View source for I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025

[[Category:WalkthroughsSpecific]]
= The course = 
== The venue ==
This page describes the contents of the ''Dynamo''-specific part of the course "I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025", which will take part at the premises of the Centro Nacional de Biotecnología in Madrid, from the 9th to the 12th of December 2025.
== Contents == 
Whole pipelines for cryo-ET processing will be covered in the Scipion-related area of the course (days 1 and 2). The ''Dynamo'' part will covered selected parts of the pipeline.

= Installation of Dynamo and Matlab =
== Dynamo on your own laptop == 
To follow the course in your own laptop, please install '''[https://drive.google.com/file/d/1x5he7ctkC4BUCNFhfXLk6heggGohELoM/view?usp=drive_link the Dynamo for Matlab version]''' as explain in [[ Downloads ]] page.

= Computing resources = 

== Laptops ==
Participants can use their own laptops to complete the Dynamo part of the course. For this, participants need to have and active '''Matlab installation''' and an Dynamo installation.
* For Matlab, we advise the (R2025b version). If you don't have a license through your home institution, a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available] from the Mathworks company. 
* '''The Dynamo Download link is currently down''', we will update it later today  (17:00 ECT): 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 
 
''Dynamo'' is delivered as a single .tar file. To install it, move the file to the location where you want to install ''Dynamo'', then open a Matlab session and type after the Matlab prompt:

 <tt>  >> tar -xvf dynamo_temp_1.1.579.tar </tt>

to untar the installation file. ''Dynamo'' will be installed in the folder that contained the .tar. If we call this folder <DYNAMO_ROOT>, you can activate ''Dynamo'' in your MATLAB session by typing:

<tt> >> run dynamo_activate.m </tt>

when you are in that folder, or with 

 <tt> >> run <DYNAMO_ROOT>/dynamo_activate.m </tt>

if you are in some other folder. Wait while some packages are compiled. Activate it again.

== Amazon machines ==

If you want to follow the course with virtual machines provided by the course, follow this instructions.

=== Entering in the AWS Machine ===

Access the link of your AWS Machine provided by the organizers, that appears in the [https://docs.google.com/spreadsheets/d/15o8IUOSsNjGHxK0Bmi1QBfI9KCCWCpX603R4l_rn6KA/edit?gid=653170857#gid=653170857 Google Sheet]. After introducing your password (also given in the same google sheet), you will have entered in the AWS Machine.

Before accessing, it may be helpful to set the browser zoom  to 50% or less and refresh the website. This will help later to visualize some GUIs in a friendlier way.

=== Activating Dynamo Standalone ===

Once you have accessed the AWS Machine, you need to activate Dynamo Standalone. Open the terminal emulator and type the next command:

<pre>
source /home/student/dynamo-v-1.1.579/dynamo_activate_linux_shipped_MCR.sh
</pre>

After some lines asserting the correct addition of several paths and tests, it should appear as the last line: "Dynamo is ready for standalone use in your Linux system".

=== Initializing Dynamo Standalone ===

For a specific explanation of the Standalone see [https://www.dynamo-em.org//w/index.php?title=Standalone]. 
Once dynamo has been initialized, you can enter in dynamo by typing

<pre>
dynamo 
</pre>
 
You can also type

<pre>
dynamo x
</pre>

so dynamo will open a GUI console, instead of using the terminal, nevertheless the first option is strongly reccommended for some Walkthroughs.


=== Solution of some possible minor cons of working in a laptop ====

Working with AWS Machine in the Work Shop may entails some minor cons that you may encounter. Here we present the most common ones so you can solve them quickly.

==== Problem opening a GUI Window ====

If you are working on a small laptop screen, opening a GUI window, for example when typing the "dcp" command to start a project, may make appear it with the header of the window hidden on the top of the screen:

[[File:Problem GUI Window Hidden.png|thumb|center|600px|The open GUI Window appears hidden in the AWS Machine. Pressing Alt+Click will make it possible to move it so it is possible to access to the header of the window.]]

A quick way of solving it is pressing Alt+Click on the window and move it down until the header appears so it is possible to change its size.

==== Problem pressing right click in a MAC laptop with no external mouse ====

For some walkthroughs, like "Walkthrough on GUI based tilt series alignment", you need to do '''secondary click''' on the "View" botton:

[[File:View Button.png|thumb|center|450px|Necessity of right clicking view button]]

In general, this corresponds to doing a ''right click'', but if you are working on a MAC laptop with no external mouse, just press with two fingers on the trackpad at the same time.

Note that sometimes the GUI does not refresh itself and in this case, doing right click on the "View" botton will not work. To manually refresh the GUI and load all of the previous results into it, you need to do a '''primary click''' on the "View" bottom first. After that, you can do '''right click''' and you should be able to access the "View" panel as usual.

=== Unzipping some of the data ===

In the amazon machines, the data for the walkthrough on Geometry aware template matching is in a zipped file, so in order to access it, we need to unzip it. To do so, open a terminal and write:

<tt> cd  /home/student/data/TemplateMatchingGUI

unzip MCP_walkthrough_data.zip </tt>

== 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 ):
{| 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 || {{Template:DownloadLinkTemplateMatchingBasic}} (750MB)
|-
| Template Matching (GUI) || {{Template:DownloadLinkTemplateMCP}} (7.6GB)
|-
| Alignment of tilt series || {{Template:DownloadLinkAWFHIV1TS}} (600MB)
|-
| Virus like particles ||  {{Template:DownloadLinkVLPs}} (4.6GB)
|-
| Spherical geometries || {{Template:DownloadLinkBasicHIVTomo}}  (64 MB)
|-
| Principal Component Analysis || Data generated locally by Dynamo
|-
| Complete walkthrough on FHV virus || {{Template:DownloadLinkFHV}} (2GB)
|-
| Walkthrough on hexagonal lattice coherence through neighborhood analysis || {{Template:DownloadLinkNeighborhoodData}}
|-
| High-resolution HIV1 || {{Template:DownloadLinkHighResHIV1}} (48Gb)
|}

= Time schedule =

{| class="wikitable" 
|+ Day 3 (Morning) 11th of December
|-
! Module !! Time !! Subject
|-
| 1 || 09:30 - 10:30|| Hands-on tutorial. First steps and formats.
|-
| 2 || 10:30 - 11:00|| [[Starters guide (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Starters Guide: subtomogram averaging]]
|-
| coffee || 11:00 - 11:30 || Coffee Break
|-
| 2 || 11:30 - 12:30||  Starters Guide: subtomogram averaging (continuation).
|-
|  SBGrid || 12:30 - 13:00 || SBGrid Consortium presentation (Estrella Giménez)
|}


{| class="wikitable" 
|+ Day 3 (Afternoon)  11th of December
|-
| 3 ||14:00 - 14:30  || General modelling
|-
| 3a ||14:30 - 15:00  || [[Walkthrough_on_filament_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Filaments]] <br/>  Additional material: [[Walkthrough model workflow reuse (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Coordinated extraction from several filaments]]
|-
| 3b || 15:00 - 15:15 || [[Walkthrough_on_vesicle_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Models: Vesicles ]] 
|-
| 3c || 15:15 - 15:30 || [[Walkthrough_on_membrane_models (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Models: Surfaces ]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 4 || 16:00 - 17:30 || [[Getting a Structure from Multiple Tomograms of HIV Capsids (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Virus like particles]] or [[Walkthrough for lattices on vesicles (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Spherical geometries]]
|}


The presentation introducing the automatic tilt series alignment, template matching, and principal component analysis walkthroughs can be found [https://docs.google.com/presentation/d/1cf3Me75olaY_hQYKI9NjfpZHmHgr5Wad/edit?usp=drive_link&ouid=117959272098462742941&rtpof=true&sd=true here].


{| class="wikitable" 
|+ Day 4, Morning: 12th of December (Friday)
|-
| 5a || 09:30 - 09:45 || Presentation of FHV: Advanced starters guide
|-
| 5b || 09:45 - 11:00 || [[Complete walkthrough on FHV virus (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Hands-on tutorial: Advanced starters guide ]]
|-
| coffee  || 11:00 - 11:30 || Coffee break 
|-
| 5b || 11:30 - 12:00 ||   Hands-on tutorial: Advanced starters guide (continued)
|-
| 6a || 12:00 - 12:20 || [[Walkthrough on manual marker clicking (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: Manual]] 
|-
| 6b || 12:20 - 12:40 || [[Walkthrough on GUI based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: GUI ]]
|-
| 6c || 12:40 - 13:00 || [[Walkthrough on command line based tilt series alignment (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Alignment of tilt series: command line]]
|}


{| class="wikitable" 
|+ Day 4, Afternoon session:  12th of December (Friday)
|-
! Module !! Time !! Subject
|-
| 7a || 14:00 - 15:00 || [[Walkthrough for template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Template Matching]]
|-
| 7b || 15:00 - 15:30 || [[Walkthrough for GUI-based template matching (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025) | Geometry aware template Matching]]
|-
| coffee || 15:30 - 16:00 || Coffee Break
|-
| 8  || 16:00- 17:00 ||  [[Walkthrough on PCA through the command line (I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging 2025)| Principal Component Analysis ]]
|}

= Instructors =
* Daniel Castano-Diez (CSIC Bilbao, Spain).
* Raffaele Coray (CSIC Bilbao, Spain).
* Laura García-Cornejo (CSIC Bilbao, Spain).
* Andrés Molina (CSIC Bilbao, Spain).
* Miguel Sánchez López-Cuervo (CSIC Bilbao, Spain).