Difference between revisions of "Materials Basel 2016"

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Materials for
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Theory will be presented on synthetic data generated on the fly by ''Dynamo''. Then, the shown theory can be applied on real data sets brought by the participants themselves, or the data sets prepared in the instructor file share under:
==General Introduction ==
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<tt>/Users/gast/mountedData/workshop2016</tt>
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==Program==
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===General Introduction===
  
 
Wednesday afternoon.
 
Wednesday afternoon.
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** {{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.
  
==Data management and modeling==
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===Data management and modeling===
 
Thursday morning.
 
Thursday morning.
  
*  [http://{{SERVERNAME}}/w/doc/misc/modelMembrane tutorial on ] membrane modeling with <tt> dmslice </tt>
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*  [http://{{SERVERNAME}}/w/doc/misc/modelMembrane tutorial on] membrane modeling with <tt> dmslice </tt>
 
* Filament models with <tt>dtmslice</tt>
 
* Filament models with <tt>dtmslice</tt>
 
** [http://{{SERVERNAME}}/w/doc/misc/modelFilament tutorial ]
 
** [http://{{SERVERNAME}}/w/doc/misc/modelFilament tutorial ]
 
** [[Filament model | walkthrough]]
 
** [[Filament model | walkthrough]]
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* Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]])
 
* Further work: catalogue
 
* Further work: catalogue
  
==Classification==
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===Classification===
 
Thursday afternoon session.
 
Thursday afternoon session.
* PCA
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* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.]
* Multirefererence Analysis [[Walkthrough basic multireference|walkthrough]]
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* Multirefererence Analysis <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx  Basic concepts.]  <br />[[Walkthrough basic multireference|walkthrough]]
 
* Further work
 
* Further work
 
** Commandline operations with PCA
 
** Commandline operations with PCA
  
==Additional tools==
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.
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===Additional tools===
 
Friday morning session.
 
Friday morning session.
* Subboxing {{pdftutorial|subboxing_symmetry|tutorial}}
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* Subboxing
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*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
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*: Basic subboxing {{pdftutorial|subboxing_multireference_PCA|tutorial}}
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*: advanced subboxing tutorial: combining with MRA ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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*: suggested data set: prd1 Capsides (in the folder of isolated particles)
 
* Manual alignment.
 
* Manual alignment.
 
* [[Workshop exercises| Exercises]]
 
* [[Workshop exercises| Exercises]]
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== Data sets ==
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In the directory <tt>/Users/gast/mountedData/workshop2016</tt> there are folders with real data sets representing typical situations. There are both tomograms and already extracted [[data folder]]s.
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*D1 to D4 are tomograms described [http://{{SERVERNAME}}/w/doc/workshops/2016/Datasets.pdf here].
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*D5-D6 are folders containing different formatted data folders.
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An additional data set of [http://www.sciencedirect.com/science/article/pii/S0969212615004931 5ht3] particles is available through [https://drive.google.com/open?id=0BwunkvGgI_EpUnlqSF9EVXVwVVk this Google drive link]. This data sets includes several thousands of particles. If you want to work with the whole data set, it is a good idea to download it directly into your CSCS account.
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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 10:12, 19 August 2016

Theory will be presented on synthetic data generated on the fly by Dynamo. Then, the shown theory can be applied on real data sets brought by the participants themselves, or the data sets prepared in the instructor file share under: /Users/gast/mountedData/workshop2016


Program

General Introduction

Wednesday afternoon.

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

after the coffee break:

  • 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.

Data management and modeling

Thursday morning.

Classification

Thursday afternoon session.

.

Additional tools

Friday morning session.

Data sets

In the directory /Users/gast/mountedData/workshop2016 there are folders with real data sets representing typical situations. There are both tomograms and already extracted data folders.

  • D1 to D4 are tomograms described here.
  • D5-D6 are folders containing different formatted data folders.

An additional data set of 5ht3 particles is available through this Google drive link. This data sets includes several thousands of particles. If you want to work with the whole data set, it is a good idea to download it directly into your CSCS account.

Exercises

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