Difference between revisions of "EMBO workshop 2016"

From Dynamo
Jump to navigation Jump to search
(Created page with "''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 i...")
 
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
''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 centralize all information relative to the course in this page.
+
==Computers==
 +
We will be using two different computing resources:
  
−
== Accessing the computers==
+
* [[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.
  
−
== Teaching materials==
+
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 16:51, 31 August 2016

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

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:
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

after the second coffee break

Data management and modeling

Wednesday 31 August (first part).

Classification

Wednesday 31 August (second part).

Additional tools

Thursday, 1 September.

Retrieved from "https://wiki.dynamo.biozentrum.unibas.ch/w/index.php?title=EMBO_workshop_2016&oldid=1205"