View source for SciLife Lab Workshop for Subtomogram Averaging 2023

[[Category:WalkthroughsSpecific]]

= Workshop =

The SciLife Lab Workshop for Subtomogram Averaging 2023 will take place at the premises of the SciLifeLab between the 26th and the 28th of October. <br />.
The aim of the workshop will be to provide participants with detailed hands-on training in all aspects of computational cryo electron tomography. <br />

We will start from scratch, describing the general workflows of tomography, then exploring the concrete procedures that <it>Dynamo</it> implements to tackle them. We will thus discuss different tools for alignment of tilt series, creation of tomograms, location of particles and design of subtomogram averaging projects. On the second day, we will focus on a particular case, 
The third day will be devoted to discuss specific applications suggested by the research lines of participants. 

= Materials =

Users will bring their own laptops in order to connect via ssh to the computing resources facilitated by the SciLifeLab. The details of the connection protocol will be specified later

== 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), a licence free trial version is available. 
* Dynamo 
* Chimera
We will publish here the links to these relevant versions of those packages.

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

= Flash Presentations =

Participants will be asked to prepare a <it>flash presentation </it> (one or two slides for a presentation of about two minutes) to briefly present their interest in cryo electron tomography.

= Schedule =

This schedule is orientative. We are in the process of designing the definitive schedule and contents, which will be adapted to the profile of the registered applicants.

{| class="wikitable"
! colspan="4" | '''Day 1'''
|-
|'''Time '''
|'''Activity
|'''Topic'''
|'''Comment'''
|-
| 09:00 - 10:00
| Presentation
| Introduction
|
|-
| 14:30 - 15:30
| Tutorial
| [[Walkthrough_on_GUI_based_tilt_series_alignment_(EMBO2021)| Tilt series alignment with GUI]]
|
|-
| 15:30 - 15:45
| Break
| 
|
|-
| 15:45 - 16:45
| Tutorial
| [[Walkthrough_on_command_line_based_tilt_series_alignment_(EMBO2021) | Tilt series alignment with command line]]
| 
|-
| 16:45 - 17:00
| Break
|
|
|-
| 17:00 - 17:30
| Tutorial
| [[Walkthrough_on_filament_models | Models for filaments]]
|
|-
| 17:30 - 18:00
| Tutorial
| [[Walkthrough_on_membrane_models | Models for surfaces]]
|
|-
| Optional: 18:00
| Tutorial
| [[Walkthrough for template matching | Template matching]]
|
|-
! colspan="4" | '''Day 2'''
|-
|'''Time (London)'''
|'''Activity
|'''Topic'''
|'''Comment'''
|-
| 09:00 - 09:15
| Presentation
| Introduction
|
|-
| 14:15 - 15:30
| Tutorial
| [[Starters_guide_(EMBO2021) | Starters guide]]
| 
|-
| 15:30 - 15:45
| Break
|
|
|-
| 15:45 - 17:45
| Tutorial
| [[Advanced_starters_guide_(EMBO2021) | Advanced starters guide]]
| Take a 15 min break individually during this tutorial
|-
| 17:45 - 18:00
| Presentation
| Closing remarks
|
|-
| Optional: 18:00
| Tutorials
| [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids_(walkthrough) | Virus like particles]] or [[Walkthrough for lattices on vesicles| Spherical geometries]]
|
|-
! colspan="4" | '''Day 3'''
|-
|'''Time (London)'''
|'''Activity
|'''Topic'''
|'''Comment'''
|-
| 9:00 - 11:15
| Flash Presentations
| Application cases
| Each participant presents their past/ongoing/intended research that involves tomography.
|}

= Instructors =
* Daniel Castaño Díez (Instituto Biofisika, Bilbao, Spain)..
* Raffaele Coray (Instituto Biofisika, Bilbao, Spain).
* Alma Vivas Lago (Instituto Biofisika, Bilbao, Spain).