Difference between revisions of "''Dynamo''workshop at the New York Structural Biology Center 2016"

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{{DISPLAYTITLE: ''Dynamo'' workshop at the New York Structural Biology Center 2016 }}
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The NYSBC offer a two-day compact course on the use of the ''Dynamo'' software for subtomogram averaging and tomography. This workshop provides hands-on training in all practical aspects of sub-tomogram averaging, encompassing all stages of the pipeline: tomogram visualization and archiving, particle picking, averaging, refinement and classification. No previous experience will be required.
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An additional day will be offered for those interested in deepening the topics presented during the first two days.
  
 
= Registration =
 
= Registration =
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Participants are welcome to bring along their own laptops.
 
Participants are welcome to bring along their own laptops.
  
''Dynamo'' can be run as standalone (in Linux)  or inside the commercial Matlab software (Linux or Mac). For this course, we ask participants to get beforehand a trial license for Matlab.  Please, perform the installation of the latest version of ''Dynamo'' on your laptop before the course.  
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''Dynamo'' can be run as standalone (in Linux)  or inside the commercial Matlab software (Linux or Mac). For this course, we ask participants to get beforehand a trial license for Matlab.  Please, perform the [[Installation|installation]] of the [[Downloads|latest version]] of ''Dynamo'' on your laptop before the course.  
  
Also, we encourage participants to check beforehand if they have access to GPU machines through their home institution.
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Also, we encourage participants to check beforehand if they have access to GPU machines through their home institution.  
  
 
= Program =
 
= Program =
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This program is provisional.
  
 
==Introduction: alignment projects==
 
==Introduction: alignment projects==
Wednesday 7th of December (afternoon).
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* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]
 
* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon]
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** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects.
 
** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects.
  
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==Data management and modeling==
  
==Data management and modeling==
 
Thursday 8th December (morning).
 
  
 
*  [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt>
 
*  [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt>
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==Classification==
 
==Classification==
Thursday 8th December (afternoon).
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* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.]  
 
* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.]  
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==Additional tools==
 
==Additional tools==
Friday, 9th of September (morning)
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We offer an extra day for those interested in working with their own data, or discussing with the instructors more advanced topics.  
 
We offer an extra day for those interested in working with their own data, or discussing with the instructors more advanced topics.  
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* Subboxing
 
* Subboxing
 
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
 
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
*: Basic subboxing {{pdftutorial|subboxing_multireference_PCA|tutorial}}
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*: Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
*: advanced subboxing tutorial: combining with MRA ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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*: advanced subboxing tutorial: combining with MRA{{pdftutorial|subboxing_multireference_PCA|tutorial}}
 
*: suggested data set: prd1 Capsides (in the folder of isolated particles)
 
*: suggested data set: prd1 Capsides (in the folder of isolated particles)
 
* Manual alignment.
 
* Manual alignment.
 
* [[Workshop exercises| Exercises]]
 
* [[Workshop exercises| Exercises]]
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= Organizers =
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Alex Noble,  NYSBC, New York.
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=Instructors=
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* Alex Noble,  NYSBC, New York.
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* Daniel Castaño-Díez, BioEM lab, Biozentrum, University of Basel.

Latest revision as of 15:09, 9 December 2016


The NYSBC offer a two-day compact course on the use of the Dynamo software for subtomogram averaging and tomography. This workshop provides hands-on training in all practical aspects of sub-tomogram averaging, encompassing all stages of the pipeline: tomogram visualization and archiving, particle picking, averaging, refinement and classification. No previous experience will be required.

An additional day will be offered for those interested in deepening the topics presented during the first two days.

Registration

To be announced.

Requirements

Participants are welcome to bring along their own laptops.

Dynamo can be run as standalone (in Linux) or inside the commercial Matlab software (Linux or Mac). For this course, we ask participants to get beforehand a trial license for Matlab. Please, perform the installation of the latest version of Dynamo on your laptop before the course.

Also, we encourage participants to check beforehand if they have access to GPU machines through their home institution.

Program

This program is provisional.

Introduction: alignment projects

  • 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.

Data management and modeling

Classification

Additional tools

We offer an extra day for those interested in working with their own data, or discussing with the instructors more advanced topics.

Organizers

Alex Noble, NYSBC, New York.

Instructors

  • Alex Noble, NYSBC, New York.
  • Daniel Castaño-Díez, BioEM lab, Biozentrum, University of Basel.