Difference between revisions of "Materials Basel 2016"
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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: | |
| − | + | <tt>/Users/gast/mountedData/workshop2016</tt> | |
| − | |||
| − | * | + | ==Program== |
| − | * | + | |
| − | * Basic walkthrough: creating a catalogue, picking particles, launching a project. | + | ===General Introduction=== |
| + | |||
| + | Wednesday afternoon. | ||
| + | |||
| + | * [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: | * Further work: | ||
| − | ** commandline tutorial | + | ** {{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== | + | ===Data management and modeling=== |
| − | Thursday morning | + | Thursday morning. |
| − | * | + | * [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 ] | ||
| + | ** [[Filament model | walkthrough]] | ||
| + | * Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]]) | ||
* Further work: catalogue | * Further work: catalogue | ||
| − | ==Classification== | + | ===Classification=== |
| − | Thursday afternoon | + | Thursday afternoon session. |
| − | * PCA | + | * PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] |
| − | * Multirefererence Analysis | + | * Multirefererence Analysis <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] <br />[[Walkthrough basic multireference|walkthrough]] |
| − | * | + | * Further work |
| − | ** Commandline operations with PCA | + | ** Commandline operations with PCA |
| + | |||
| + | . | ||
| + | |||
| + | ===Additional tools=== | ||
| + | Friday morning session. | ||
| + | * 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]] | ||
| + | |||
| + | == Data sets == | ||
| + | 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. | ||
| + | *D1 to D4 are tomograms described [http://{{SERVERNAME}}/w/doc/workshops/2016/Datasets.pdf here]. | ||
| + | *D5-D6 are folders containing different formatted data folders. | ||
| + | |||
| + | 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 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
Contents
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:
Data management and modeling
Thursday morning.
- 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
Friday morning session.
- 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
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.
