Single Particle Short Course
March 2-6, 2020
NCCAT offered a 1 week workshop focused on the theory and practice of single-particle analysis. The mornings were filled with lectures and stimulating round table discussions. The afternoons provided hands-on practicals to reinforce fundamental concepts and topics covered earlier in the day.
Short-course Agenda
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) [lecture slides][lecture video] |
| 11:15 – 11:30 | Break |
| 11:30 – 12:15 | Roundtable 1 – SEMC conference room Introductions and course overview Short course attendees [roundtable slides] |
| 12:15 – 13:30 | Lunch |
| 13:30 – 14:15 | Lecture 2 – SEMC conference room cryoVR for sample preparation Brenda Gonzalez & Jiahui Dong (Purdue University) [lecture slides][lecture video] |
| 14:15 – 14:30 | Break |
| 14:30 – 18:00
14:30 – 18:00 |
Practical 1 – SEMC conference room Support films and grids Practical 2 – SEMC conference room Plunge freezers and Chameleon SEMC/NCCAT Staff [schedule] |
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 Ed Eng (NCCAT/NYSBC) [lecture slides][lecture video] |
| 10:45 – 11:00 | Break |
| 11:00 – 12:00 | Roundtable 2 – SEMC conference room cryoEM Facility building SEMC/NCCAT Staff [roundtable slides][roundtable video] |
| 12:00 – 13:30 | Lunch |
| 13:30 – 17:30 | Practical 3 – SEMC conference room TEM microscopes SEMC/NCCAT Staff [schedule] |
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) [lecture slides 1 lecture slides 2 lecture slides 3 lecture slides 4] [lecture notes SPR lecture notes reconstruction lecture notes fourier2D-3D lecture notes fourier1D lecture notes phase contrast lecture notes complex numbers] [lecture video] |
| 11:30 – 11:45 | Break |
| 11:45 – 12:30 | Lecture 5 – NYSBC conference room Data Analysis and reconstruction workflow Amedee des Georges (ASRC/CUNY) [lecture slides][lecture video] |
| 12:30 – 13:15 | Lunch & Roundtable 3 – NYSBC conference room Current algorithms to deal with SPA reconstruction Fred Sigworth, Amedee des Georges [roundtable video] |
| 13:15 – 13:30 | Group photo |
| 13:30 – 17:00
13:30 – 17:00 |
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) [lecture slides][lecture video] |
| 10:45 – 11:45 | Lecture 7 – NYSBC conference room Validation Methods Tom Walz (Rockefeller University) [lecture slides][lecture video] |
| 11:45 – 12:15 | Roundtable 4 – NYSBC conference room EM challenges and new frontiers Rich Hite, Tom Walz [rountable video] |
| 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 [summary slide] |
| 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) [lecture slides][lecture video] |
| 18:00 – 20:00 | Reception Group dinner [directions] |
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) [lecture slides][lecture video] |
| 10:45 – 11:45 | Lecture 10 – NYSBC conference room Coordinate Refinement and Validation Gira Bhabha & Damian Ekiert (New York University) [lecture slides][lecture video] |
| 11:45 – 12:00 | Practical 5 setup – SEMC conference room Making biological conclusions from cryoEM reconstructions. Oli Clarke [pre-practical instructions] |
| 12:00 | Lunch (pizza lunch) – SEMC conference room working lunch through practical |
| 12:00 – 15:45 | Practical 5 – SEMC conference room Coot and model building Oli Clarke & SEMC Staff [practical slides] |
| 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 |
