Difference between revisions of "EMBO workshop 2016"
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===General Introduction=== | ===General Introduction=== | ||
| − | Tuesday 30 August 2016 | + | Tuesday 30 August 2016. |
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* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon] | * [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon] | ||
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===Data management and modeling=== | ===Data management and modeling=== | ||
| − | Wednesday 31 August | + | Wednesday 31 August (first part). |
* [http://{{SERVERNAME}}/w/doc/misc/modelMembrane tutorial on] membrane modeling with <tt> dmslice </tt> | * [http://{{SERVERNAME}}/w/doc/misc/modelMembrane tutorial on] membrane modeling with <tt> dmslice </tt> | ||
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===Classification=== | ===Classification=== | ||
| − | + | Wednesday 31 August (second part). | |
| + | |||
* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] | * 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]] | * Multirefererence Analysis <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] <br />[[Walkthrough basic multireference|walkthrough]] | ||
Revision as of 15:50, 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 (first part).
- tutorial on membrane modeling with dmslice
- Filament models with dtmslice
- Reusing model workflows ( walkthrough)
- Further work: catalogue
Classification
Wednesday 31 August (second part).
- 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
