SciLifeLab Workshop for Cryo Electron Tomography Processing
Contents
Workshop
The SciLifeLab Dynamo workshop will take place from October the 24th to October the 27th in the SciLifeLab at Stockholm.
The workshop provides hands-on training in all practical aspects of tomography and sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this four-day course.
Computing resources
Laptops
Participants will bring their own laptops to access a SciLifeLab server which will host the data. However, each participant should also instal in their laptop prior to the workshop:
- Matlab (R2023a version), licence free trial version is available.
- Dynamo : prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:
https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html
Access to SciLifeLab resources
Credentials
To access the local desktop use the user and password that will be written in the whiteboard.
Each Windows OS PC has an Matlab 2019a executable with a parallel tool box installed.
A Chimera executable is locally available. To have an accelarated performance, there is the alternative to VNC Connect remote desktop software. Further instruction will be given for the interested users.
Load and run Dynamo from Matlab
In order to activate Dynamo, first open Matlab with a doble click
run Z:\SLL-STA-2023\Software\Dynamo\1.1.539\dynamo_activate.m
Data
In the PC, open a new Cywin-bash terminal (double-click on the icon).
Make sure to change dir to your user located in disk C:
cd /cygdrive/c/Users/MYUSER
Here, you replace MYUSER with the actual username (it will be available in the dashboard).
To create your working directory:
mkdir workplace-XX
Here, you replace XX with the number of your PC tower.
To copy the data into your local directory:
scp -r ws05@login.cryoem.se:/mnt/cephfs/home/ws05/workshop-sweden/dynamo_classics ./workplace-XX
It will ask for a password that will be also written in the whiteboard.
Time Schedule
- On the first day we will present the basic tools in the Dynamo environment.
- The second day will be devoted to a hands-on guide on two practical cases:
- Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol. Biosci. 5:82.
- Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo Scaramuzza S, Castaño-Díez D (2021). PLoS biology. 19(8):e3001318.
- On the third day participants are encouraged to make a flash presentation (3 mins, max. slides) describing their past or planned research in tomography. We will study the particular cases of interest of each participant, and identify tools of possible relevance inside the Dynamo environment, designing with the participants viable processing workflows combining Dynamo and other packages.
| Module | Time | Subject |
|---|---|---|
| 0 | 09:00 - 10:00 | Research Talk |
| 1 | 10:00 - 10:45 | General introduction: Hands on |
| 2 | 11:00 - 12:30 | Starters Guide: subtomogram averaging |
| 3 | 13:30 - 14:00 | General modelling |
| 3a | 14:00 - 14:30 | Models: Filaments Additional material: Coordinated extraction from several filaments |
| 3b | 14:30 - 14:45 | Models: Vesicles |
| 3c | 14:45 - 15:00 | Models: Surfaces |
| Module | Time | Subject |
|---|---|---|
| 4 | 9:15 - 10:30 | Template Matching |
| 5a | 11:45 - 12:30 | Alignment of tilt series: Manual |
| Module | Time | Subject |
|---|---|---|
| 5b | 13:30 - 14:15 | Alignment of tilt series: GUI |
| 5c | 14:15 - 15:00 | Alignment of tilt series: command line |
| 6 | 15:30 - 16:15 | Principal Component Analysis |
| FHV | 16:15 - 17:30 | Complete walkthrough on FHV virus |
| HIV1 light | 17:30 - 18:00 | Spherical geometry: multiple liposomes |
| Module | Time | Subject |
|---|---|---|
| FT | 09:00 - 11:00 | Flash Talks |
| HIV1 | 11:15 - 12:00 | High Resolution workflow for HIV1 |
| HIV1 light | 11:15 - 12:00 | Virus like particles or Spherical geometries |
