Difference between revisions of "Göttingen Workshop 2024"
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= Workshop = | = Workshop = | ||
| − | This workshop will take place from April the 10 to April the 12th 2024. | + | This workshop will take place from April the 10 to April the 12th 2024 in the European Neuroscience Institute (ENI), Room 2.006. |
| − | 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 | + | 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. |
= Computing resources = | = Computing resources = | ||
== Laptops == | == Laptops == | ||
| − | + | For the first two days, participants will bring their own laptops . However, each participant should also install in their laptop prior to the workshop: | |
* (R2024a version), a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available]. | * (R2024a version), a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available]. | ||
* [https://www.dynamo-em.org//w/index.php?title=Downloads#Beta_Version 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://www.dynamo-em.org//w/index.php?title=Downloads#Beta_Version 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: | ||
| Line 15: | Line 15: | ||
Then, | Then, | ||
| − | >> tar -xvf dynamo_temp_1.1. | + | >> tar -xvf dynamo_temp_1.1.532.tar |
Launch the installed package inside MATLAB. | Launch the installed package inside MATLAB. | ||
| Line 24: | Line 24: | ||
* [https://www.cgl.ucsf.edu/chimera/download.html Chimera] | * [https://www.cgl.ucsf.edu/chimera/download.html Chimera] | ||
| + | |||
| + | == 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): | ||
| + | {| class="wikitable" | ||
| + | |+ 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) | ||
| + | |- | ||
| + | | Walkthrough on hexagonal lattice coherence through neighborhood analysis || https://drive.google.com/drive/folders/1jberboXIRNp32GvZ14XV_6N2R-tnYESD | ||
| + | |- | ||
| + | |} | ||
== Access to computational resources== | == 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 = | = Time Schedule = | ||
| Line 35: | Line 69: | ||
** [https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001318''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. | ** [https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001318''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. | + | * 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. |
{| class="wikitable" | {| class="wikitable" | ||
| Line 42: | Line 76: | ||
! Module !! Time !! Subject | ! Module !! Time !! Subject | ||
|- | |- | ||
| − | | 0 || 09: | + | | 0 || 09:30 - 10:00|| Research Talk |
|- | |- | ||
| 1 || 10:00 - 10:45|| General introduction: Hands-on guide to basic tools. <br/> | | 1 || 10:00 - 10:45|| General introduction: Hands-on guide to basic tools. <br/> | ||
| Line 48: | Line 82: | ||
[https://wiki.dynamo.biozentrum.unibas.ch/w/doc/misc/introductionTablesAndData.pdf Basic formats for data and metadata] | [https://wiki.dynamo.biozentrum.unibas.ch/w/doc/misc/introductionTablesAndData.pdf Basic formats for data and metadata] | ||
|- | |- | ||
| − | | 2 || 11:00 - 12:30 || [[Starters guide | Starters Guide: subtomogram averaging]] | + | | 2 || 11:00 - 12:30 || [[Starters guide (Göttingen 2024) | Starters Guide: subtomogram averaging]] |
|- | |- | ||
| Line 59: | Line 93: | ||
| 3c || 15:30 - 16:30 || [[Walkthrough_on_membrane_models | Models: Surfaces ]] | | 3c || 15:30 - 16:30 || [[Walkthrough_on_membrane_models | Models: Surfaces ]] | ||
|} | |} | ||
| − | |||
{| class="wikitable" | {| class="wikitable" | ||
| Line 66: | Line 99: | ||
! Module !! Time !! Subject | ! Module !! Time !! Subject | ||
|- | |- | ||
| − | | 4 || 09: | + | | 4 || 09:30 - 10:15 || [[Walkthrough for template matching (Göttingen 2024) | Template Matching]] |
|- | |- | ||
| − | | 5 || 10:15 - 11:30 || [[Walkthrough on PCA through the command line | + | | 5 || 10:15 - 11:30 || [[Walkthrough on PCA through the command line (Göttingen 2024) | Principal Component Analysis ]] |
|- | |- | ||
| 6a || 11:30 - 12:00 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]] | | 6a || 11:30 - 12:00 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]] | ||
| Line 76: | Line 109: | ||
| 6c || 12:30 - 12:45 || [[Walkthrough_on_command_line_based_tilt_series_alignment | Alignment of tilt series: command line]] | | 6c || 12:30 - 12:45 || [[Walkthrough_on_command_line_based_tilt_series_alignment | Alignment of tilt series: command line]] | ||
|} | |} | ||
| − | |||
{| class="wikitable" | {| class="wikitable" | ||
| Line 82: | Line 114: | ||
|- | |- | ||
! Module !! Time !! Subject | ! Module !! Time !! Subject | ||
| − | | | + | |- |
| + | | Neigh || 13:30 - 14:00 || [[ Walkthrough on hexagonal lattice coherence through neighborhood analysis| Neighborhood analysis ]] <br/> | ||
| + | |- | ||
| + | | FHV || 14:00- 17:00 || [[Complete walkthrough on FHV virus (Göttingen 2024) | FHV]] | ||
|- | |- | ||
|} | |} | ||
| Line 90: | Line 125: | ||
|- | |- | ||
! Module !! Time !! Subject | ! Module !! Time !! Subject | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| + | | HIV1-Introduction || 9:30 - 10:00 || HIV1 presentation:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br/> | ||
| + | |- | ||
| + | | HIV1-0 || 10:00 - 10:20 || | ||
| + | [[ High resolution walkthrough with HIV1 (Göttingen 2024) | High Resolution workflow for HIV1: Overall view ]] </br> | ||
| + | |- | ||
| + | | HIV1-a || 10:20 - 10:50 || Preprocessing (presentation) <br/> | ||
| + | |- | ||
| + | | HIV1-ai || 10:40 - 11:20 || Preprocessing (individual work) <br/> | ||
| + | |- | ||
| + | | HIV1-ap || 11:20 - 11:30 || Preprocessing (Discussionn) <br/> | ||
| + | |- | ||
| + | |- | ||
| + | | HIV1-b || 11:30 - 11:45 || Dynamo manipulations (presentation) | ||
| + | |- | ||
| + | | HIV1-b || 11:45 - 12:30 || Dynamo manipulations (individual work) | ||
| + | |- | ||
| + | | Lunch || 12:30 - 13:30 || Lunch <br/> | ||
| + | |- | ||
| + | | HIV1-b || 13:30 - 13:45 || Dynamo manipulations (discussion) | ||
| + | |- | ||
| + | | HIV1-c || 13:45 - 16:45 || Refinement and binding with Relion | ||
| + | |- | ||
| + | | agur || 16:45 - 17:00 || Final remarks | ||
|} | |} | ||
| − | |||
Additional material: <br/> | Additional material: <br/> | ||
Latest revision as of 14:01, 12 April 2024
Contents
Workshop
This workshop will take place from April the 10 to April the 12th 2024 in the European Neuroscience Institute (ENI), Room 2.006.
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.
Computing resources
Laptops
For the first two days, participants will bring their own laptops . However, each participant should also install in their laptop prior to the workshop:
- (R2024a version), a 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
Then,
>> tar -xvf dynamo_temp_1.1.532.tar
Launch the installed package inside MATLAB.
>> run <DYNAMO_ROOT>/dynamo_activate.m
Wait while some packages are compiled. Activate it again.
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 | 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) |
| Walkthrough on hexagonal lattice coherence through neighborhood analysis | https://drive.google.com/drive/folders/1jberboXIRNp32GvZ14XV_6N2R-tnYESD |
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 | 09:30 - 10:00 | Research Talk |
| 1 | 10:00 - 10:45 | General introduction: Hands-on guide to basic tools. |
| 2 | 11:00 - 12:30 | Starters Guide: subtomogram averaging |
| 3 | 13:30 - 14:00 | General modeling |
| 3a | 14:00 - 14:45 | Models: Filaments Additional material: Coordinated extraction from several filaments |
| 3b | 14:45 - 15:30 | Models: Vesicles |
| 3c | 15:30 - 16:30 | Models: Surfaces |
| Module | Time | Subject |
|---|---|---|
| 4 | 09:30 - 10:15 | Template Matching |
| 5 | 10:15 - 11:30 | Principal Component Analysis |
| 6a | 11:30 - 12:00 | Alignment of tilt series: Manual |
| 6b | 12:00 - 12:30 | Alignment of tilt series: GUI |
| 6c | 12:30 - 12:45 | Alignment of tilt series: command line |
| Module | Time | Subject |
|---|---|---|
| Neigh | 13:30 - 14:00 | Neighborhood analysis |
| FHV | 14:00- 17:00 | FHV |
| Module | Time | Subject |
|---|---|---|
| HIV1-Introduction | 9:30 - 10:00 | HIV1 presentation:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing |
| HIV1-0 | 10:00 - 10:20 | |
| HIV1-a | 10:20 - 10:50 | Preprocessing (presentation) |
| HIV1-ai | 10:40 - 11:20 | Preprocessing (individual work) |
| HIV1-ap | 11:20 - 11:30 | Preprocessing (Discussionn) |
| HIV1-b | 11:30 - 11:45 | Dynamo manipulations (presentation) |
| HIV1-b | 11:45 - 12:30 | Dynamo manipulations (individual work) |
| Lunch | 12:30 - 13:30 | Lunch |
| HIV1-b | 13:30 - 13:45 | Dynamo manipulations (discussion) |
| HIV1-c | 13:45 - 16:45 | Refinement and binding with Relion |
| agur | 16:45 - 17:00 | Final remarks |
Additional material:
- Coordinated extraction from several vesicles
- 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).
- Alma Vivas-Lago (CSIC Bilbao, Spain).
