Difference between revisions of "Copenhagen Workshop on Cryo Electron Tomography 2024"
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The workshop data (see next section) has been downloaded in the desktop folder workshop_data.<br><br> | The workshop data (see next section) has been downloaded in the desktop folder workshop_data.<br><br> | ||
− | Once connected, you can activate Dynamo by open a terminal and running: source dynamo_tests/dynamo_activate_linux.sh<br> | + | Once connected, you can activate Dynamo by open a terminal and running: <code>source dynamo_tests/dynamo_activate_linux.sh<\code><br> |
Once Dynamo is activated, you can open the Dynamo standalone by running the command: dynamo | Once Dynamo is activated, you can open the Dynamo standalone by running the command: dynamo | ||
Revision as of 08:58, 24 January 2024
Contents
Workshop
This workshop will take place from January the 24th to January the 26th in Copenhagen.
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 an Amazon 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 Amazon resources
The information on how to access the amazon session will be given during the workshop.
Dynamo has been installed on the desktop in the folder dynamo_tests.
The workshop data (see next section) has been downloaded in the desktop folder workshop_data.
Once connected, you can activate Dynamo by open a terminal and running: source dynamo_tests/dynamo_activate_linux.sh<\code>
Once Dynamo is activated, you can open the Dynamo standalone by running the command: dynamo
Workshop data
The data that will be used during the workshop can be downloaded using the google drive link: https://drive.google.com/drive/folders/10lZjjKj1tMfVL_RYJioaK12ji3_RdrNT?usp=drive_link
In detail, the data for the respective modules is as follows (for a total of about 8GB):
Module and data source
Module
Data source
Starters Guide: subtomogram averaging
Data generated locally by Dynamo
Models: Filaments
Data generated locally by Dynamo
Models: Vesicles
Data generated locally by Dynamo
Models: Surfaces
Data generated locally by Dynamo
Template Matching
https://drive.google.com/drive/folders/1EXXGPMQZhD0lKurzaQ6Nz0Vypj3WUkJP?usp=drive_link (750MB)
Alignment of tilt series
https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg4UX_dDLHHIhhbp9?usp=drive_link (600MB)
Virus like particles
https://drive.google.com/drive/folders/1Vr108rtKI7knFOmzL06-nfFm1KCKdq4e?usp=drive_link (4.6GB)
Spherical geometries
https://drive.google.com/drive/folders/1arrd1KcscsvCDEasmNISShujWjWCYjlw?usp=drive_link (64 MB)
Principal Component Analysis
Data generated locally by Dynamo
Complete walkthrough on FHV virus
https://drive.google.com/drive/folders/10j1mGTV-4srVV2Hg98eWkAPhPeAbU5BQ?usp=drive_link (2GB)
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.
Day 1, 24.01.23 (Afternoon): Presentations
Module
Time
Subject
Talk
14:00 - 14:50
Presentation: Dynamo
Talk
14:50 - 15:30
Presentation: Denoising in cryo electron tomography (Ricardo Righetto)
--
15:30 - 15:50
Coffe break
Flash
15:50 - 18:00
Flash talks from participants
--
19:00
Course dinner
Day 2 25.01.23 (Morning) General tools
Module
Time
Subject
Talk
09:00 - 10:00
Presentation: Segmentation (Ricardo Righetto)
1
10:00 - 10:30
General introduction: Hands on
--
10:30 - 10:50
Coffe break
2
11:00 - 12:30
Starters Guide: subtomogram averaging
Day 2, 25.01.23 (Afternoon): Modelling
Module
Time
Subject
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
--
15:00 - 15:20
Coffe break
HIV1 light
15:20 - 18:00
Virus like particles or Spherical geometries
Day 3 26.01.23 (Morning) General Tools
Module
Time
Subject
4
9:15 - 10:30
Template Matching
--
10:30 - 10:50
Coffe break
Talk
10:50 - 11:45
Presentation: Segmentation II (Ricardo Righetto)
5a
11:45 - 12:30
Alignment of tilt series: Manual
Day 3 26.01.23 (Afternoon): Practical cases
Module
Time
Subject
5b
13:30 - 14:15
Alignment of tilt series: GUI
5c
14:15 - 15:00
Alignment of tilt series: command line
--
15:00 - 15:20
Coffe break
6
15:20 - 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