Difference between revisions of "PSI Workshop 2023"

From Dynamo
Jump to navigation Jump to search
 
(32 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 +
[[Category:WalkthroughsSpecific]]
 +
 
= Workshop =
 
= Workshop =
 
The PSI Dynamo workshop will take place from August the 16th to August the 18th in the Paul Scherrer Institute.
 
The PSI Dynamo workshop will take place from August the 16th to August the 18th in the Paul Scherrer Institute.
Line 7: Line 9:
  
 
== Laptops ==
 
== Laptops ==
−
Participants will bring their own laptops to access a PSI server which will host the data. However, each participant should also instal 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:
 
* (R2023a version), a [https://ch.mathworks.com/campaigns/products/trials.html licence free trial version is available].  
 
* (R2023a 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 ]
+
* [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
 +
 +
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.
 +
 
 +
 
 
* [https://www.cgl.ucsf.edu/chimera/download.html Chimera]
 
* [https://www.cgl.ucsf.edu/chimera/download.html Chimera]
  
 
== Access to PSI resources==
 
== Access to PSI resources==
−
We will publish here a brief guide describing the steps to follow to access the computing resources.
+
[https://intranet.psi.ch/en/emf/2023-tomoworkshop This guide] describes the steps to follow to access the computing resources inside PSI.
  
 
= Time Schedule =
 
= Time Schedule =
Line 31: Line 47:
 
|  0 || 09:00 - 10:00|| Research Talk
 
|  0 || 09:00 - 10:00|| Research Talk
 
|-
 
|-
−
| 1 || 10:00 - 10:45|| General introduction: Hands on  
+
| 1 || 10:00 - 10:45|| General introduction: Hands-on guide to basic tools. <br/>
 +
[https://wiki.dynamo.biozentrum.unibas.ch/w/doc/misc/conceptsSheet.pdf Basic Dynamo jargon] <br/>
 +
[https://wiki.dynamo.biozentrum.unibas.ch/w/doc/misc/introductionTablesAndData.pdf Basic formats for data and metadata]
 +
 
 
|-
 
|-
 
| 2 || 11:00 - 12:30 || [[Starters guide | Starters Guide: subtomogram averaging]]
 
| 2 || 11:00 - 12:30 || [[Starters guide | Starters Guide: subtomogram averaging]]
 
|-
 
|-
  
−
| 3 || 13:30 - 14:00 || General modelling
+
| 3 || 13:30 - 14:00 || General modeling
 
|-
 
|-
−
| 3a ||14:00 - 14:30 || [[Walkthrough_on_filament_models | Models: Filaments]]
+
| 3a ||14:00 - 14:45 || [[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 ]]
+
| 3b || 14:45 - 15:30 || [[Walkthrough_on_vesicle_models | Models: Vesicles ]]  
 
|-
 
|-
−
| 3c || 14:45 - 15:00 || [[Walkthrough_on_membrane_models | Models: Surfaces ]]
+
| 3c || 15:30 - 16:30 || [[Walkthrough_on_membrane_models | Models: Surfaces ]]
 
|}
 
|}
  
  
 
{| class="wikitable"  
 
{| class="wikitable"  
−
|+ Day 1 (Afternoon) General Tools
+
|+ Day 2 (Morning) General Tools
 
|-
 
|-
 
! Module !! Time !! Subject
 
! Module !! Time !! Subject
 
|-
 
|-
−
| 4 || 15:15 - 15:45 || [[Walkthrough for template matching (PSI 2023) | Template Matching]]
+
| 4 || 09:00 - 10:15 || [[Walkthrough for template matching (PSI 2023) | Template Matching]]
 
|-
 
|-
−
| 5 || 15:45 - 16:15 || [[Walkthrough on PCA through the command line | Principal Component Analysis ]]
+
| 5 || 10:15 - 11:30 || [[Walkthrough on PCA through the command line PSI 2023 | Principal Component Analysis ]]
 
|-
 
|-
−
| 6a || 16:15 - 16:45 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]]
+
| 6a || 11:30 - 12:00 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]]  
 
|-
 
|-
−
| 6b || 16:45 - 17:15 || [[Walkthrough_on_GUI_based_tilt_series_alignment | Alignment of tilt series: GUI ]]
+
| 6b || 12:00 - 12:30 || [[Walkthrough_on_GUI_based_tilt_series_alignment | Alignment of tilt series: GUI ]]
 
|-
 
|-
−
| 6c || 17:15 - 17:45 || [[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]]
  
 
|}
 
|}
  
−
{| class="wikitable"
 
−
|+ Day 2 (Morning):  Practical cases
 
−
|-
 
−
! Module !! Time !! Subject
 
−
|-
 
−
| FHV || 09:00 - 11:00 || [[Advanced starters guide (PSI 2023)| Complete walkthrough on FHV virus]]
 
−
|-
 
−
| HIV1 || 11:15 - 13:00 || High Resolution workflow for HIV1: preprocessing
 
−
|}
 
  
 
{| class="wikitable"  
 
{| class="wikitable"  
Line 78: Line 88:
 
! Module !! Time !! Subject
 
! Module !! Time !! Subject
 
|-
 
|-
−
| HIV1 || 14:00 - 15:30 || [[ HIV1_workshop | High Resolution workflow for HIV1: Dynamo manipulations ]]
+
| FHV || 13:30 - 15:30 || [[Advanced starters guide (PSI 2023)| Complete walkthrough on FHV virus]]
 
|-
 
|-
−
| HIV1 || 15:45 - 17:00 || High Resolution workflow for HIV1: binding with Relion
+
| HIV1 || 15:45 - 17:00 || High Resolution workflow for HIV1: preprocessing <br/>
 +
[[ HIV1 Walkthrough (PSI 2023)| High Resolution workflow for HIV1: Dynamo manipulations ]] </br>
 +
High Resolution workflow for HIV1: binding with Relion
 
|}
 
|}
 +
 +
 +
Additional material: <br/>
 +
* [[Walkthrough for lattices on vesicles | 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).

Latest revision as of 13:20, 2 December 2024


Workshop

The PSI Dynamo workshop will take place from August the 16th to August the 18th in the Paul Scherrer Institute.

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:

  • (R2023a 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 PSI resources

This guide describes the steps to follow to access the computing resources inside PSI.

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 guide to basic tools.

Basic Dynamo jargon
Basic formats for data and metadata

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


Day 2 (Morning) General Tools
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


Day 2 (Afternoon): Practical cases
Module Time Subject
FHV 13:30 - 15:30 Complete walkthrough on FHV virus
HIV1 15:45 - 17:00 High Resolution workflow for HIV1: preprocessing

High Resolution workflow for HIV1: Dynamo manipulations
High Resolution workflow for HIV1: binding with Relion


Additional material:

Instructors

  • Daniel Castano-Diez (CSIC Bilbao, Spain).
  • Raffaele Coray (CSIC Bilbao, Spain).
  • Alma Vivas-Lago (CSIC Bilbao, Spain).
Retrieved from "https://www.dynamo-em.org//w/index.php?title=PSI_Workshop_2023&oldid=5313"