Difference between revisions of "EMBO workshop 2016"
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''Dynamo'' will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data. | ''Dynamo'' will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data. | ||
| − | We will | + | ==Computers== |
| + | We will be using two different computing resources: | ||
| − | + | * [[Workstations EMBO 2016| Local Linux workstations]] | |
| + | * [[GPUs EMBO 2016 |Remote GPUs]] | ||
== Data sets == | == Data sets == | ||
| + | In the directory <tt>/g/embo2016/data/DYNAMO</tt> there are folders with real data sets representing typical situations. There are both tomograms and already extracted [[data folder]]s. | ||
| + | *T1 to T4 are tomograms described [http://{{SERVERNAME}}/w/doc/workshops/2016/Datasets.pdf here]. | ||
| + | *P1-P2 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. |
| + | |||
| + | ==Program== | ||
| + | |||
| + | ===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. | ||
| + | |||
| + | after the second coffee break | ||
| + | |||
| + | * Introduction to the use of [[GPUs EMBO 2016 | remotely located GPUs]] | ||
| + | |||
| + | ===Data management and modeling=== | ||
| + | Wednesday 31 August (first part). | ||
| + | |||
| + | * [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt> | ||
| + | * Filament models with <tt>dtmslice</tt> | ||
| + | ** [http://{{SERVERNAME}}/w/doc/misc/modelFilament.pdf tutorial ] | ||
| + | ** [[Filament model | walkthrough]] | ||
| + | * Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]]) | ||
| + | * Further work: catalogue | ||
| + | |||
| + | ===Classification=== | ||
| + | Wednesday 31 August (second part). | ||
| + | |||
| + | * 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]] | ||
Latest revision as of 17:51, 31 August 2016
Dynamo will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data.
Contents
Computers
We will be using two different computing resources:
Data sets
In the directory /g/embo2016/data/DYNAMO there are folders with real data sets representing typical situations. There are both tomograms and already extracted data folders.
- T1 to T4 are tomograms described here.
- P1-P2 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.
Program
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:
after the second coffee break
- Introduction to the use of remotely located GPUs
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
