SPA Short course2020-02-22T01:19:09+00:00
  • 1 week.

  • Morning lectures.

  • Afternoon practicals.

  • March 2-6, 2020.

  • At no cost.

  • Room and board NOT included.

Note, registration has closed for the 2020 offering. New applicants will automatically be placed on the livestream mailing list.

Questions? Email nccatinfo [at] nysbc.org.

Apply

Sponsors

Single Particle Short Course
March 2-6, 2020

NCCAT will be offering a 1 week workshop focused on the theory and practice of single-particle analysis. The mornings will have lectures and stimulating round table discussions. The afternoons provide hands-on practicals to reinforce fundamental concepts and topics covered earlier in the day.

Short-course Agenda ver. 2020.02.13

Day 1: Monday, March 2, 2020

09:00 – 09:30 Registration and Welcome – SEMC conference room
09:50 – 10:00 Opening – NYSBC conference room
10:00 – 11:15 Keynote / Lecture 1 – NYSBC conference room
Intro and overview of SPA
Joachim Frank (Columbia University)
11:15 – 11:30 Break
11:30 – 12:15 Roundtable 1 – SEMC conference room
Introductions and course overview
Short course attendees
12:15 – 13:30 Lunch
13:30 – 14:15 Lecture 2 – SEMC conference room
cryoVR for sample preparation
Brenda Gonzalez & Jiahui Dong (Purdue University)
14:15 – 14:30 Break
14:30 – 17:00

14:30 – 17:00

Practical 1 – SEMC conference room
Support films and grids
Practical 2 – SEMC conference room
Plunge freezers and Chameleon
SEMC/NCCAT Staff

Day 2: Tuesday, March 3, 2020

09:00 – 09:30 Registration/Information desk – SEMC conference room
09:45 – 10:45 Lecture 3 – NYSBC conference room
Microscopes and tools of the trade
SEMC/NCCAT Staff
10:45 – 11:00 Break
11:00 – 12:00 Roundtable 2 – SEMC conference room
cryoEM Facility building
SEMC/NCCAT Staff
12:00 – 13:30 Lunch
13:30 – 17:00 Practical 3 – SEMC conference room
TEM microscopes
SEMC/NCCAT Staff

Day 3: Wednesday, March 4, 2020

09:00 – 09:30 Registration/Information desk – SEMC conference room
09:45 – 10:35

10:40 – 11:30

Lecture 4 – NYSBC conference room
Algorithms and foundational math PartI:
     derivation/explanation of the CTF, FTs.
Algorithms and foundational math PartII:
reconstruction, classification, maximum likelihood.
Fred Sigworth (Yale University)
11:30 – 11:45 Break
11:45 – 12:30 Lecture 5 – NYSBC conference room
Data Analysis and reconstruction workflow
Amedee des Georges (ASRC/CUNY)
12:30 – 13:15 Lunch & Roundtable 3 – NYSBC conference room
Current algorithms to deal with SPA reconstruction
Fred Sigworth, Amedee des Georges & others
13:15 – 13:30 Group photo
13:30 – 17:00

13:30 – 17:00
by appointment

Practical 4 – SEMC conference room
CryoEM on Demand (processing in the cloud using AWS)Practical 3B – Krios control room
TEM microscopes (continued) – Krios operations
SEMC/NCCAT Staff

Day 4: Thursday, March 5, 2020

09:00 – 09:30 Registration/Information desk – SEMC conference room
09:45 – 10:45 Lecture 6 – NYSBC conference room
Interpretation and Limitations of SPA
Rich Hite (Memorial Sloan Kettering Cancer Center)
10:45 – 11:45 Lecture 7 – NYSBC conference room
Validation Methods
Tom Walz (Rockefeller University)
11:45 – 12:15 Roundtable 4 – NYSBC conference room
EM challenges and new frontiers
Rich Hite, Tom Walz & others
12:15 – 13:30 Lunch
13:30 – 15:45 Practical 4B – SEMC conference room
CryoEM on Demand (wrap-up)
mini-roundtable: Results, resolution and EM maps
SEMC/NCCAT Staff
13:30 – 17:00
by appointment
Practical 3C – Krios control room
TEM microscopes (continued) – Krios operations
Time reserved for data collection of select student projects
15:45 – 17:00 Lecture 8 – SEMC conference room
EMDataResource: Structure Data Archiving, Validation Challenges
Cathy Lawson (Rutgers University)
18:00 – 20:00 Reception
Group dinner

Day 5: Friday, March 6, 2020

09:00 – 17:00 Registration/Information desk – SEMC conference room
room available all day except for practicals
09:45 – 10:45 Lecture 9 – NYSBC conference room
Fitting Atomic Models
Oli Clarke (Columbia University)
10:45 – 11:45 Lecture 10 – NYSBC conference room
Coordinate Refinement and Validation
Gira Bhabha & Damian Ekiert (New York University)
11:45 – 12:15 Roundtable 4 – NYSBC conference room
Making biological conclusions from cryoEM reconstructions.
Gira Bhabha, Damian Ekiert, Oli Clarke & others
12:15 – 12:30 Lunch (pizza lunch) – SEMC conference room
working lunch through practical
12:30 – 15:45 Practical 5 – SEMC conference room
Coot and model building
Oli Clarke & SEMC Staff
13:45 – 15:45
by appointment
Practical 3D – Krios control room
TEM microscopes (continued) – Krios operations
Time reserved for data collection of select student projects
SEMC/NCCAT Staff
15:45 – 16:15 Closing and farewell