Winter Boot Camp 2018

5th Annual Interdisciplinary Quantitative Biology Winter Boot Camp 

Cryo-Electron Tomography

January 8 - 12, 2018

Center for Integrative Proteomics Research | Room 120 | Map  
Busch Campus, Rutgers University 
GPS: 679 Hoes Lane, Piscataway

Faculty, Staff, Type 6 and 9 Graduate Students, Guests:  Faculty/Staff parking options

Non-Type 6 or 9 Students:  Student parking options

 

 What is Cryo-Electron Tomography?

Cryo-electron tomography is an experimental technique to obtain a three-dimensional representation of a sample preserved in amorphous ice. A biological specimen (such as a protein, nucleic acid, macromolecular complex, virion, organelle, or cell) is vitrified in a thin film of aqueous solution. This process preserves the native state of the specimen through the imaging process. A series of transmission electron microscopy images of the specimen are obtained while tilting the specimen to various angles. Information from each of these images is merged computationally to reconstruct a three-dimensional volume. This volume can be analyzed by segmentation, quantitation, or by combining information from several tomograms of the same specimen through the process of sub-tomogram alignment and averaging. Cryo-electron tomography can be applied to biological questions over a range of resolutions from cell ultrastructure to the fine structure of individual macromolecules. With the use of subtomogram averaging, atomic models can be obtained for some systems.

Read more about the various electron microscopy techniques for the determination of three-dimensional structures at PDB101

Read more about the Cryo-Electron Microscopy and Tomography facility at the Center for Integrative Proteomics Research here.

   

WHAT WILL BOOT CAMP BE LIKE?

Boot Camp is designed to augment education for quantitative and biological scientists. Our overarching goal is to introduce students of all ages to the value of integrating biology and medicine with mathematics, physics, chemistry, computer science, statistics and biostatistics, and engineering.

The immersive one-week Boot Camp experience will provide broad introductory exposure to the language, culture, and experimental/theoretical underpinnings of cell biology, macromolecular biochemistry/biophysics, structural biology, computational biology, systems biology, and bioinformatics.  

Instruction will take the form of:

Morning lectures focused on the theory and practice of cryo-electron tomography. Participants will be introduced to fundamental concepts in cryo-electron tomography from sample preparation to data analysis. Experts in the field will discuss the latest applications of cryotomography to cell biology, microbiology, and structural biology.

Afternoon sessions devoted to hands-on training in sample preparation/cryo-preservation and in silico tutorials that will take participants from raw tomographic images to sub-tomogram averaged 3D structures of biological assemblies.

PROGRAM

The official program for the 2018 Winter Boot Camp can be found here.

WHO CAN ATTEND?

Students (undergraduate and graduate), staff, faculty, and colleagues in industry. Lectures open to all. Participants in dry lab exercises must register to attend (Mac or Linux laptop required).

HOW CAN I REGISTER?

If you are a student:

Register for this 1-credit Pass/Fail Winter Session course by:

  1. Registering on the Boot Camp website by Dec. 15th at 3 PM. We will inform you by Dec. 18th if you have been accepted as a full-time participant. Lectures will be open to the general public.
  2. If you are given approval to take the course,

a. Send an email with your name, RUID, and course number to Michelle Sanghera at msanghera@iqb.rutgers.edu. If you do not have a Rutgers ID number, please go here to request one.

b. Register on WebReg:

Undergraduate Level: 01:556:480
Graduate Level: 16:848:601
 
You will be given a special permission number at that time and your late registration fees will be waived.
If you are NOT a student: 
  1. Registering on the Boot Camp website. We will inform you by Dec. 18th if you have been accepted as a full-time participant. Lectures will be open to the general public.

DEADLINE FOR REGISTRATION:  Friday, December 15th at 3 PM.

Attendance will be limited to 25 full-time participants, so register now!

REMOTE CONNECT INSTRUCTIONS FOR LIVE-STREAMING LECTURES

SOFTWARE

Boot Camp Participants will be using their own laptops (Mac or Linux; not Windows) for their project research and visualizations.

Please make sure you have the following software installed PRIOR to the start of Boot Camp: 

Web Browser: current generation Firefox, Google Chrome, Safari, or Internet Explorer
Java: latest version. More info at java.com
UCSF Chimera: free for academic use; follow the download and installation information at https://www.cgl.ucsf.edu/chimera/download.html
Word processing, slide making/presenting, and spreadsheet software: Word, Powerpoint, and Excel or any tools with similar functionality.
IMODhttp://bio3d.colorado.edu/imod/download.html
Dynamo https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Downloads
EMAN2 http://blake.bcm.edu/emanwiki/EMAN2/Install

 

DEMO DATA

Please download the following demo data for Boot Camp Workshops

Recommended items: 

  • Power supply cords 
  • External mouse (very useful for structural visualization)
  • External participants will have the option to use WiFi as Guests.
  • Also, please note that no laptops will be available to be handed out as loaners during Boot Camp.

SAKAI SITE 

Once you have been accepted into Boot Camp, use the link here to join the 2018 Winter Boot Camp Sakai site. Rutgers participants log-in with your NETID. External registrants will be given Guest log-in information. Once you log-in, please follow the instructions here to make the site easily accessible. If you have any complications, please contact Michelle Sanghera at msanghera@iqb.rutgers.edu to request access. 

HOW DO I PREPARE FOR BOOT CAMP?

  1. Familiarize yourself with the parking arrangement that applies to you:
    1. Faculty/staff: Park in faculty/staff lots as usual (shown in yellow-green on the map). 
    2. Students with parking permits: Permitted parking options
    3. Visitors: Pull up in the circle in front of CABM (as described in the directions for being dropped off) and call 848-445-0103 to get your week-long parking permit.
  2. Remember to bring your laptops to Boot Camp every day.
  3. Since this is Boot Camp, start your day with 1,000 push-ups per day (optional) 

SURVEY:

Participants of the course can fill out the survey here.

ORGANIZERS:

Rutgers, The State University of New Jersey
Institute for Quantitative Biomedicine
RCSB Protein Data Bank  

QUESTIONS?

Email events@iqb.rutgers.edu