Difference between revisions of "EMBO workshop 2016"
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== 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.
Contents
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:
Data management and modeling
Wednesday 31 August 2016
- tutorial on membrane modeling with dmslice
- Filament models with dtmslice
- Reusing model workflows ( walkthrough)
- Further work: catalogue
Classification
Thursday afternoon session.
- PCA Basic concepts.
- Multirefererence Analysis
Basic concepts.
walkthrough - Further work
- Commandline operations with PCA
.
Additional tools
Thursday, 1 September.
- Subboxing
- motivation slide: extraction of vertices from icosahedral viruses
- Basic subboxing tutorial
- advanced subboxing tutorial: combining with MRA (tutoriall)
- suggested data set: prd1 Capsides (in the folder of isolated particles)
- Manual alignment.
- Exercises