Difference between revisions of "SciLifeLab Workshop for Cryo Electron Tomography Processing"
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In order to activate Dynamo, type inside Matlab: | In order to activate Dynamo, type inside Matlab: | ||
| − | <tt> Z:\SLL-STA-2023\Software\Dynamo\1.1.539\dynamo_activate.m <tt> | + | <tt> Z:\SLL-STA-2023\Software\Dynamo\1.1.539\dynamo_activate.m <\tt> |
= Time Schedule = | = Time Schedule = | ||
Revision as of 13:33, 24 October 2023
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:
User: dumo6457
Password: wildness8-crimson8
Each Windows OS pc has an Matlab 2019a executable with parallel tool box installed.
Load and run Dynamo from Matlab
In order to activate Dynamo, type inside Matlab:
Z:\SLL-STA-2023\Software\Dynamo\1.1.539\dynamo_activate.m <\tt>
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 |
| 3b | 14:30 - 14:45 | Models: Vesicles |
| 3c | 14:45 - 15:00 | Models: Surfaces |
| Module | Time | Subject |
|---|---|---|
| 4 | 15:15 - 15:45 | Template Matching |
| 5 | 15:45 - 16:15 | Principal Component Analysis |
| 6a | 16:15 - 16:45 | Alignment of tilt series: Manual |
| 6b | 16:45 - 17:15 | Alignment of tilt series: GUI |
| 6c | 17:15 - 17:45 | Alignment of tilt series: command line |
| Module | Time | Subject |
|---|---|---|
| FHV | 09:00 - 11:00 | Complete walkthrough on FHV virus |
| HIV1 | 11:15 - 13:00 | High Resolution workflow for HIV1 : preprocessing |
| Module | Time | Subject |
|---|---|---|
| HIV1 | 14:00 - 15:30 | High Resolution workflow for HIV1: Dynamo manipulations] |
| HIV1 | 15:45 - 17:00 | High Resolution workflow for HIV1: binding with Relion |
