2025 Tsinghua Spring School
Contents
Workshop
The practical hands on Dynamo workshop will take place on the 3rd, 4th and 5th of March of 2025.
Contents
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 three-days course.
Venue
Computing resources
We will publish here instructions for the access to the computing resources.
Workshop data
The data that will be used during the workshop can be downloaded through the SACO server of CSIC. In detail, the data for the respective modules is as follows (for a total of about 61 Gb ):
| 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://saco.csic.es/s/LAXyQgWnrLNFiym (750MB) |
| Template Matching (GUI) | https://saco.csic.es/s/SmymKiHxswSoyoP (7.6GB) |
| Alignment of tilt series | https://saco.csic.es/s/rWWRdGkYmbntywB (600MB) |
| Virus like particles | https://saco.csic.es/s/9mcg9wAZXqYe9FB (4.6GB) |
| Spherical geometries | https://saco.csic.es/s/smSJXzxNA2ynw8K (64 MB) |
| Principal Component Analysis | Data generated locally by Dynamo |
| Complete walkthrough on FHV virus | https://saco.csic.es/s/wmbDNPi2YcYFjKb (2GB) |
| Walkthrough on hexagonal lattice coherence through neighborhood analysis | https://saco.csic.es/s/T9EzcQ3qLxz9g4k |
| High-resolution HIV1 | SACO link (48Gb) / https://saco.csic.es/s/JN5LGP4BbKSn9F8 |
Access to computational resources
On the third day, a more advanced tutorial will be completed. For this we will to access a server which will host the data. Access details will be updated here.
Time Schedule
- On the first two days, we will present the basic tools in the Dynamo environment.
- The third 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. 2 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 | 13:00 - 14:00 | Hands-on tutorial. First steps and formats. |
| 1 | 14:00 - 15:30 | Starters Guide: subtomogram averaging |
| 咖啡 | 15:30 - 16:00 | Coffee Break |
| 3 | 16:00 - 16:15 | General modeling |
| 3a | 16:15 - 16:45 | Models: Filaments Additional material: Coordinated extraction from several filaments |
| 3b | 16:45 - 17:00 | Models: Vesicles |
| 3c | 17:00 - 17:30 | Models: Surfaces |
| 4a | 13:30 - 14:15 | Presentation of FHV: Advanced starters guide |
| 4b | 14:30 - 15:30 | Hands-on tutorial: Advanced starters guide |
| 咖啡 | 15:30 - 16:00 | Coffee break |
| 5a | 15:30 - 16:00 | Alignment of tilt series: Manual |
| 5b | 16:30 - 17:00 | Alignment of tilt series: GUI |
| 5c | 17:00 - 17:30 | Alignment of tilt series: command line |
| Module | Time | Subject |
|---|---|---|
| 4 | 19:00 - 20:00 | Template Matching |
| 5 | 20:00 - 21:00 | Geometry aware template Matching |
| Module | Time | Subject |
|---|---|---|
| Neigh | 13:30 - 14:00 | Neighborhood analysis |
| PCA | 14:30- 15:30 | Principal Component Analysis |
| 咖啡 | 15:30 - 16:00 | Coffee break. |
| Spheres | 16:00- 17:30 | Virus like particles or Spherical geometries |
| Module | Time | Subject |
|---|---|---|
| HIV1-0 | 19:00 - 19:15 | HIV1 presentation:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing |
| HIV1-1 | 19:15 - 20:45 | |
| agur | 20:45 - 21:00 | Final remarks |
Additional material:
- Programmatic GUI customization for template matching
- Walkthrough on creation of 3d scenes
- Walkthrough on placement of averages on table positions
Instructors
- Daniel Castano-Diez (CSIC Bilbao, Spain).
- Raffaele Coray (CSIC Bilbao, Spain).
- Andrés Molina (CSIC Bilbao, Spain).
