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. | |
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. | 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. | ||
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== Laptops == | == Laptops == | ||
Participants will bring their own laptops to access a PSI server which will host the data. However, each participant should also install in their laptop prior to the workshop: | Participants will bring their own laptops to access a PSI server which will host the data. 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]. |
* [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: | ||
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Wait while some packages are compiled. Activate it again. | Wait while some packages are compiled. Activate it again. | ||
| − | |||
* [https://www.cgl.ucsf.edu/chimera/download.html Chimera] | * [https://www.cgl.ucsf.edu/chimera/download.html Chimera] | ||
| − | == Access to | + | == Access to computational resources== |
| − | + | We will describe here the computational resources. | |
= Time Schedule = | = Time Schedule = | ||
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| 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]] | ||
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{| class="wikitable" | {| class="wikitable" | ||
|+ Day 3 (Afternoon): Practical cases | |+ Day 3 (Afternoon): Practical cases | ||
| + | |- | ||
| + | ! Module !! Time !! Subject | ||
| + | | FHV || 13:30- 17:00 || FHV | ||
| + | |- | ||
| + | |} | ||
| + | |||
| + | {| class="wikitable" | ||
| + | |+ Day 3 (Afternoon): Practical case: High resolution | ||
|- | |- | ||
! Module !! Time !! Subject | ! Module !! Time !! Subject | ||
Revision as of 11:49, 28 February 2024
Contents
Workshop
This workshop will take place from April the 10 to April the 12th 2024.
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 PSI server which will host the data. 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_1.1.530.tar
Launch the installed package inside MATLAB.
>> run <DYNAMO_ROOT>/dynamo_activate.m
Wait while some packages are compiled. Activate it again.
Access to computational resources
We will describe here the computational resources.
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. 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 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 | 09:00 - 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 | FHV | 13:30- 17:00 | FHV |
|---|
| Module | Time | Subject | HIV1 | 09:00 - 17:00 | High Resolution workflow for HIV1: preprocessing High Resolution workflow for HIV1: Dynamo manipulations |
|---|
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).
