View source for SciLifeLab Workshop for Cryo Electron Tomography Processing

= 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), [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://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html 
* [https://www.cgl.ucsf.edu/chimera/download.html Chimera]

== Access to SciLifeLab resources==



=== Credentials ===

To access the local desktop use the user and password that will be written in the whiteboard. 

Each Windows OS PC has an Matlab 2019a executable with a parallel tool box installed.

A Chimera executable is locally available. To have an accelarated performance, there is the alternative to VNC Connect remote desktop software. Further instruction will be given for the interested users.

=== Load and run Dynamo from Matlab ===

In order to activate Dynamo, first open Matlab with a doble click <br>

<code> run Z:\SLL-STA-2023\Software\Dynamo\1.1.539\dynamo_activate.m  </code>

=== Data ===

In the PC, open a new Cywin-bash terminal (double-click on the icon).

Make sure to change dir to your user located in disk C:<br>
<code> cd /cygdrive/c/Users/MYUSER </code> <br>
Here, you replace <tt>MYUSER</tt> with the actual username (it will be available in the dashboard).

To create your working directory:

<code> mkdir workplace-XX</code> <br>
Here, you replace <tt>XX</tt> with the number of your PC tower.

To copy the data into your local directory:<br>
<code> scp -r ws05@login.cryoem.se:/mnt/cephfs/home/ws05/workshop-sweden/dynamo_classics  ./workplace-XX</code><br>

It will ask for a password that will be also written in the whiteboard.

= Time Schedule =

* On the first day we will present the basic tools in the Dynamo environment.    
* The second day will be devoted to a hands-on guide on two practical cases:
** [https://doi.org/10.3389/fmolb.2018.00082''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.
** [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. 

{| class="wikitable" 
|+ 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 (SciLifeLab 2023) | Starters Guide: subtomogram averaging ]]
|-

| 3 || 13:30 - 14:00 || General modelling
|-
| 3a ||14:00 - 14:30  || [[Walkthrough_on_filament_models | Models: Filaments]] <br> Additional material: [[Walkthrough model worfklow reuse | Coordinated extraction from several filaments]]
|-
| 3b || 14:30 - 14:45 || [[Walkthrough_on_vesicle_models | Models: Vesicles ]]
|-
| 3c || 14:45 - 15:00 || [[Walkthrough_on_membrane_models | Models: Surfaces ]]
|}


{| class="wikitable" 
|+ Day 2 (Morning) General Tools
|-
! Module !! Time !! Subject
|-
| 4 || 9:15 - 10:30 || [[Walkthrough for template matching (SciLifeLab 2023) | Template Matching]]
|-
| 5a || 11:45 - 12:30 || [[Walkthrough on manual marker clicking (SciLifeLab 2023)| Alignment of tilt series: Manual]]
|-
|}

{| class="wikitable" 
|+ Day 2 (Afternoon):  Practical cases
|-
! Module !! Time !! Subject
|-
| 5b || 13:30 - 14:15 || [[Walkthrough_on_GUI_based_tilt_series_alignment (SciLifeLab 2023)| Alignment of tilt series: GUI ]]
|-
| 5c || 14:15 - 15:00 ||[[Walkthrough_on_command_line_based_tilt_series_alignment (SciLifeLab 2023)| Alignment of tilt series: command line]]
|-
| 6 || 15:30 - 16:15 || [[Walkthrough on PCA through the command line (SciLifeLab 2023)| Principal Component Analysis ]]
|-
| FHV || 16:15 - 17:30 || [[Complete walkthrough on FHV virus (SciLifeLab 2023)| Complete walkthrough on FHV virus]]
|-
| HIV1 light || 17:30 - 18:00 ||   [[Walkthrough for lattices on vesicles (EMBO2023)| Spherical geometry: multiple liposomes]]
|}

{| class="wikitable" 
|+ Day 3 (Morning):  Practical cases
|-
! Module !! Time !! Subject
|-
| FT || 09:00 - 11:00 || Flash Talks
|-
| HIV1 || 11:15 - 12:00 || [[HIV1 workshop | High Resolution workflow for HIV1  ]]
|-
| HIV1 light || 11:15 - 12:00 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (EMBO2023) | Virus like particles]] or [[Walkthrough for lattices on vesicles (EMBO2023)| Spherical geometries]] 
|}