffee Break and Panel Discussion
11:00-12:15 Student Talks
12:15-14:00 Lunch
14:00-15:00 General Chalk Talk
15:00-17:30 Breakout Sessions or Project time
18:00-20:00 Dinner, Social, or Poster Session
20:00-22:00 Project Time or Special Evening Sessions
Weekend Activities: See below.

Please look here for a draft of the Detailed Schedule, qbSS17.

Application Process

The application process will involve submitting a CV, a 1-page statement of interest, and completing a form online. No letters of reference are necessary in the first round of applications, but these may be requested in the application review stage. Applications will be reviewed by the organizers of each course. Organizers have been instructed to look for students who are diverse in background and training, but who demonstrate a keen interest in quantitative methods to study biological systems.

Applications for the 2017 q-bio Summer School are now open! Applications are due February 3, 2017 (extended deadline).

To apply now, visit here.

Application Selection Criteria

All applications to attend will be evaluated by the course organizers as a whole. At the time of application and in their letter of interest (limited to 1-page), students are asked to indicate the specific courses they are most interested to attend. This information will be used to ensure that the student body represents a diverse range of backgrounds, interests, experiences and scientific training. This information will also be used to aid scheduling for breakout discussions and the project mentoring activities. Most importantly, we are looking for students who show a strong promise to use tools learned at the summer school in their ongoing research endeavors. We strongly encourage applications (1) from experimentalists who wish to learn computational tools to understand their data and (2) from computational scientists who would like to explore new biological problems to which to apply their training. Since group projects are a key aspect of the program, students must be willing and able to engage with other researchers in multi-disciplinary investigations. We expect a mix of students at different levels of their training: some students will be admitted on the basis of past experience and strong publication records, while others will be admitted based upon their enthusiasm and potential for future research in their current position. Students should make sure to address how specific summer school topics are expected to relate to their past, present and future research objectives.

Application review will begin late February, 2017. Only students who apply on time will be considered during the initial selection phase. Late applicants and students not accepted in the initial phase will be placed on a wait list in case of cancellations or scheduling conflicts. 'Space is limited to 30 external students on the CSU campus. Historically, approximately one in three applications are accepted for attendance at the summer school.

The q-bio summer school does not discriminate on the basis of race, age, color, religion, national origin or ancestry, sex, gender, disability, veteran status, genetic information, sexual orientation, or gender identity or expression.

Intended Audience

Each of the the four theme areas of the q-bio summer school requires basic familiarity with ordinary differential equations. We will be cover basic and some more advanced results in nonlinear dynamics and stochastic processes. We will also spend a significant amount of time developing and using computational tools. However, the main aim of the school is to develop biological insight and use these mathematical/computational tools to solve biological problems. Students with some familiarity with differential equations who are willing to learn and are interested in the biological questions will benefit from the program. Student with extensive knowledge of the math and with a deep interest in the biological questions will also benefit. We hope to attract both of these categories of students to attend the course. We believe that students with strong mathematical backgrounds and those with strong training in the biological sciences can work together, learn from one another, and help us to strengthen the q-bio community as a whole. The summer school may not be an optimal match for someone who is interested only in the math (i.e., this is not a dynamical systems summer school but a q-bio summer school). However, we will cover some modern data analysis methods, and we hope that even those people who have seen dynamical systems before will learn a few new tools or approaches.

The 2016 q-bio Summer School at CSU

Registration Fees

Estimated fees to attend the q-bio Summer School are:

Registration: $700.00.
Lodging and Meals: $1300.00. This includes 16 nights lodging and most meals.
Students are responsible for their travel expenses both to the school and between the school and the q-bio Student Symposium.

Scholarships are available to cover registration and to reduce the lodging fees. Please indicate your financial need on the school application.

About the CSU Campus

The q-bio Summer School will be held at the Colorado State University in Fort Collins. Founded in 1870 under the Morrill Act of 1862, the Fort Collins CSU campus now enrolls 25,600 on-campus students.

The q-bio Summer School will be held in the new, Suzanne and Walter Scott, Jr. Bioengineering Building. This $75-million, 122,000-square-foot building, completed in Fall of 2013, houses office and lab space for about 40 faculty scientists from several departments and colleges; all engaged in Systems and Synthetic Biology, Bioanalytical Devices, and Biomedical Engineering. The building, which has been built to LEED Gold standards, also includes state-of-the-art classrooms, teaching labs, and small design studio computer labs where student teams will work on course projects.

School Lodging

Students at the q-bio Summer School in Fort Collins will be housed in the Academic Village Honors dormitories (a short, but pleasant walk from the school classrooms). Two lodging options are available: suite-style single and suite-style double. A description and floor plans for the dormitories are located here. Prices will depend upon room type.

Daily breakfast and lunch are included with the lodging fee and will be served at the Rams Horn at the Academic Village. This center features 8 different food venues including a Mongolian Grill, Tex-Mex station, pasta, deli, salad bar, and more.

On campus students will have access to the CSU recreation center located across the intramural fields from the dormitories. The Rec Center is home to the single largest strength training facility in the state. It also features two 38-foot-tall rock-climbing towers and a bouldering wall/cave, an aquatic center that boasts a 12-foot-tall climbing wall, lazy river and 35-person spa, two massage rooms, cardio-weight areas measuring over 24,000 square feet, four exercise studios and a three-lane indoor track.

Nearby Attractions

CSU is in Fort Collins is located 65 miles (105km) north of Denver, and on the edge of the Front Range of the Rocky Mountains. Fort Collins is a midsize city of 150,000, which has frequently been ranked one of the best towns in the USA by numerous sources. Fort Collins is located along the Poudre river and has limitless outdoor opportunities for hiking, rafting, kayaking, water skiing, rock climbing, and bicycling. The city's thriving beer culture supports many fantastic microbreweries, including the New Belgium Brewing Company, the Odell Brewing Company, the Fort Collins Brewery, Equinox Brewing, Funkwerks, Anheuser-Busch, and several brewpubs. Fort Collins has an impressive selection of restaurants and quality fine arts programs, and the resources of Denver are just over an hour’s drive away.

Weekend Activities

A couple group weekend activities will be planned, but there is lots more to do:

There is plenty to do right in Fort Collins. Check out the the Fort Collins Old Town a short walk from campus, and be sure to look up special events
Check out a bicycle from the Fort Collins Bike Library and ride some of the 30+ miles of beautiful paved bike trails right in Fort Collins.
Go for morning trail runs at Horsetooth Mountain, Lory State Park, or on one of the many other local trails.
Go for a white water rafting adventure with one of several local Fort Collins rafting companies.
Rent a fishing boat, ski boat, kayak, paddle board or wave runner at the Horsetooth Reservoir Marina just five miles from campus.
Tour the New Belgium Brewery.
Go to Rocky Mountain National Park to hike, climb, or just sit in a mountain meadow to watch the elk herds.
Go to Denver to visit the many museums, zoo, theater, and much more.
Catch a Colorado Rockies game at Coors field or a Colorado Rapids game at Dick's Sporting Goods Park
Take a weekend road trip to see Steamboat Hot-springs (3h,15min), Great Sand Dunes National Park (5hr), Arches and Canyonlands National Parks (7hr), or plan a post-school trip to Tetons and Yellowstone National Parks (8hr).

Bike/Boat Rentals near Fort Collins

How to contact the organizers

For scientific questions, please email Brian Munsky (munsky at engr dot colostate dot edu).

For administrative questions, please email qbio_summer_school@colostate.edu to contact the q-bio program coordinator.

2017qbSS

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