Difference between revisions of "Materials Basel 2017"

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This page is provided as a generic orientation of the contents of the practical hands-on sessions. The final material will be updated before the beginning of the course.
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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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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:
 
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<tt>/Users/gast/mountedData/workshop2017</tt>
 
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==Program==
 
==Program==
  
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The course will start around 10:30, 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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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.
  
 
===General Introduction===
 
===General Introduction===
  
 
Wednesday afternoon.
 
Wednesday afternoon.
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Guided presentation:
  
 
* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]
 
* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]
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after the coffee break:  
 
after the coffee break:  
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Working on your own:
  
 
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
 
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
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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.
  
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===Data management and modeling===
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===Geometric modeling===
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Thursday morning.
 
  
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*  [http://{{SERVERNAME}}/w/doc/misc/modelMembrane tutorial on] membrane modeling with <tt> dmslice </tt>
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Thursday morning / afternoon.
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Short guided presentation:
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*  [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt>
 
* Filament models with <tt>dtmslice</tt>
 
* Filament models with <tt>dtmslice</tt>
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** [http://{{SERVERNAME}}/w/doc/misc/modelFilament tutorial ]
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** [http://{{SERVERNAME}}/w/doc/misc/modelFilament.pdf tutorial ]
 
** [[Filament model | walkthrough]]
 
** [[Filament model | walkthrough]]
 
* Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]])
 
* Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]])
 
* Further work: catalogue
 
* Further work: catalogue
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Working on your own:
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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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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>
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=== Creation of 3D scenes ===
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Friday morning
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Working on your own:
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* [[Walkthrough on creation of 3d scenes | Walkthrough on the FHV data set]] (~1hour)
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Further support material.
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* [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data).
  
 
===Classification===
 
===Classification===
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Thursday afternoon session.
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Friday afternoon
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Short guided presentation:
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* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.]  
 
* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.]  
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* Multirefererence Analysis  <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx  Basic concepts.]  <br />[[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]] (~10 min)
 
* Further work
 
* Further work
 
** Commandline operations with PCA
 
** Commandline operations with PCA
  
 
===Additional tools===
 
===Additional tools===
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Friday morning session.
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Friday afternoon session.
 
* Some tools for tilt series alignment, reconstruction, CTF correction.
 
* Some tools for tilt series alignment, reconstruction, CTF correction.
 
* Subboxing
 
* Subboxing
 
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
 
*: 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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*: Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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*: advanced subboxing tutorial: combining with MRA ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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*: advanced subboxing tutorial: combining with MRA {{pdftutorial|subboxing_multireference_PCA|tutorial}}
 
*: suggested data set: prd1 Capsides (in the folder of isolated particles)
 
*: 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/workshop2017</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.
 
  
 
== 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.

Latest revision as of 08:58, 25 August 2017

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

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.

General Introduction

Wednesday afternoon.

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.

Geometric modeling

Thursday morning / afternoon.

Short guided presentation:

Working on your own:

Template matching

Friday morning.

Working on your own:

Creation of 3D scenes

Friday morning

Working on your own:

Further support material.

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

Classification

Friday afternoon

Short guided presentation:

Additional tools

Friday afternoon session.

Exercises

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

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