Difference between revisions of "SciLifeLab Workshop for Cryo Electron Tomography Processing"

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| 5 || 15:45 - 16:15 || [[Walkthrough on PCA through the command line | Principal Component Analysis ]]
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| 5 || 15:45 - 16:15 || [[Walkthrough on PCA through the command line (SciLifeLab 2023)| Principal Component Analysis ]]
 
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| 6a || 16:15 - 16:45 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]]
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| 6a || 16:15 - 16:45 || [[Walkthrough on manual marker clicking (SciLifeLab 2023)| Alignment of tilt series: Manual]]
 
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| FHV || 09:00 - 11:00 || [[Advanced starters guide | Complete walkthrough on FHV virus]]
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| FHV || 09:00 - 11:00 || [[Advanced starters guide (SciLifeLab 2023)| Complete walkthrough on FHV virus]]
 
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| HIV1 || 11:15 - 13:00 || High Resolution workflow for HIV1: preprocessing
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| HIV1 || 11:15 - 13:00 || High Resolution workflow for HIV1 : preprocessing
 
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| HIV1 || 14:00 - 15:30 ||[High Resolution workflow for HIV1 (SciLifeLab 2023) | High Resolution workflow for HIV1: Dynamo manipulations]
 
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| HIV1 || 15:45 - 17:00 || High Resolution workflow for HIV1: binding with Relion
 
| HIV1 || 15:45 - 17:00 || High Resolution workflow for HIV1: binding with Relion
 
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Revision as of 07:49, 20 October 2023

Workshop

The SciLifeLab Dynamo workshop will take place from October the 24th to October the 27th in the SciLifeLab at Stockholm.

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 SciLifeLab 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 SciLifeLab resources

We will publish here a brief guide describing the steps to follow to access the computing resources.

Time Schedule

  • 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 (Morning) General tools
Module Time Subject
0 09:00 - 10:00 Research Talk
1 10:00 - 10:45 General introduction: Hands on
2 11:00 - 12:30 Starters Guide: subtomogram averaging
3 13:30 - 14:00 General modelling
3a 14:00 - 14:30 Models: Filaments
3b 14:30 - 14:45 Models: Vesicles
3c 14:45 - 15:00 Models: Surfaces


Day 1 (Afternoon) General Tools
Module Time Subject
4 15:15 - 15:45 Template Matching
5 15:45 - 16:15 Principal Component Analysis
6a 16:15 - 16:45 Alignment of tilt series: Manual
6b 16:45 - 17:15 Alignment of tilt series: GUI
6c 17:15 - 17:45 Alignment of tilt series: command line
Day 2 (Morning): Practical cases
Module Time Subject
FHV 09:00 - 11:00 Complete walkthrough on FHV virus
HIV1 11:15 - 13:00 High Resolution workflow for HIV1 : preprocessing
Day 2 (Afternoon): Practical cases
Module Time Subject
HIV1 14:00 - 15:30 High Resolution workflow for HIV1: Dynamo manipulations]
HIV1 15:45 - 17:00 High Resolution workflow for HIV1: binding with Relion
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