Boot Camp 2017

Interdisciplinary Boot Camp in Quantitative Biology


JANUARY 3-13, 2017

Single Particle Cryo-Electron Microscopy

Proteomics, Room 120

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Overview

The Center for Integrative Proteomics Research, home to the Institute for Quantitative Biomedicine and the Graduate Program in Quantitative Biomedicine, hosts an annual boot camp to augment interdisciplinary undergraduate and graduate education for students and scientists of all levels interested in bringing quantitative approaches to challenges in biological research. The goal is to introduce participants to the value of integrating quantitative biology education with that afforded by other disciplines of study, including mathematics, physics, computer science, statistics, chemistry, engineering, medicine, and the life sciences.

The immersive two-week Boot Camp of 2017 will focus on single particle cryo-electron microscopy (CryoEM). CryoEM enables determination of three-dimensional structures of large biological macromolecules, macromolecular complexes, and cell components of biological interest.  Recent advances in CryoEM have made it possible to visualize extremely complex systems, thereby enhancing our understanding of biology at the molecular level.

Boot camp might interest you if you have ever:

  • wondered how to use your talents to help solve challenging structural problems in biology that require interdisciplinary team efforts
  • wondered how people can get high resolution images of complex cellular machines, even without the need to grow crystals
  • wondered what kinds of job opportunities are associated with being part of interdisciplinary teams of scientists working on challenging problems – and how to get such jobs
  • wished you could figure out who might be valuable partners for collaboration

 

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Boot Camp Basics

Week 1 (Jan. 3-6, 2017): Sample preparation and image collection

Week 2 (Jan. 9-13, 2017): Image processing, model fitting/making, validation, and deposition in databases

Program Options and How to Sign Up:

  1. Choose your preferred program option:

    1. The immersive Weeks 1 and 2, 2-credit option (for students)
      1. Experience a unique form of education and fun!  Take big chances in a Pass/Fail format, doing exciting things that may be out of your areas of familiarity – without worrying about grades.
      2. Listen to talks and engage in hands-on exercises preparing and characterizing samples for purity, solubility, and concentration prior to imaging.  
      3. Flash-freeze samples and examine them in the cryo-electron microscope.  At this stage, students may also examine samples prepared in advance corresponding to their own research efforts.
      4. Learn how to collect and analyze images of biological machines.
      5. Listen to talks and then take the driver’s seat learning how to determine high resolution CryoEM structures.
      6. Become a member of an interdisciplinary team, doing the detective work to unfold the secrets of intricate molecular machines.
      7. There will be 4 teams, each with its own project to solve, You will learn to make decisions regarding how to successfully navigate the steps involved with sample preparation, data collection and processing to reach a high resolution 3D structure of your complex.  
      8. Use graphical display software to visualize data as 3D molecular structures.
      9. You will learn to analyze your results by using statistics for validation along with fitting and validating available models. What does your model say about the biology?
      10. Share information and insights with teammates and the larger group as a means to understand how the process reveals how these 4 cellular machines work. You may also explore how suitable your own sample might be for CryoEM studies.
      11. Work with other participants to prepare a final presentation of the technical and biological aspects of the structure determinations corresponding to each of the 4 teams’ macromolecular machines.
      12. Participate in career development sessions and use your new skills at networking events during Boot Camp.
    1. The immersive Weeks 1 and 2, pay-to-participate option (for staff, postdocs, and faculty)
      1. You are invited and encouraged to participate in Boot Camp, like the registered students, as team members on a mission to learn as much as you can about the process involved in determining the structures and functions of your cellular machines by CryoEM
      2. Learn from the 4 samples chosen for the program and ask and learn how suitable your own sample might be for CryoEM studies.
    2. The immersive Week 2-only, pay-to-participate option (for staff, postdocs, faculty, and researchers from industry or private businesses)
      1. Join in at the stage where we take you through the process of analyzing hundreds of images of a cellular machine and learn how to obtain and process CryoEM images to produce high resolution structures.
      2. Learn how to visualize your team’s machinein a way that will highlight features of interest that you would like to study and convey this information to others.
      3. Perform simulations of your molecular machine in action to help model its abilities.
      4. Participate in the final analyses and take part in group’s presentation.
      5. Enjoy social and networking events within the context of Boot Camp.
      6. Talk with Dennis Thomas about your own research interests and samples regarding the suitability of your samples and possible studies using the cryo-electron microscope.
    3. The drop-in-when-you’d-like option (for all interested individuals)
      1. Drop in to any lectures, career development and networking events, and the final presentation at no cost on a space-available basis during Boot Camp.  Due to the significant amount of mentoring required, hands-on exercises will be limited to fully registered participants only.
      2. Join career development and networking sessions.
      3. Attend the final group presentations to see what the groups have accomplished using CryoEM. We hope for a lively discussion period where the pitfalls and advantages of this process can be discussed.
  2. Sign up:

    1. Deadlines
      1. Before Dec. 15th at noon: ALL people interested in attending the immersive 1- and/or 2-week program (for all categories) must register FIRST on the Boot Camp Registration page.  
      2. By Dec. 16th at 5 PM: 40 1- and 2-week full participants (of categories A, B, and C above) will be informed that they have been selected.  You will then need to fully establish your participation according to your particular status (described below).  All others will be placed on a Waiting List.  Please note the deadlines in bold character.  If you do not register in time, your position will be offered to the next person on the waiting list.  
      3. All others are welcome to attend as Drop-in participants (or to sign up for a future Boot Camp, possibly in Summer 2017).
    2. The immersive Weeks 1 and 2, 2-credit option (for students)
      1. Obtain a Special Permission number by contacting Michelle Sanghera at msanghera@iqb.rutgers.edu.
      2. Register on Rutgers’ Winter Session Registration page before it closes Dec. 21st at 4 PM.  This registration will appear on your transcript.
      3. The cost will be that of 2 credits + $83 for student fees.  (The costs are detailed here.)

        Note 1: For graduate students, tuition can either come from your first-year course-credit allowance (i.e., as a teaching assistant or graduate fellow) or from lab funds (and will count toward the credits required for your Master’s and/or Ph.D. degree).

        Note 2: For undergraduates, this cost will be in addition to your annual tuition fees.  You may wish to discuss with your counselor ways in which you might take Boot Camp as one of your electives.

        Note 3: If you are a graduate student in the GSBS, you will also need to fill out a "student exchange program" form in order to get the credits transferred to your Spring 2017 transcript.  As part of the process, you will need to gather approval signatures from your advisor, the GSBS dean (gsbspisc@gsbs.rutgers.edu), and Gail Ferstandig Arnold (gfarnold@iqb.rutgers.edu).
    3. The immersive Weeks 1 and 2, pay-to-participate option (for postdocs, staff, and faculty)
      1. A sliding fee will be charged depending upon your possible participation in teaching during Boot Camp.  Contact Michelle Sanghera msanghera@iqb.rutgers.edu for details.
    4. The immersive Week 2-only, pay-to-participate option (postdocs, staff, faculty, and researchers from industry and private businesses)
      1. If you are a postdoc, staff member, or faculty member, a sliding fee will be charged depending upon your possible participation in teaching.  Contact Michelle Sanghera msanghera@iqb.rutgers.edu for details.
      2. If you are from industry, a fixed fee will be charged.  Contact Michelle Sanghera msanghera@iqb.rutgers.edu for details.
    5. The drop-in-when-you’d-like option (for all interested individuals)
      1. Members of the Rutgers community are encouraged to attend individual lectures, career development and networking events, and the final presentation at no cost on a space-available basis.

Program

View the program

Schedule

View the schedule

Space-Limited Events

Most events will be in Proteomics room 120 where there will be seats for ~100 people.  40 people will be allowed to participate in the immersive 1- and 2-week programs and others will be welcome to drop in to attend individual lectures, career development and networking events, and the final presentation at no cost on a space-available basis.

Software Needed

Boot Camp Participants will be using their own laptops to access Linux servers using VNC.  Users will also need a 3 button mouse to do the work as touchpads will be problematic for the various tasks that need to be done with the mouse pointer.

  1. Mac users can use the Mac built in VNC client in Finder
  2. Windows users download TightVNC from http://www.tightvnc.com/download.php

In addition, users will also run local applications for some tasks.  Please download and install the following software

  1. Chimera - https://www.cgl.ucsf.edu/chimera/download.html
  2. EMAN2 - http://ncmi.bcm.edu/ncmi/software/counter_222/software_133

FAQ

 1. Do I need to take any prerequisites?

No prerequisites are required.  The material will be presented assuming that you are capable but not knowledgeable.

2. How many hours a day will Boot Camp be?

Boot Camp will go from roughly 9 AM-5 PM both weeks (not including the weekend).  A few social evening events will be planned.

3. What will I need to do to earn the 2 credits and pass the course?

To earn 2 credits, you will be expected to participate in the full spectrum of activities from 9 AM-5 PM of both weeks, as a member of a team and a contributor to the whole group.

4. What can I attend without being registered?

As a non-registered individual, you are free to attend any of the morning lectures, career development and networking sessions, coffee sessions, and the final presentation on a space-available basis.

Sakai Site

Use the following link to join the 2017 Boot Camp Sakai site: https://sakai.rutgers.edu/portal/directtool/2c080c22-445d-46a1-a49a-de4f01eb7438
Log in with your NETID.  External users must select Email Login and request access before entry.  Contact Michelle Sanghera (msanghera@iqb.rutgers.edu) to request access.

CryoEM Facility

Learn more about the CryoEM facility here

Contact Us

Please send all questions and comments to: bootcamp@iqb.rutgers.edu