4th q-bio Summer School Themes

Spatiotemporal modeling of cellular regulatory systems

This series of lectures will be focused on modeling of signal-transduction systems.

Lecturers:

  • William S. Hlavacek
  • Bridget S. Wilson
  • Elaine L. Bearer
  • James R. Faeder

Stochastic biochemistry

In this theme, we will explore stochasticity in the modeling of biochemical systems. In particular, we will concentrate on the effects that small numbers of important molecules (i.e. genes, RNAs and proteins) have on the dynamics of living cells. We will review experimental manifestations of stochastic effects in molecular biology, as can be measured using single cell and single molecule techniques. We will discuss the most recent analytical and numerical methods that are used to model these systems and show how these methods can improve interpretation of experimental data. We will study how different cellular mechanisms control and/or exploit randomness in order to survive in uncertain environments. Similarly, we will explore how single-cell measurements of cell-to-cell variability can reveal more information about underlying cellular mechanisms.

This section of the summer school will include a number of instructor-suggested group projects, in which students will apply various numerical techniques to formulate, identify and solve stochastic models for gene regulatory systems. Students will then apply these tools to model experimental flow cytometry or other single-cell data. Access and knowledge of Matlab will be helpful, but is not strictly necessary.

This section of the summer school is organized by Brian Munsky. Please address all questions about this section of the summer school to its organizer.

Lecturers Include

Topics Include

  • Introduction to Stochasticity. The importance of stochasticity in gene regulatory networks. Key examples from the literature.
  • Discussion of the importance of stochasticity in small populations. Stochastic Phenomena: switching, focusing, resonance, filtering.
  • The effects of positive and negative feedback.
  • The physics behind stochastic chemical kinetics.
  • Connection between deterministic and stochastic reaction rates.
  • Derivation of the Master Equation for discrete stochastic processes.
  • Solving the Chemical Master Equation: exact solutions for linear propensity functions,
  • Kinetic Monte Carlo algorithms: Tau Leaping. Chemical Langevin equation. Time separation schemes. Hybrid methods.
  • Density Computation Approaches: Finite State projections techniques, Moment Generating Function Techniques, Moment Closure Techniques, Fokker Planck equation.
  • Simplification of complex biochemical processes.
  • Switch rate analyses, waiting/completion times.
  • Single cell measurement techniques: flow cytometry, fluorescence microscopy, time lapse microscopy.
  • Using fluctuations to infer system mechanisms and parameters.
  • History of Stochastic Modeling in Physics.
  • Signal Processing in Biochemical networks.
  • Synthetic Biology

Multiscale modeling of biomolecules

The general theme of this lecture track is multiscale modeling of biomolecules. It will feature four lectures:

  • S. 'Gnana' Gnanakaran: general overview - how multiscale modeling approaches have been applied to study a wide variety of biological problems
  • Partha Ramakrishnan: quantum mechanical and molecular modeling approaches with special emphasis on molecular recognition during host-pathogen and nanomaterial-protein Interactions
  • Anurag Sethi: Molecular dynamics and network theory approaches with special emphasis on signaling and intrinsically disordered proteins
  • Giovanni Bellesia: Coarse-grained and statistical mechanical approaches with special emphasis on biofuels and membrane physics

Other topics

In addition to lectures in the three main tracks (spatiotemporal modeling of cellular regulatory systems, stochastic biochemistry and multiscale modeling of biomolecules), there will be lectures on additional subjects.

4th q-bio Summer School Logistics

Travel Information

Flying in

You can fly either to Albuquerque airport (ABQ) or to Santa Fe airport (SAF). Service to SAF is limited and tends to be expensive, though the airport is closer. From our personal experience, you may want to avoid the last flight of the day to either of the airports, and especially to Santa Fe. Both airports are quite small by big-city standards, and rebooking may be a problem if your flight is cancelled or delayed due to weather or other problems.

Getting to Los Alamos/Santa Fe from the airports

Shuttle service to Los Alamos from either airport costs in excess of $80, and a reservation is needed in advance. Shuttle service is offered by two companies:

  • Roadrunner Shuttle (+1 505 424-3367)
  • LA Shuttle (+1 505 695-9407)

Shuttle service to Santa Fe from ABQ is offered by Sandia Shuttle Express. A reservation can be made online or by calling +1 888 775-5696.

If you wish to rent a car, you are eligible for the LANL contracted rate from Hertz, because the q-bio Summer School is sponsored by Los Alamos National Laboratory (LANL). Simply provide the LANL Hertz corporate discount number 72120 at the time of reservation and, more importantly, rental. Renting from Hertz is likely to be cheaper than other rental options because there is no surcharge for a one-way rental and full insurance is included in the LANL contracted rate. The Hertz car rental drop-off/pick-up location in Los Alamos is the Los Alamos County Airport, which has no commercial air service. Hertz rents only to those 21 years old or older.

Driving time to Los Alamos from Santa Fe and Albuquerque airports is about one and two hours, respectively. Traveling on a shuttle will take longer.

Local Transportation

  • Atomic City Transit provides free bus service within Los Alamos.
  • New Mexico Park & Ride commuter bus service connects Los Alamos to Pojoaque and Santa Fe (Blue Route). The one-way fare is $3. Exact change is required. There is no weekend service.
  • The New Mexico Rail Runner train connects Santa Fe to Albuquerque. The downtown Albuquerque train station is connected to the Albuquerque airport (ABQ) via ABQ Ride city bus (Route 50) and the free Airport Express Route 350 shuttle. The one-way city bus fare in Albuquerque is $1.
  • Santa Fe Trails provides bus service within Santa Fe. The one-way city bus fare in Santa Fe is $1.

Parking

If you are bringing your own car, there is ample parking near the site of the summer school. Parking is free but by permit only. Permits will be made available.

Transportation to the q-bio Conference

The site of the q-bio Conference is the campus of St. John's College in Santa Fe, which can be reached via public transportation. A van will be provided for transport/storage of luggage.

Visiting Los Alamos National Laboratory

Badging requirements

  • If you are approved by DOE to visit LANL, you must pick up a visitor badge at the LANL Badge Office before coming onto any other LANL property. The Badge Office is located in the Otowi Building (Technical Area 3, Building 261). The Badge Office hours are 7:30-15:30 Mon-Fri and CLOSED Wed 11-12:30.
  • If you are a US citizen, to receive a badge, you must provide proof of citizenship. The only proof accepted is a) a US passport or b) a government issued photo ID and a birth certificate.
  • If you are not a US citizen, to receive a badge, you must provide photo ID, a valid passport, and visa documentation.
  • When on LANL property, you must wear your badge at all times, clearly visible above the waist.
  • You must swipe your badge at a badge reader before entering any building. You may enter only approved buildings.

Laptops

To carry a non-LANL owned laptop (and many other non-LANL owned electronic devices) onto LANL property, you must complete Form 1897. You may complete this form upon arrival.

While on LANL property, please

  • Turn off Wi-Fi
  • Turn off or tape over camera
  • Use up-to-date anti-virus software
  • Carry a completed Form 1897 with your laptop (and other electronic devices)

Cameras

Please do not use or carry a camera onto LANL property. If your mobile phone is equipped with a camera, do not use it. See below for more information about mobile phones.

Mobile phones

To carry a mobile phone onto LANL property you will need to complete Form 1897. This form can be completed upon arrival. While on LANL property, please

  • Do not use your camera, if your phone has one.
  • Do not carry your phone into buildings where mobile phones are not allowed, such as the T Division building (Technical Area 3, Building 123). Lock boxes are available outside such buildings.
  • Carry a completed Form 1897 with your phone.

Backpacks and other bags

All unidentified backpacks, purses, lunch pails and other bags will be confiscated and destroyed if left unattended. Please tag your bag upon arrival. Tags will be made available.

How to Find the Lecture Hall

The site of the summer school is Room 203A/B in the Los Alamos Research Park building at 4200 W Jemez Rd (map). This room is around the corner from Hot Rocks Java Cafe, a coffee and sandwich shop with free Wi-Fi. Across from the building is Technical Area 3 (TA-3) of Los Alamos National Laboratory (LANL). The building sits on the rim of Los Alamos Canyon (map). The lecture hall is a designated open area and a DOE-issued ID badge is not required to enter the lecture hall. If you are arriving at the Transit Center via either Atomic City Transit bus or NMDOT Park & Ride bus, you will need to walk along Jemez Rd to the Los Alamos Research Park building; see this map (Building 4200 is your destination). If you are walking uphill after passing the intersection with Diamond Drive, you will be going in the correct direction. Please do not wander onto property of Los Alamos National Laboratory without a DOE-issued ID badge!!

About the surrounding area: The network of hiking trails throughout Los Alamos can be accessed from the research park. One can drive from the research park to the Pajarito Mountain ski/mountain biking area in about 10 minutes. By car, one can reach sites such as the Santa Fe National Forest, Bandelier National Monument, and the Valles Caldera National Preserve in less than 30 minutes.

  • Map - the Los Alamos Research Park is at the top of the map, a bit to the left from the center; the building number is 4200.
  • Parking permits will be available upon request.
  • Wireless and wired internet access will be available at the classroom. A printer will also be available.

 

4th q-bio Summer School Students

Group Picture

Summer School 2010 participants

Students

  1. Alexey V. Akimov, Rice University
  2. Dipak Barua, Los Alamos National Laboratory
  3. Julio M. Belmonte, Indiana University
  4. Eyal Ben-Isaac, Weizmann Institute of Science
  5. Paul B. Bogdan, Carnegie Mellon University
  6. Rosemary Braun, National Cancer Institute
  7. Anat Burger, University of California, San Diego
  8. Paolo Cazzaniga, University of Milan-Bicocca
  9. Antoine Delmotte, Imperial College of Science, Technology and Medicine
  10. Alexei Finski, Harvard University
  11. Michael M. de Freitas, Rutgers University
  12. Jianfu Guo, Institute for Computational Biology, Shanghai
  13. Jean Hausser, Universität Basel
  14. Kentaro Hayashi, Keio University
  15. Jiankui He, Rice University
  16. Yuejun Kang, Los Alamos National Laboratory
  17. Kimberly Kanigel-Winner, University of New Mexico
  18. Chunbo Lou, University of California, San Francisco
  19. Simon Mehalek, University of New Mexico
  20. Maria Mateescu, EPFL
  21. Michael Nip, University of California, Santa Barbara
  22. Stephen T. Payne, Duke University
  23. Mario J. Paz, University of New Mexico
  24. Barak Peleg, Weizmann Institute of Science
  25. Dario Pescini, University of Milan-Bicocca
  26. Erin M. Rivera, New Mexico State University
  27. Henry Romero, University of Colorado
  28. Erwin Schoof, The Institute of Cancer Research
  29. Samantha Schwartz, University of New Mexico
  30. Jonghyeon Shin, University of Minnesota
  31. Piyou Song, University of New Mexico
  32. Alvin Tamsir, University of California, San Francisco
  33. Abhinav Tiwari, Rice University
  34. W. Duncan Wadsworth, University of New Mexico
  35. Sheng Wu, University of California, Santa Barbara
  36. Xiaojing Yang, University of California, San Francisco
  37. Christoph Zimmer, University of Heidelberg

Student Pictures

Henry Romero
Christoph Zimmer
Erin Rivera
Alexei Finski
Michael Nip
Kentaro Hayashi
Michael de Freitas
Erwin Schoof
Sheng Wu
Jianfu Guo
Abhinav Tiwari
Paul Bogdan
Julio Belmonte
Jonghyeon Shin
Sam Schwartz
Duncan Wadsworth
Jiankui He
Dario Pescini
Paolo Cazzaniga
Yuejun Kang
Maria Mateescu
Rosemary Braun
Dipak Barua
Simon Mehalek
Mario Paz
Antoine Delmottte
Anat Burger
Chunbo Lou
Alexey Akimov
Eyal Ben-Isaac
Jean Hausser
Kim Kanigel
Stephen Payne
Barak Peleg
Xiaojing Yang
Alvin Tamsir

 

4th q-bio Summer School Schedule

Schedule Overview

Unless otherwise noted, the school schedule will consist of approximately 3 hours of lectures in the morning. A typical schedule will look like

  • 9:00-10:45 -- Lecture One
  • 10:45-11:00 -- Break
  • 11:00-12:45 -- Lecture Two

Afternoons will be left for other activities, such as ad hoc lectures, student talks (please come prepared to give an informal talk about your research), discussions, and study sessions, work on homework projects, continuation of the participants' regular academic work, and recreation. A classroom with wireless internet access will be reserved for the school participants for all afternoons during the school program. Additionally, we expect the students to spend some of the afternoons with the school faculty, most of whom are scientists at LANL, familiarizing themselves with the workings of the research institution and potentially starting collaborative research with the faculty.

Detailed schedule

July 25 - Sunday
Arrive in Los Alamos

Week 1

July 26 - Monday
Opening remarks - 8:00 AM
Lecture 1, Ruy Ribeiro, Dynamics of CD4+ T cells in HIV-1 infection
Lecture 2, Brian Munsky, Stochastic effects in systems biology: theoretical foundations and experimental results (part 1) Slides--Part1
Lunch discussion with lecturers
Student Talk 1 - Christoph Zimmer
July 27 - Tuesday
Lecture 3, S. 'Gnana' Gnanakaran, How multiscale modeling approaches have been applied to study a wide variety of biological problems
Lecture 4, William S. Hlavacek, Rule-based modeling (slides)
Lunch discussion with lecturers
Student Talk 2 - Erin Rivera
14:00-15:00, Jasmin Fisher, Microsoft Research Cambridge -- q-bio seminar talk.
Student Talk 3 - Kentaro Hayashi
Student Talk 4 - Abhinav Tiwari
July 28 - Wednesday
Lecture 5, Tanmoy Bhattacharya, Phylogenetics (slides)
Lecture 6, Brian Munsky, Stochastic effects in systems biology: theoretical foundations and experimental results (part 2) Slides--Part2
Lunch discussion with lecturers
Student Talk 5 - Anat Burger
Student Talk 6 - Erwin Schoof
Student Talk 7 - Paolo Cazzaniga
Student Talk 8 - Dario Pescini
July 29 - Thursday
Lecture 7, Alan S. Perelson, How to model a viral infection
Lecture 8, Bridget S. Wilson, Protein clustering
Lunch discussion with lecturers
Student Talk 9 - Sam Schwartz
Student Talk 10 - Duncan Wadsworth
Student Talk 11 - Jean Hausser
Student Talk 12 - Jiankui He
July 30 - Friday
Lecture 9, Bette Korber, HIV vaccine design
Lecture 10, Anurag Sethi, Molecular dynamics and network theory approaches with special emphasis on signaling and intrinsically disordered proteins
Lunch discussion with lecturers
Student Talk 13 - Michael Nip
Student Talk 14 - Michael de Freitas
Student Talk 15 - Julio Belmonte
Student Talk 16 - Maria Mateescu
July 31 and August 1 (Saturday and Sunday)
Ideas for weekend activities -- TBA

Week 2

August 2 - Monday
Lecture 11, Cynthia Reichhardt, Computational Modeling of Directed Motion in Self-Driven Systems such as Bacteria and Cells
Lecture 12, Helen Wearing, University of New Mexico
Lunch discussion with lecturers
Guest Lecture - Ramit Mehr (slides)
Student Talk 17 - Alvin Tamsir
Student Talk 18 - Barak Peleg
August 3 - Tuesday
Lecture 13a, Arjun Raj, Measuring cell-to-cell variability with fluorescence microscopy and single molecule Fluorescence In Situ Hybridization (FISH) techniques.
Lecture 13b, Babs Marrone, Measuring cell-to-cell variability with flow cytometry and fluorescence activated cell sorting. (slides)
Lecture 14, Thomas Leitner, Molecular evolution: tracing HIV epidemics and the origin of the domestic dog
Lunch discussion with lecturers
Student Talk 22 - Rosemary Braun
Student Talk 23 - Antoine Delmotte
14:00-15:00, Arjun Raj, University of Pennsylvania -- q-bio seminar talk A single molecule view of cell fate: FISHing for worm guts
August 4 - Wednesday
Lecture 15, Partha Ramakrishnan, Quantum mechanical and molecular modeling approaches with special emphasis on molecular recognition during host-pathogen and nanomaterial-protein Interactions
Lecture 16A, Jim Werner, Fluorescence Correlation Spectroscopy (FCS) and 3 Dimensional Molecule Tracking:
Lecture 16B, Brian Munsky, Using single-cell variability data (FISH and Flow Cytometry) to identify parameters and mechanisms of gene regulatory systems.
Lunch discussion with lecturers
Lecture 17, Arthur D. Lander, Biological Pattern and Growth: Mechanism and Control
Student Talk 24 - Xiaojing Yang
Student Talk 25 - Chunbo Lou
August 5 - Thursday
Lecture 18, Ryan Gutenkunst, Inferring population history and natural selection from genomic data
Lecture 19, Giovanni Bellesia, Coarse-grained and statistical mechanical approaches with special emphasis on biofuels and membrane physics
Lunch discussion with lecturers
"Guest Lecture" - Ramit Mehr
Student Talk 26 - Eyal Ben Isaac
Special Talk - Mac Hyman, Tulane/Los Alamos, Good choices for great careers (this talk will start at 4 PM) (slides)
August 6 - Friday
Lecture 20, Ilya Nemenman, Signal processing in biochemical networks, Part 1.
Lecture 21, Ilya Nemenman, Signal processing in biochemical networks, Part 2.
Lunch discussion with lecturers
Student Talk 27 - Paul Bogdan
Student Talk 28 - Arfu Guo
Student Talk 29 - Jonghyeon Shin
Student Talk 30 - Sheng Wu
August 7 and 8 (Saturday and Sunday)
Ideas for weekend activities -- TBA

Week 3

August 9 - Monday
Lecture 22, Anton Zilman, History of Stochastic Modeling in Physics.
Lecture 23, Anton Zilman, Advanced stochastic analyses: Fokker Planck equation, Moment Generating Functions, etc...
Lunch - Panel discussion on the Necessary Complexity of Biological Models: Tanmoy Bhattacharya, Gnanakaran, S, Byron Goldstein, Ryan Gutenkunst, Ilya Nemenman
Lecture 24, Elaine L. Bearer, Cellular dynamics: inside and outside
Student Talk 34 - Mario Paz
Student Talk 35 - Kimberly Kanigel-Winner
August 10 - Tuesday
Lecture 25, James R. Faeder, University of Pittsburgh School of Medicine
Lecture 26, Christopher A. Voigt, CANCELLED - Replacement 1/2 talk to be given by Alvin Tamsir. Synthetic biology
Lunch discussion with lecturers
14:00-15:00, Chris Bystroff, Rensselaer Polytechnic Institute -- q-bio seminar talk (this talk will take place in Room 203A/B of the Los Alamos Research Park building)
Lecture 27, Tomasz Lipniacki, Polish Academy of Sciences
August 11 - Wednesday
Depart to Santa Fe for the q-bio Conference -- Students will take a NM Park & Ride bus to Santa Fe in the morning ($3 exact change is required); organizers will arrange for separate transport of luggage to the conference site. A van will be waiting with an organizer at the school hotel at 8:15 am for transport of luggage to the site of the conference.

4th q-bio Summer School Lecturers

Lecturers

Other Senior Participants

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