Difference between revisions of "EMBO workshop 2016"

From Dynamo
Jump to navigation Jump to search
Line 8: Line 8:
  
 
== Teaching materials==
 
== Teaching materials==
 +
 +
===General Introduction===
 +
 +
Tuesday 30 August 2016
 +
 +
 +
* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]
 +
 +
* [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats.
 +
* [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''.
 +
 +
after the coffee break:
 +
 +
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
 +
* Further work:
 +
** {{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.
 +
 +
===Data management and modeling===
 +
Wednesday 31 August 2016
 +
 +
*  [http://{{SERVERNAME}}/w/doc/misc/modelMembrane tutorial on] membrane modeling with <tt> dmslice </tt>
 +
* Filament models with <tt>dtmslice</tt>
 +
** [http://{{SERVERNAME}}/w/doc/misc/modelFilament tutorial ]
 +
** [[Filament model | walkthrough]]
 +
* Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]])
 +
* Further work: catalogue
 +
 +
===Classification===
 +
Thursday afternoon session.
 +
* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.]
 +
* Multirefererence Analysis  <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx  Basic concepts.]  <br />[[Walkthrough basic multireference|walkthrough]]
 +
* Further work
 +
** Commandline operations with PCA
 +
 +
.
 +
 +
===Additional tools===
 +
Thursday, 1 September.
 +
* Subboxing
 +
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
 +
*: Basic subboxing {{pdftutorial|subboxing_multireference_PCA|tutorial}}
 +
*: advanced subboxing tutorial: combining with MRA ({{pdftutorial|subboxing_symmetry|tutorial}}l)
 +
*: suggested data set: prd1 Capsides (in the folder of isolated particles)
 +
* Manual alignment.
 +
* [[Workshop exercises| Exercises]]

Revision as of 14:49, 24 August 2016

Dynamo will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data.

We will centralize all information relative to the course in this page... information is coming soon.

Accessing the computers

Data sets

Teaching materials

General Introduction

Tuesday 30 August 2016


  • 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

Wednesday 31 August 2016

Classification

Thursday afternoon session.

.

Additional tools

Thursday, 1 September.