Difference between revisions of "EMBO workshop 2021"

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The tutorials listed here take place virtually on the 11th and 13th of September of 2021 (14:00-18:30) as part of the EMBO workshop for Image processing in cryoEM.
+
The tutorials listed here take place virtually on the 11th and 13th of September of 2021 (14:00-18:30, London time) as part of the EMBO workshop for Image processing in cryoEM.
  
 
=Connect to Guacamole and run Dynamo=
 
=Connect to Guacamole and run Dynamo=
Line 28: Line 28:
 
where XX stands for your actual workshop participant number.
 
where XX stands for your actual workshop participant number.
  
−
=== Load and run Dynamo ===
+
=== Data location ===
−
 
 
−
First you load the '''standalone''' version of ''Dynamo'' with the command:
 
−
<tt> module load dynamo/v1.1.524</tt>
 
−
and then it can be run by simply typing:
 
−
<tt> dynamo</tt>
 
−
 
 
−
[[File:embo_2021_5.png|thumb|center|300px|Dynamo console started.]]
 
  
−
''Dynamo'' specific commands are then typed into this so called ''Dynamo console''. For example, try to type the ''Dynamo'' command
 
−
<tt>dynamo_version</tt>
 
−
to see the current version that you are using. Note: Copy paste of commands from your local desktop into the dynamo standalone console on the remote Linux XFCe desktop might not always work. We suggest to additionally open the tutorials that you will be working on in a browser inside the remote Linux XFCe desktop itself, in case you need to copy paste long commands.
 
−
 
−
Type the following command to check how many CPU your machine has. You might use this number later for tasks that require parallel processing:
 
−
 
−
<tt>mbparse.multicore.checkPhysicalCores</tt>
 
−
 
−
=== Data location ===
 
 
The data used in the tutorials is already available for you. Move to the directory of the corresponding practical using the command:
 
The data used in the tutorials is already available for you. Move to the directory of the corresponding practical using the command:
  
Line 62: Line 46:
 
[[File:embo_files.png|thumb|center|500px|files]]
 
[[File:embo_files.png|thumb|center|500px|files]]
  
−
During the ''Dynamo'' workshop, work only within those two directories.
+
During the ''Dynamo'' workshop, work '''only''' within these two directories.
 +
 
 +
=== Load and run Dynamo ===
 +
 
 +
To use ''Dynamo'', first load the '''standalone''' version of ''Dynamo'' with the command:
 +
<tt> module load dynamo/v1.1.524</tt>
 +
Then it can be run by simply typing:
 +
<tt> dynamo</tt>
 +
 
 +
[[File:embo_2021_5.png|thumb|center|300px|Dynamo console started.]]
 +
 
 +
''Dynamo'' specific commands are then typed into this so called ''Dynamo console''. For example, try to type the ''Dynamo'' command
 +
<tt>dynamo_version</tt>
 +
to see the current version that you are using. Type the following command to check how many CPUs your machine has. You might use this number later for tasks that require parallel processing (e.g., alignment projects):
 +
 
 +
<tt>mbparse.multicore.checkPhysicalCores</tt>
 +
 
 +
'''Note:''' Copy paste of commands from your local desktop into the dynamo standalone console on the remote Linux XFCe desktop might not always work. We suggest to additionally open the tutorials that you will be working on in a browser inside the remote Linux XFCe desktop itself, in case you need to copy paste long commands.
 +
 
 +
'''Note:''' We suggest to open a new tab in the terminal (''File -> Open Tab''), in which you navigate to the same directory. You can then use this tab for normal linux commands so you do not have to quit ''Dynamo'' every time you want to do something else (e.g., running alignment projects or using chimera). Be aware that if you press ctrl+c within the ''Dynamo'' console you exit ''Dynamo'' and lose your workspace.
  
 
=== Chimera ===
 
=== Chimera ===
−
To use chimera use the following command (replace 'myFile.mrc' with your file) in the normal terminal (outside 'Dynamo').
+
To use chimera, use the following command (replace 'myFile.mrc' with your file) in the normal terminal (outside ''Dynamo'').
  
 
  <tt>/usr/local/bin/chimera myFile.mrc</tt>
 
  <tt>/usr/local/bin/chimera myFile.mrc</tt>
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! colspan="4" | '''Day 1'''
 
! colspan="4" | '''Day 1'''
 
|-
 
|-
−
|'''Time'''
+
|'''Time (London)'''
 
|'''Activity
 
|'''Activity
 
|'''Topic'''
 
|'''Topic'''
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| 14:30 - 15:30
 
| 14:30 - 15:30
 
| Tutorial
 
| Tutorial
−
| [[Walkthrough on GUI based tilt series alignment | Tilt series alignment with GUI]]
+
| [[Walkthrough_on_GUI_based_tilt_series_alignment_(EMBO2021)| Tilt series alignment with GUI]]
 
|
 
|
 
|-
 
|-
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| 15:45 - 16:45
 
| 15:45 - 16:45
 
| Tutorial
 
| Tutorial
−
| [[Walkthrough on command line based tilt series alignment | Tilt series alignment with command line]]
+
| [[Walkthrough_on_command_line_based_tilt_series_alignment_(EMBO2021) | Tilt series alignment with command line]]
−
| Skip last part "On the fly reconstruction of particles"
+
|  
 
|-
 
|-
 
| 16:45 - 17:00
 
| 16:45 - 17:00
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|
 
|
 
|-
 
|-
−
| 17:00 - 17:45
+
| 17:00 - 17:30
 
| Tutorial
 
| Tutorial
 
| [[Walkthrough_on_filament_models | Models for filaments]]
 
| [[Walkthrough_on_filament_models | Models for filaments]]
 
|
 
|
 
|-
 
|-
−
| 17:45 - 18:30
+
| 17:30 - 18:00
 
| Tutorial
 
| Tutorial
 
| [[Walkthrough_on_membrane_models | Models for surfaces]]
 
| [[Walkthrough_on_membrane_models | Models for surfaces]]
 
|
 
|
 
|-
 
|-
−
| Optional:
+
| Optional: 18:00
 
| Tutorial
 
| Tutorial
 
| [[Walkthrough for template matching | Template matching]]
 
| [[Walkthrough for template matching | Template matching]]
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! colspan="4" | '''Day 2'''
 
! colspan="4" | '''Day 2'''
 
|-
 
|-
−
|'''Time'''
+
|'''Time (London)'''
 
|'''Activity
 
|'''Activity
 
|'''Topic'''
 
|'''Topic'''
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| 14:15 - 15:30
 
| 14:15 - 15:30
 
| Tutorial
 
| Tutorial
−
| [[Starters_guide_(workshop_version) | Starters guide (workshop version)]]
+
| [[Starters_guide_(EMBO2021) | Starters guide]]
 
|  
 
|  
 
|-
 
|-
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|
 
|
 
|-
 
|-
−
| 15:45 - 18:15
+
| 15:45 - 17:45
 
| Tutorial
 
| Tutorial
−
| [[advanced starters guide | Advanced starters guide]]
+
| [[Advanced_starters_guide_(EMBO2021) | Advanced starters guide]]
 
| Take a 15 min break individually during this tutorial
 
| Take a 15 min break individually during this tutorial
 
|-
 
|-
−
| 18:15 - 18:30
+
| 17:45 - 18:00
 
| Presentation
 
| Presentation
 
| Closing remarks
 
| Closing remarks
 
|
 
|
 
|-
 
|-
−
| Optional:
+
| Optional: 18:00
 
| Tutorials
 
| Tutorials
 
| [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids_(walkthrough) | Virus like particles]] or [[Walkthrough for lattices on vesicles| Spherical geometries]]
 
| [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids_(walkthrough) | Virus like particles]] or [[Walkthrough for lattices on vesicles| Spherical geometries]]
 
|
 
|
 
|}
 
|}

Latest revision as of 17:07, 11 September 2021

The tutorials listed here take place virtually on the 11th and 13th of September of 2021 (14:00-18:30, London time) as part of the EMBO workshop for Image processing in cryoEM.

Connect to Guacamole and run Dynamo

Credentials

Please refer to your personal course material to access your two sets of credentials:

  1. A set of credentials to enter Guacamole (the platform for connecting via browser). These are common to all participants.
  2. A set of course credentials to enter the actual machines on which the course will be done: the EMBO21 UserID. These are unique to each participant.

Connect to Guacamole

To connect to Guacamole, first go to the following link in your browser: 

https://login.cryst.bbk.ac.uk/guacamole/#/

At this stage you should maximize your browser window, otherwise you might have visualization problems when opening Dynamo. You should see the following window. Enter your Guacamole credentials.

Entering guacamole server.

Connect to your machine

Now you need to select a machine. Please then click on +em and then +Servers - Public and select your dedicated server (in this example it is Zeus-0-14).

Select a machine.

When you select the machine, you will prompted to use your EMBO21 UserID

Entering your personal course credentials.

This should access your virtual Linux XFCe desktop, which should look like this in your browser

Linux XFCe desktop

If you open a terminal (with the terminal icon) you can test by typing 

pwd

that you are in the correct path, which should be: 

 /d/embo2021/u/emboXX

where XX stands for your actual workshop participant number.

Data location

The data used in the tutorials is already available for you. Move to the directory of the corresponding practical using the command: 

cd prac-5

or 

cd prac-6

respectively. Double-check if the data is present by typing 

ls

You should see the following files in both directories:

files

During the Dynamo workshop, work only within these two directories.

Load and run Dynamo

To use Dynamo, first load the standalone version of Dynamo with the command: 

 module load dynamo/v1.1.524

Then it can be run by simply typing: 

 dynamo
Dynamo console started.

Dynamo specific commands are then typed into this so called Dynamo console. For example, try to type the Dynamo command 

dynamo_version

to see the current version that you are using. Type the following command to check how many CPUs your machine has. You might use this number later for tasks that require parallel processing (e.g., alignment projects): 

mbparse.multicore.checkPhysicalCores

Note: Copy paste of commands from your local desktop into the dynamo standalone console on the remote Linux XFCe desktop might not always work. We suggest to additionally open the tutorials that you will be working on in a browser inside the remote Linux XFCe desktop itself, in case you need to copy paste long commands.

Note: We suggest to open a new tab in the terminal (File -> Open Tab), in which you navigate to the same directory. You can then use this tab for normal linux commands so you do not have to quit Dynamo every time you want to do something else (e.g., running alignment projects or using chimera). Be aware that if you press ctrl+c within the Dynamo console you exit Dynamo and lose your workspace.

Chimera

To use chimera, use the following command (replace 'myFile.mrc' with your file) in the normal terminal (outside Dynamo). 

/usr/local/bin/chimera myFile.mrc

Schedule

The course is divided into short presentations and tutorials, as described in the time schedule below. For the presentations, we all meet in the main room. The tutorials are structured as follows:

  1. Demonstration: All students stay connected to the main room for the first minutes, where the goals of the tutorial are briefly explained.
  2. Individual work: Students go the assigned breakout rooms to work on the material independently. An instructor will be assigned to each breakout room to help with questions.
  3. Closure: During the last 5 minutes we come back to the general breakout room to wrap up the tutorial.
Day 1
Time (London) Activity Topic Comment
14:00 - 14:30 Presentation Introduction
14:30 - 15:30 Tutorial Tilt series alignment with GUI
15:30 - 15:45 Break
15:45 - 16:45 Tutorial Tilt series alignment with command line
16:45 - 17:00 Break
17:00 - 17:30 Tutorial Models for filaments
17:30 - 18:00 Tutorial Models for surfaces
Optional: 18:00 Tutorial Template matching
Day 2
Time (London) Activity Topic Comment
14:00 - 14:15 Presentation Introduction
14:15 - 15:30 Tutorial Starters guide
15:30 - 15:45 Break
15:45 - 17:45 Tutorial Advanced starters guide Take a 15 min break individually during this tutorial
17:45 - 18:00 Presentation Closing remarks
Optional: 18:00 Tutorials Virus like particles or Spherical geometries
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