The Tenth q-bio Summer School - Colorado
The 2016 q-bio Summer School in Fort Collins will be held July 11-23!
In 2015, we added a new campus of the q-bio Summer School at the Colorado State University in Fort Collins, CO. Three overlapping courses will be offered ranging from the analysis of complexity in biological systems to the inference of stochastic models from single-cell measurements and to the modeling of dynamics of leukemic cancers. Over two weeks, students will attend:
- ten invited 1-hour research seminars;
- ten invited 1.5-hour general lectures;
- six to eight panel discussions on topics ranging from scientific collaborations to career decisions;
- 30 hours of in-depth instruction during breakout discussions including expert panel discussions, chalk talks, computer/experimental lab demonstrations;
- 20 student oral presentations;
- a catered poster session;
- 20+ hours of mentored project work and project presentations;
- formal and informal networking opportunities and more.
For questions about the Fort Collins Campus of the q-bio Summer School, contact Dr. Brian Munsky.
- 1 Themes
- 2 Selection Procedure
- 3 Intended Audience
- 4 Organizers
- 5 Lecturers
- 6 Career Discussion Panelists
- 7 Examples of Past Lectures
- 8 Open Events
- 9 Students
- 10 Campus Schedule
- 11 Software
- 12 About the CSU Campus
- 13 School Lodging
- 14 Nearby Attractions
- 15 Weekend Activities
- 16 Local Sponsors
These are the main topics to be covered at the Fort Collins branch of the q-bio Summer School. Applicants wishing to attend the Fort Collins campus do not need to commit in advance to one of these specific course. All students at the Fort Collins campus will have the opportunity to attend all general lectures, but will separate into the three themes for special hands-on training and project work.
- The 2016 qbSS in Fort Collins will include a much greater emphasis on, and allotment of time for, course projects. A list of possible mentors and project themes will made be available at the time of application. Students are encouraged to request a specific project mentor 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.
All applications to attend the CSU campus 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. No letters of reference are necessary in the first round of applications.
Application review will begin late February, 2016. 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. Approximately one in three applications are accepted for attendance at the CSU branch of 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.
Each of the the three 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.
- Prof. Rosemary Braun, Northwestern University
- Prof. Marek Kimmel, Rice University
- Prof. Brian Munsky,Colorado State University
- Prof Ashok Prasad, Colorado State University
- Prof. Patrick Shipman, Colorado State University
- Prof. Douglas Shepherd, University of Colorado Denver
- Prof. Sabrina Spencer, University of Colorado at Boulder
Invited Lecturers at the 2016 q-bio Summer School (CSU Campus) will include:
- David Axelrod, Rutgers University
- Rosemary Braun, Northwestern University
- Seth Corey, Northwestern University
- Cecilia Dinis Behn, Colorado School of Mines
- James Ferrell, Stanford University
- Thomas Gedeon, Montana State University
- Steve Haase, Program in Cell and Molecular Biology, Duke University
- Alexandra Jilkine, Notre Dame
- Marek Kimmel, Rice University
- Joel Kralj, University of Colorado Boulder
- Francis Motta, Dept. of Mathematics, Duke University
- Brian Munsky, Colorado State University
- Andrzej Polanski, Silesian University of Technology
- Ashok Prasad, Colorado State University
- Steve Presse, Indiana University and Purdue University
- Michael Savageau University of California, Davis
- Douglas Shepherd, University of Colorado Denver
- Patrick Shipman, Colorado State University
- Sabrina Spencer, University of Colorado Boulder
- Tim Stasevich, Colorado State University
- Simon Tavener, Colorado State University
- Roy Wollman, University of California San Diego
Career Discussion Panelists
- David Axelrod, Professor of Genetics, Rutgers University
- Asa Ben-Hur, Associate Professor of Computer Science, Colorado State University
- Rosemary Braun, Assistant Professor of Bio-statistics, Northwestern University
- Dan Bush, Vice Provost of Faculty Affairs and Professor of Biology, Colorado State University
- David Dandy Department Head, Chemical and Biological Engineering, Colorado State University
- Ellen Fisher, Professor of Chemistry and Senior Faculty Advisor for Research, Colorado State University
- Steve Haase, Director of the Duke University Program in Genetics and Genomics and Lead Biologist and co-founder of Mimetics, LLC.
- Todd Headley, President, CSU Ventures
- Matthew Hickey, Graduate Program Director, Department of Health and Exercise Science, Colorado State University
- Shing Ho, Professor and Chair of the Department of Biochemistry and Molecular Biology, Colorado State University
- Susan P James, Department Head and Professor of Mechanical Engineering, Colorado State University
- Michael Kirby, Professor of Mathematics, Colorado State University
- Mark Mdowik, CSU Assistant Vice President for Research and Industry Partnerships
- Erin Osborne Nishimura, Assistant Professor of Biochemistry, Colorado State University
- Mario G Oyola, President of the CSU Postdoc Association
- Jean Peccoud, Associate Professor of Chemical and Biological Engineering, Colorado State University
- Jessica Prenni, Associate Professor of Biochemistry and Molecular Biology, Director of Proteomics and Metabolomics Facility, Colorado State University
- Steve Presse, Assistant Professor of Physics, Indiana University-Purdue University Indianapolis
- Ken Reardon, Professor, Chemical and Biological Engineering, CSU; Founder of OptiEnz Sensors
- Melissa Reynolds, Associate Professor of Chemistry, Colorado State University
- Jacob Roberts, Professor and Chair of Physics, Colorado State University
- Michael Savageau, Distinguished Professor of Biomedical Engineering, UC Davis
- Patrick Shipman, Associate Professor of Mathematics, Colorado State University
- Tim Stasevich Assistant Professor of Biochemisty, Colorado State Uniersity
- Stuart Tobet, Professor of Cell and Molecular Biology, Colorado State University
- Mark Wdowik, CSU Assistant Vice President for Research and Industry Partnerships
- Carol Wilusz, Professor of Microbiology, Immunology and Pathology, Colorado State University
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
The 2016 q-bio Summer School will feature several events that are open to the CSU graduate student and research community.
- q-bio Summer School Poster Session, 17:30-19:00, Monday, July 11, Scott Atrium (space is limited and registration is required - register here),
- Career Discussion Panels, 09:45-10:45 in Scott 229. Please register here.
- July 12, 2016: Choosing the right research project
- July 13, 2016: Finding a good postdoc position
- July 14, 2016: Balancing work and family in a research career
- July 15, 2016: Applying for grants and fellowships
- July 18, 2016: Building multidisciplinary collaborations
- July 19, 2016: Navigating the tenure process in academia
- July 20, 2016: Resolving conflicts in Mentor/Mentee Relationships
- July 21, 2016: Intellectual Property and Entrepreneurship
- Morning q-bio Seminars, 08:30-09:30, Monday (July 11) through Friday (July 22), Schedule
- Afternoon q-bio Seminars, 14:00-15:00, Monday (July 11) through Friday (July 22), Schedule
Single Cell Gene Regulation
- Merzu Belete, University of Houston ,firstname.lastname@example.org
- Matthew Boryczka, Colorado State University, email@example.com
- Rebecca Brouwers, University of Edinburgh, Rebecca.Brouwers@ed.ac.uk
- Minghan Chen, Virginia Tech, firstname.lastname@example.org
- Taylor Firman, University of Denver, Taylor.Firman@du.edu
- Mahan Ghafari, Emory University, email@example.com
- Sina Jaznai, Indiana University-Purdue University at Indianapolis, firstname.lastname@example.org
- Kenneth Lyon, CSU, email@example.com
- Mingwei Min, University of Colorado - Boulder, firstname.lastname@example.org
- Qiuyan Shao, Texas A&M University, email@example.com
- Mohammad Tanhaemami, Colorado State University, firstname.lastname@example.org
- Mona Tonn, Imperial College, London, email@example.com
- David Wallace-Bradley, Rice University, firstname.lastname@example.org
- Martijn Wehrens, FOM Institute AMOLF, email@example.com
- Wenlong Xu, Colorado State University, firstname.lastname@example.org
- Elaheh Alizadeh, Colorado State University, email@example.com
- Wojciech Bensz, Silesian University of Technology, firstname.lastname@example.org
- Kerrigan Blake, University of California, Irvine, email@example.com
- Dhananjay (Danny) Dhokarh, Mayo Clinic, firstname.lastname@example.org
- Tegan Emerson, Colorado State University, email@example.com
- Albertas Janulevicius, University of Groningen, firstname.lastname@example.org
- Monika Kurpas, Silesian University of Technology, Faculty of Automatic Control, Electronics and Computer Science, email@example.com
- Xiaoyu Liu, Colorado State University, firstname.lastname@example.org
- Aaron Prescott, University of Tennessee - Knoxville, email@example.com
- Yu-Hsuan Shih, University of Cincinnati, firstname.lastname@example.org
- Niccolò Totis, University of Turin (Italy), email@example.com
- Jialiang Wu, Yale University, firstname.lastname@example.org
Complex Biological Systems
- Wes Galbraith, Colorado State University, email@example.com
- Krishna Kanhaiya, Åbo Akademia (Finland), firstname.lastname@example.org
- Tina Kelliher, Duke University, email@example.com
- Santosh Manicka, Indiana University Bloomington, firstname.lastname@example.org
- Chengzhe Tian, University of Copenhagen, email@example.com
- Ariadne Whitby, Imperial College London, firstname.lastname@example.org
- Maxwell Wilson, Princeton University, email@example.com
- Michael Wolfe, University of Michigan, firstname.lastname@example.org
- Kun Xiong, University of Arizona, email@example.com
- Xueping Zhao, University of South Carolina, firstname.lastname@example.org
The daily schedule a the CSU campus 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, q-bio16, Fort Collins.
Many of the lectures at the 2015 q-bio Summer School in Fort Collins will make use of different software packages. We recommend coming to the summer school with the following pre-installed:
- Mathworks Matlab or GNU Octave
- A Python distribution such as Anaconda or Enthought Canopy
- Design Space Toolbox V2
About the CSU Campus
The new campus of 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 offie 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.
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.
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.
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).