Difference between revisions of "Materials Basel 2017"

From Dynamo
Jump to navigation Jump to search
 
(5 intermediate revisions by the same user not shown)
Line 41: Line 41:
  
 
* For the morning session: complete the  [[advanced starters guide]] (~2 hours) <br / > the data can be found in  <br /><tt> ~/data/data/crop.rec</tt> <br /> a central file is available in <br /> <tt>~/clab-share/data/crop.rec</tt>
 
* For the morning session: complete the  [[advanced starters guide]] (~2 hours) <br / > the data can be found in  <br /><tt> ~/data/data/crop.rec</tt> <br /> a central file is available in <br /> <tt>~/clab-share/data/crop.rec</tt>
* In the afternoon, after the research talks, we will focus on the extraction of particles  [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]]  (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hivv/v17.rec'''</tt>
+
* In the afternoon, after the research talks, we will focus on the extraction of particles  [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]]  (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec'''</tt>
 
 
wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec
 
 
 
Before going for lunch, please write in a '''linux terminal''':
 
 
 
<tt>''' /clab-share/bringDataLocal.sh'''</tt>
 
  
 
===Template matching===
 
===Template matching===
  
Thursday morning.
+
Friday morning.
  
 
Working on your own:  
 
Working on your own:  
  
 
* We will follow this [[Walkthrough for template matching | walkthrough]] for automated identification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc'''</tt>
 
* We will follow this [[Walkthrough for template matching | walkthrough]] for automated identification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc'''</tt>
 
===Classification===
 
 
Friday morning
 
 
Short guided presentation:
 
 
* 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]] (~10 min)
 
* Further work
 
** Commandline operations with PCA
 
  
 
=== Creation of 3D scenes ===
 
=== Creation of 3D scenes ===
Line 79: Line 62:
  
 
* [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data).
 
* [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data).
 +
 +
===Classification===
 +
Friday afternoon
 +
 +
Short guided presentation:
 +
 +
* 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]] (~10 min)
 +
* Further work
 +
** Commandline operations with PCA
  
 
===Additional tools===
 
===Additional tools===
Friday morning session.
+
Friday afternoon session.
 
* Some tools for tilt series alignment, reconstruction, CTF correction.
 
* Some tools for tilt series alignment, reconstruction, CTF correction.
 
* Subboxing
 
* Subboxing
Line 90: Line 83:
 
* Manual alignment.
 
* Manual alignment.
 
* [[Workshop exercises| Exercises]]
 
* [[Workshop exercises| Exercises]]
 
== Data sets ==
 
In the directory <tt>/Users/gast/mountedData/workshop2017</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 ==
 
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
 
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.

Latest revision as of 08:58, 25 August 2017

This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described here

Program

The course will start at 10 o'clock, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.

General Introduction

Wednesday afternoon.

Guided presentation:

  • tutorial on basic elements: help, data and metadata formats.
  • tutorial on the basic concept in Dynamo alignment: the project.

after the coffee break:

Working on your own:

  • 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.

Geometric modeling

Thursday morning / afternoon.

Short guided presentation:

Working on your own:

Template matching

Friday morning.

Working on your own:

Creation of 3D scenes

Friday morning

Working on your own:

Further support material.

  • Walkthrough on depiction and manipulation of triangulations (synthetic data).

Classification

Friday afternoon

Short guided presentation:

Additional tools

Friday afternoon session.

Exercises

Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.