Difference between revisions of "2025 Tsinghua Spring School"

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= Workshop =
 
= Workshop =
−
The practical hands on Dynamo workshop will take place on the 3rd, 4th and 5th of March of 2025.
+
The practical hands on Dynamo workshop took place on the 3rd, 4th and 5th of March of 2025.
 +
 
 +
[[File:workshopTsinghua2025.jpeg|thumb|center|700px| Group photo.]]
  
 
== Contents ==  
 
== Contents ==  
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== Workshop data ==
 
== 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
+
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 ):
−
 
 
−
In detail, the data for the respective modules is as follows (for a total of about 8GB):
 
 
{| class="wikitable"  
 
{| class="wikitable"  
 
|+ Module and data source
 
|+ Module and data source
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| Models: Surfaces || 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)
+
| Template Matching || https://saco.csic.es/s/LAXyQgWnrLNFiym (750MB)
 
|-
 
|-
−
| Template Matching (GUI) || https://drive.google.com/file/d/1ME2r6cDw6_sJVtFPTFTgOVBWIuQn44Wl/view?usp=drive_link (7.6 GB)
+
| Template Matching (GUI) || https://saco.csic.es/s/SmymKiHxswSoyoP (7.6GB)
 
|-
 
|-
−
| Alignment of tilt series || https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg4UX_dDLHHIhhbp9?usp=drive_link (600MB)
+
| Alignment of tilt series || https://saco.csic.es/s/rWWRdGkYmbntywB (600MB)
 
|-
 
|-
−
| Virus like particles || https://drive.google.com/drive/folders/1Vr108rtKI7knFOmzL06-nfFm1KCKdq4e?usp=drive_link (4.6GB)
+
| Virus like particles || https://saco.csic.es/s/9mcg9wAZXqYe9FB (4.6GB)
 
|-
 
|-
−
| Spherical geometries || https://drive.google.com/drive/folders/1arrd1KcscsvCDEasmNISShujWjWCYjlw?usp=drive_link (64 MB)
+
| Spherical geometries || https://saco.csic.es/s/smSJXzxNA2ynw8K  (64 MB)
 
|-
 
|-
 
| Principal Component Analysis || Data generated locally by Dynamo
 
| 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)
+
| Complete walkthrough on FHV virus || https://saco.csic.es/s/wmbDNPi2YcYFjKb (2GB)
−
|-
 
−
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || https://drive.google.com/drive/folders/1jberboXIRNp32GvZ14XV_6N2R-tnYESD
 
 
|-
 
|-
−
| HIgh-resolution HIV1 || Copy from local storage (48 GB)
+
| 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
 
|}
 
|}
  
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! Module !! Time !! Subject
 
! Module !! Time !! Subject
 
|-
 
|-
−
|  0 || 13:00 - 10:00|| XXXX
+
|  0 || 13:00 - 14:00|| Hands-on tutorial. First steps and formats.
 
|-
 
|-
−
| 1 || 14:00 - 15:00|| [[Starters guide (Göttingen 2024) | Starters Guide: subtomogram averaging]]
+
| 1 || 14:00 - 15:30|| [[Starters guide (Tsinghua Spring School 2025) | Starters Guide: subtomogram averaging]]
 
|-
 
|-
−
| 咖啡 || 15:00 - 15:30 || Coffe Break
+
| 咖啡 || 15:30 - 16:00 || Coffee Break
 
|-
 
|-
−
| 3 || 15:30 - 16:00 || General modeling
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| 3 || 16:00 - 16:15 || General modeling
 
|-
 
|-
−
| 3a ||16:00 - 16:3- || [[Walkthrough_on_filament_models | Models: Filaments]] <br/>  Additional material: [[Walkthrough model worfklow reuse | Coordinated extraction from several filaments]]
+
| 3a ||16:15 - 16:45 || [[Walkthrough_on_filament_models | Models: Filaments]] <br/>  Additional material: [[Walkthrough model worfklow reuse | Coordinated extraction from several filaments]]
 
|-
 
|-
−
| 3b || 16:30 - 17:00 || [[Walkthrough_on_vesicle_models | Models: Vesicles ]]  
+
| 3b || 16:45 - 17:00 || [[Walkthrough_on_vesicle_models | Models: Vesicles ]]  
 
|-
 
|-
 
| 3c || 17:00 - 17:30 || [[Walkthrough_on_membrane_models | Models: Surfaces ]]
 
| 3c || 17:00 - 17:30 || [[Walkthrough_on_membrane_models | Models: Surfaces ]]
 
|}
 
|}
 +
  
 
{| class="wikitable"  
 
{| class="wikitable"  
−
|+ Day 1 (Evening) Real data
+
|+ Day 2 (Afternoon) Practical cases
 +
|-
 +
| 4a || 13:30 - 14:15 || Presentation of FHV: Advanced starters guide
 +
|-
 +
| 4b || 14:30 - 15:30 || [[Complete walkthrough on FHV virus (Tsinghua Spring School 2025) | Hands-on tutorial: Advanced starters guide]]
 +
|-
 +
| 咖啡 || 15:30 - 16:00 || Coffee break
 
|-
 
|-
−
! Module !! Time !! Subject
+
| 5a || 15:30 - 16:00 || [[Walkthrough on manual marker clicking (Tsinghua Spring School 2025) | Alignment of tilt series: Manual]]
 
|-
 
|-
−
| 4 || 19:00 - 19:15 || Advanced starters guide: presentation
+
| 5b || 16:30 - 17:00 || [[Walkthrough on GUI based tilt series alignment (Tsinghua Spring School 2025) | Alignment of tilt series: GUI ]]
 
|-
 
|-
−
| 5 || 19:15 - 21:00 || Advanced starters guide  (FHV tutorial)
+
| 5c || 17:00 - 17:30 || [[Walkthrough on command line based tilt series alignment (Tsinghua Spring School 2025) | Alignment of tilt series: command line]]
 
|}
 
|}
−
 
  
 
{| class="wikitable"  
 
{| class="wikitable"  
−
|+ Day 2  (Afternoon) Alignment of tilt series
+
|+ Day 2  (Evening) Real data
 
|-
 
|-
−
| 6 || 13:30 - 14:30 || Continuation of FHV
+
! Module !! Time !! Subject
 
|-
 
|-
−
| 7a || 14:30 - 15:00 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]]  
+
| 4 || 19:00 - 20:00 || [[Walkthrough for template matching (Tsinghua Spring School 2025) | Template Matching]]
 
|-
 
|-
−
| 7b || 15:00 - 15:30 || [[Walkthrough_on_GUI_based_tilt_series_alignment | Alignment of tilt series: GUI ]]
+
| 5 || 20:00 - 21:00 || [[Walkthrough for GUI-based template matching (Tsinghua Spring School 2025) | Geometry aware template Matching]]
−
-
 
−
| 咖啡 || 15:30 - 16:00 || Coffe break]  
 
−
|-
 
−
| 7c || 16:00 - 16:30 || [[Walkthrough_on_command_line_based_tilt_series_alignment | Alignment of tilt series: command line]]
 
−
|-
 
−
| 7c || 16:30 - 17:3o || Spherical geometries.
 
 
|}
 
|}
 +
 +
  
  
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! Module !! Time !! Subject
 
! Module !! Time !! Subject
 
|-
 
|-
−
| Neigh  || 13:00 - 13:30 || [[ Walkthrough on hexagonal lattice coherence through neighborhood analysis| Neighborhood analysis  ]] <br/>
+
| Neigh  || 13:30 - 14:00 || [[ Walkthrough on hexagonal lattice coherence through neighborhood analysis (Tsinghua Spring School 2025)| Neighborhood analysis  ]] <br/>
 
|-
 
|-
−
| PCA || 13:30- 14:30 ||  Principal Component Analysis
+
| PCA || 14:30- 15:30 ||  [[Walkthrough on PCA through the command line (Tsinghua Spring School 2025)| Principal Component Analysis ]]
 
|-
 
|-
 
|咖啡  || 15:30 - 16:00 || Coffee break.
 
|咖啡  || 15:30 - 16:00 || Coffee break.
 
|-
 
|-
−
| PCA || 16:00- 17:30 || Spherical geometries
+
| Spheres || 16:00- 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (Tsinghua Spring School 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (Tsinghua Spring School 2025)| Spherical geometries]]
 
|-
 
|-
 
|}
 
|}
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! Module !! Time !! Subject
 
! Module !! Time !! Subject
 
|-
 
|-
−
| HIV1-Introduction || 19:00 - 19:15 || HIV1 presentation:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br/>
+
| HIV1-0 || 19:00 - 19:15 || HIV1 presentation:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br/>
 
|-
 
|-
−
| HIV1-0 || 19:15 - 19:30 ||  
+
| HIV1-1 || 19:15 - 20:45 ||  
−
[[ High resolution walkthrough with HIV1 (Göttingen 2024) | High Resolution workflow for HIV1: Overall view ]] </br>
+
[[ High resolution walkthrough with HIV1 (Tsinghua Spring School 2025) | High Resolution workflow for HIV1: Overall view ]] </br>
 
|-
 
|-
 
| agur || 20:45 - 21:00 || Final remarks
 
| agur || 20:45 - 21:00 || Final remarks
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Additional material: <br/>
 
Additional material: <br/>
−
* [[Walkthrough for lattices on vesicles | Coordinated extraction from several vesicles]]
+
* [[Programmatic GUI customization for template matching | Programmatic GUI customization for template matching]]
 
* [[Walkthrough on creation of 3d scenes]]
 
* [[Walkthrough on creation of 3d scenes]]
 
* [[Walkthrough on placement of averages on table positions]]
 
* [[Walkthrough on placement of averages on table positions]]

Latest revision as of 09:51, 9 April 2025


Workshop

The practical hands on Dynamo workshop took place on the 3rd, 4th and 5th of March of 2025.

Group photo.

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 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://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 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.
Day 1 (afternoon) General tools
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


Day 2 (Afternoon) Practical cases
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
Day 2 (Evening) Real data
Module Time Subject
4 19:00 - 20:00 Template Matching
5 20:00 - 21:00 Geometry aware template Matching



Day 3 (Afternoon): Practical cases
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
Day 3 (Evening): Practical case: High resolution workflow.
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

High Resolution workflow for HIV1: Overall view

agur 20:45 - 21:00 Final remarks

Additional material:

Instructors

  • Daniel Castano-Diez (CSIC Bilbao, Spain).
  • Raffaele Coray (CSIC Bilbao, Spain).
  • Andrés Molina (CSIC Bilbao, Spain).
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