Difference between revisions of "Materials Basel 2018"

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This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described [[Computers Basel 2017 | '''here''']]
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This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described [[Computers Basel 2018 | '''here''']].
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Before downloading any workshop data, please check the directory <tt>~/data</tt> since most of the needed material is already available there.
  
 
==Program==
 
==Program==
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The course will start at 10 o'clock, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.
 
The course will start at 10 o'clock, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.
  
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===Tuesday afternoon===
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=== Introduction ===
  
 
Guided presentation:  
 
Guided presentation:  
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** {{pdftutorial|commandline|tutorial}} on the use command line operations for general purposes.
 
** {{pdftutorial|commandline|tutorial}} on the use command line operations for general purposes.
 
** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects.
 
** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects.
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===Template matching===
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Tuesday afternoon.
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Working on your own:
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* We will follow this [[Walkthrough for template matching | walkthrough]] for automated identification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc'''</tt>
  
 
===Geometric modeling===
 
===Geometric modeling===
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Working on your own:
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* For the Wednesday morning session: complete the  [[advanced starters guide]] (~2 hours) <br / > the data can be found in  <br /><tt> ~/data/crop.rec</tt> <br /> a central file which you can copy is available in <br /> <tt>/clab-share/data/crop.rec</tt>
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* In the afternoon, after the research talks, we will focus on the extraction of particles  [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]]  (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec'''</tt>
  
 
Short guided presentation:
 
Short guided presentation:
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* Further work: catalogue
 
* Further work: catalogue
  
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Working on your own:
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=== Alignment and reconstruction ===
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* For the morning session: complete the  [[advanced starters guide]] (~2 hours) <br / > the data can be found in  <br /><tt> ~/data/data/crop.rec</tt> <br /> a central file is available in <br /> <tt>~/clab-share/data/crop.rec</tt>
 
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* In the afternoon, after the research talks, we will focus on the extraction of particles  [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]]  (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec'''</tt>
 
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===Template matching===
 
  
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Friday morning.
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These new features in ''Dynamo'' are at the testing stage.
  
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Working on your own:
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* [[Walkthrough on manual marker clicking  ]]
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* We will follow this [[Walkthrough for template matching | walkthrough]] for automated identification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc'''</tt>
 
  
 
=== Creation of 3D scenes ===
 
=== Creation of 3D scenes ===
  
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Friday morning
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Thursday afternoon.
  
 
Working on your own:
 
Working on your own:
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===Classification===
 
===Classification===
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Friday afternoon
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Thursday afternoon.
  
 
Short guided presentation:
 
Short guided presentation:
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** Commandline operations with PCA
 
** Commandline operations with PCA
  
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===Additional tools===
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===Additional tools and exercises===
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Friday afternoon session.
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* Getting a Structure from Multiple Tomograms:
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* Some tools for tilt series alignment, reconstruction, CTF correction.
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*: - In this [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids|exercise on VLPs]] you will be given 6 tomograms of HIV Capsids and the goal is to reach a structure in which alpha helices start to be visible.
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* Subboxing
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* [[GPUs_Basel_2018|Usage of GPUs]]
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*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
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* Subboxing:
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*: Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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*: - motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
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*: advanced subboxing tutorial: combining with MRA  {{pdftutorial|subboxing_multireference_PCA|tutorial}}
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*: - Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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*: suggested data set: prd1 Capsides (in the folder of isolated particles)
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*: - advanced subboxing tutorial: combining with MRA  {{pdftutorial|subboxing_multireference_PCA|tutorial}}
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* Manual alignment.
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*: - suggested data set: prd1 Capsides (in the folder of isolated particles)
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* [[Workshop exercises| Exercises]]
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* Manual alignment
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* [[Workshop exercises| Collection of Small Exercises]]
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== Exercises ==
 
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Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
 

Latest revision as of 21:43, 29 August 2018

This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described here.

Before downloading any workshop data, please check the directory ~/data since most of the needed material is already available there.

Program

The course will start at 10 o'clock, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.

Introduction

Guided presentation:

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

after the coffee break:

Working on your own:

  • Basic walkthrough: creating a catalogue, picking particles, launching a project.
  • Further work:
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

Template matching

Tuesday afternoon.

Working on your own:

Geometric modeling

Working on your own:

Short guided presentation:

Alignment and reconstruction

These new features in Dynamo are at the testing stage.

Creation of 3D scenes

Thursday afternoon.

Working on your own:

Further support material.

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

Classification

Thursday afternoon.

Short guided presentation:

Additional tools and exercises

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