Difference between revisions of "EMBO workshop 2018"

From Dynamo
Jump to: navigation, search
(Created page with "''Dynamo'' will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data. ==Computers== == Data sets == In the directory <tt>XXX</tt...")
 
(Data sets)
 
(8 intermediate revisions by the same user not shown)
Line 4: Line 4:
  
 
== Data sets ==
 
== Data sets ==
In the directory <tt>XXX</tt> there are folders with real data sets. Data sets:  
+
In the directory <tt>/g/embo2018/data/DYNAMO</tt> there are folders with real data sets. Data sets:  
*Tomogram 1 is called <tt>crop.rec</tt>. The data is a fraction of a tomogram.  The full tomogram was used in "Cryo-electron tomography reveals novel features of a viral RNA replication compartment." (Ertel et al.), and represents several FHV viruses docked in the outer membrane of a mitochondrion. Data can be downloaded [[Advanced_starters_guide#Downloading | here]]
+
*Tomogram 1 is called <tt>crop.rec</tt>. The data is a fraction of a tomogram.  The full tomogram was used in ''Cryo-electron tomography reveals novel features of a viral RNA replication compartment''.  (Ertel et al.), and represents several FHV viruses docked in the outer membrane of a mitochondrion. Data can be downloaded [[Advanced_starters_guide#Downloading | here]]
  
 
*Tomogram 2 is called <tt>t20s.mrc</tt>. The tomogram visualises purified T20S proteasome in solution. Data can be downloaded [[Walkthrough_for_template_matching#Data_set | here]]
 
*Tomogram 2 is called <tt>t20s.mrc</tt>. The tomogram visualises purified T20S proteasome in solution. Data can be downloaded [[Walkthrough_for_template_matching#Data_set | here]]
 +
 +
*Tomogram 3 is called <tt>v17.rec</tt>. This single tomogram is part of the data set used for the paper ''An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation'' by Schur FK, Obr M, Hagen WJ, Wan W, Jakobi AJ, Kirkpatrick JM, Sachse C, Kräusslich HG and Briggs JA. (2016). Data can be downloaded [[Walkthrough_for_lattices_on_vesicles#Data | here]]
  
 
==Program==
 
==Program==
Line 23: Line 25:
 
=====Working on your own=====
 
=====Working on your own=====
 
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
 
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
 +
 +
  
 
===Wednesday September 5th===
 
===Wednesday September 5th===
Line 29: Line 33:
  
 
=====Guided presentation:=====
 
=====Guided presentation:=====
* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]
 
 
* Walkthrough on [[Walkthrough_for_template_matching | template matching]]
 
* Walkthrough on [[Walkthrough_for_template_matching | template matching]]
 
* Overview discussion of  [[Advanced_starters_guide | Advanced starters guide]]
 
* Overview discussion of  [[Advanced_starters_guide | Advanced starters guide]]
Line 37: Line 40:
 
=====Working on your own=====
 
=====Working on your own=====
 
* Walkthrough for [[Advanced_starters_guide | Advanced starters guide]]
 
* Walkthrough for [[Advanced_starters_guide | Advanced starters guide]]
 +
 +
  
 
===Thursday September 6th:===
 
===Thursday September 6th:===
Line 50: Line 55:
 
=====Working own your own:=====
 
=====Working own your own:=====
  
*VLP project (link)
+
*Walkthrough for [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids_(walkthrough) | VLP project]]:  getting a structure from multiple tomograms of HIV capsids.
 +
 
 +
==Instructors==
 +
 
 +
*John Briggs, MRC-LMB, Cambridge, UK.
 +
 
 +
*Dustin Morado, MRC-LMB, Cambridge, UK.
 +
 
 +
*Paula Navarro, C-CINA, University of Basel, Switzerland.
 +
 
 +
*Julia Peukes, EMBL, Heidelberg, Germany.
 +
 
 +
* Giulia Zanetti, Birkbeck College, London, UK.

Latest revision as of 09:01, 5 September 2018

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

Computers

Data sets

In the directory /g/embo2018/data/DYNAMO there are folders with real data sets. Data sets:

  • Tomogram 1 is called crop.rec. The data is a fraction of a tomogram. The full tomogram was used in Cryo-electron tomography reveals novel features of a viral RNA replication compartment. (Ertel et al.), and represents several FHV viruses docked in the outer membrane of a mitochondrion. Data can be downloaded here
  • Tomogram 2 is called t20s.mrc. The tomogram visualises purified T20S proteasome in solution. Data can be downloaded here
  • Tomogram 3 is called v17.rec. This single tomogram is part of the data set used for the paper An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation by Schur FK, Obr M, Hagen WJ, Wan W, Jakobi AJ, Kirkpatrick JM, Sachse C, Kräusslich HG and Briggs JA. (2016). Data can be downloaded here

Program

Tuesday September 4th

General Introduction

Guided presentation:

after the coffee break

Working on your own
  • Basic walkthrough: creating a catalogue, picking particles, launching a project.


Wednesday September 5th

Introduction

Guided presentation:

after the coffee break

Working on your own


Thursday September 6th:

Introduction

Guided presentation
  • Overview discussion with XXX computing modi, with focus on GPUs (EMBO GPUs link).
  • Walkthrough for lattices on vesicles extraction of particles from densely packed spherical geometry.
  • Overview discussion of VLP project.
Working own your own:
  • Walkthrough for VLP project: getting a structure from multiple tomograms of HIV capsids.

Instructors

  • John Briggs, MRC-LMB, Cambridge, UK.
  • Dustin Morado, MRC-LMB, Cambridge, UK.
  • Paula Navarro, C-CINA, University of Basel, Switzerland.
  • Julia Peukes, EMBL, Heidelberg, Germany.
  • Giulia Zanetti, Birkbeck College, London, UK.