Difference between revisions of "Prato Workshop 2019"

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The login and password are written in the front board.
 
The login and password are written in the front board.
 +
 +
Create a Linux term by pressing CTRL+ALT+T.
 +
  
 
=== Starting a ''Dynamo'' session ===
 
=== Starting a ''Dynamo'' session ===
  
''Dynamo'' is already preinstalled in the file system of Diamond.  You can activate it through  
+
''Dynamo'' is already preinstalled in the file system of Prato.  You can activate it through  
 
 
<tt> module load EM/dynamo </tt>
 
  
As some visualizations are performed with Chimera you need to activate it as well
+
  <tt> source ~/ws/opt/dynamo/dynamo_activate_linux_shipped_MCR.sh </tt>
 
 
  <tt> module load chimera </tt>
 
  
 
After ''Dynamo'' and Chimera have been loaded, you can start a session with:
 
After ''Dynamo'' and Chimera have been loaded, you can start a session with:
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=== Bringing the data to the local machine ===
 
=== Bringing the data to the local machine ===
  
Some tutorials during the workshop require downloading big files from the ''Dynamo'' wiki using <tt>wget</tt>. You don't need to do that, as they have been already downloaded into the location  <tt>/dls/tmp/DynamoWorkshop/data</tt>, which is visible by all the computers in the workshop.
+
The tutorials will ask you to download some datasets.
 +
The data should be available in the folder <tt>~/ws/data/dynamo/</tt>. Check that you find three files with:
  
To speed the access to these data sets, it is convenient to make a local copy of them into your own machines. To do so, defore going to lunch, please launch the order:
+
<tt> ls ~/ws/data/dynamo/*</tt>
  
<tt>/dls/tmp/DynamoWorkshop/data/fetchDataToLocalMachine.sh</tt>  
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You should see the files <tt>crop.rec</tt>,<tt>t20s.mrc</tt> and <tt>v17.rec</tt>. Let us know if it is not the case.
  
from a linux shell. This will copy the data into the directory <tt>~/dynamo/data</tt> in your machine.
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=== Create a folder to work ===
 +
 
 +
<tt>mkdir ~/tmp </tt>
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<tt>mkdir ~/tmp/dynamo/</tt>
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<tt>cd  ~/tmp/dynamo/</tt>
  
 
== Program ==
 
== Program ==
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== Exercises ==
 
== Exercises ==
 
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
 
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
 
== Organizers ==
 
 
* Tom Burnley, STFC.
 
* Daniel Castaño-Díez, BioEM Lab, University of Basel.
 
* Colin Palmer, STFC.
 
  
 
== Instructors ==
 
== Instructors ==
  
 
*  Daniel Castaño-Díez, University of Basel.
 
*  Daniel Castaño-Díez, University of Basel.
Colin Palmer, STFC.
+
Mikhail Kudryashev, Max Planck Institute for Biophysics, Frankfurt.
* Paula Navarro, University of Basel.
 
* Stefano Scaramuzza, University of Basel.
 

Latest revision as of 08:50, 4 April 2019

This page describes the contents of the practical hands-on sessions in Prato (28th-29th April 2019).

Computers

Entering the terminal

The login and password are written in the front board.

Create a Linux term by pressing CTRL+ALT+T.


Starting a Dynamo session

Dynamo is already preinstalled in the file system of Prato. You can activate it through

 source ~/ws/opt/dynamo/dynamo_activate_linux_shipped_MCR.sh 

After Dynamo and Chimera have been loaded, you can start a session with:

 dynamo 
Opening the Dynamo console inside a linux shell with the command dynamo

Bringing the data to the local machine

The tutorials will ask you to download some datasets. The data should be available in the folder ~/ws/data/dynamo/. Check that you find three files with:

 ls ~/ws/data/dynamo/*

You should see the files crop.rec,t20s.mrc and v17.rec. Let us know if it is not the case.

Create a folder to work

mkdir ~/tmp 
mkdir ~/tmp/dynamo/
cd  ~/tmp/dynamo/

Program

Before the hands-on session, we will go to this presentation for a general introduction of the Dynamosoftware.

General Introduction

Clicking particles in the Starters guide

Guided presentation:

  • tutorial on basic elements: help, data and metadata formats.
  • tutorial on the basic concept in Dynamo alignment: the project.

Working on your own:

  • Basic walkthrough: creating a catalogue, picking particles, launching a project.
  • Advanced starters guide on a real tomogram. (~2 hours)
  • Further work:
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

Geometric modeling

Geometric modeling for surfaces and filaments

Short guided presentation:

Working on your own:

Template matching

Working on your own:

  • We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)

Adaptive bandpass filtering

Working on your own:

  • We will follow this walkthrough to create a small synthetic data set that illustrates the principles of adaptive bandpass filtering, a way of conducting a golden standard alignment procedure . (~40 mins)

Classification

Short guided presentation:

Creation of 3D scenes

Working on your own:

Further support material.

  • Walkthrough on depiction and manipulation of triangulations (synthetic data).

Additional tools

Wednesday afternoon session.

Data sets

The data sets will be updated here.

Exercises

Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.

Instructors

  • Daniel Castaño-Díez, University of Basel.
  • Mikhail Kudryashev, Max Planck Institute for Biophysics, Frankfurt.