Difference between revisions of "Dynamo Workshop CIC bioGUNE 2020"

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The Bilbao ''Dynamo'' workshop 2020 will take place from April the 29th to April the 30th at the CIC-Biogune center in Erandio, near Bilbao (Spain).
 
The Bilbao ''Dynamo'' workshop 2020 will take place from April the 29th to April the 30th at the CIC-Biogune center in Erandio, near Bilbao (Spain).
  
The workshop provides an introductory hands-on training in all practical aspects of tomography and sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this four-day course.
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The workshop provides an introductory hands-on training in all practical aspects of tomography and sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this two-day course.
  
  
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== Registration fee==
 
== Registration fee==
  
Participants will be asked to confirm their registration with the payment of a fee of 100 EUR (500 EUR for industry), which covers  registration and meals during the workshop.
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Participants will be asked to confirm their registration with the payment of a fee of 150 EUR (500 EUR for industry), which covers  registration and meals during the workshop.
  
 
== Accommodation ==
 
== Accommodation ==
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== Duration of the course ==
 
== Duration of the course ==
The course will start at 9:00 on the 29th of April. Last presentation will be at 17h00 on the 30th of April.  
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The course will start at 9:00 on the 29th of April. Last presentation will be at 18h00 on the 30th of April.  
  
 
==Computing facilities==
 
==Computing facilities==
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==Sponsors==
 
==Sponsors==
*[http://www.snf.ch FNS/SNF]  CIC-Biogune.
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*[https://www.cicbiogune.es/ CIC-Biogune], Bilbao, Spain.
 
*[http://www.snf.ch FNS/SNF]  Swiss National Science Foundation.
 
*[http://www.snf.ch FNS/SNF]  Swiss National Science Foundation.

Revision as of 15:17, 24 January 2020

The Bilbao Dynamo workshop 2020 will take place from April the 29th to April the 30th at the CIC-Biogune center in Erandio, near Bilbao (Spain).

The workshop provides an introductory hands-on training in all practical aspects of tomography and sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this two-day course.


Registration

Use this form for registration in the waiting list. Please contact us if you don't get a confirmation on the next days.

Registration fee

Participants will be asked to confirm their registration with the payment of a fee of 150 EUR (500 EUR for industry), which covers registration and meals during the workshop.

Accommodation

Please note that the travel and lodging are not covered in the workshop registration fee and participants will have to arrange it by themselves.

Program

The exact time schedule can be consulted will be published here.

Venue

The workshop will take place in the computing room of the CIC-Biogune.

Duration of the course

The course will start at 9:00 on the 29th of April. Last presentation will be at 18h00 on the 30th of April.

Computing facilities

Participants will be provided with an individual workstation and with a temporary account on a remote supercomputing system. If you wish to get used to work with Dynamo on your own laptop, you are welcome to bring it. Please, take into account the platforms where it is possible to install the current versions of the code. Also, if you have a access to a supercomputing facility in your home institution, it is a good idea to open there an account beforehand and use it during the course. Dynamo is specially suited to work on GPU systems.

Contents

The course content can be found here. As a general guideline, we will cover:

  • Alignment and reconstruction of tilt series.
  • Manual and automated particle picking in different geometries (filaments, membranes, isolated particles...).
  • Archiving and cataloguing of tilt series, tomograms and annotations.
  • Creation of subtomogram averaging projects.
  • Advanced tools in subtomogram averaging.
  • Classification methods.
  • Creation of 3d scenes.
  • Scripting in Dynamo: gentle introduction to programming.

Organization

Organizers

  • Daniel Castaño-Díez, BioEM lab, University of Basel, Switzerland.
  • Aitor Hierro, CIC-Biogune, Bilbao, Spain.
  • Adriana Rojas, CIC-Biogune, Bilbao, Spain.

Instructors

  • Soledad Baños, CIC-Biogune, Bilbao, Spain.
  • Alister Burt, ILL, Grenoble, France.
  • Daniel Castaño-Díez, BioEM Lab, University of Basel, Switzerland.
  • Carlos López, CIC-Biogune, Bilbao, Spain
  • Isaac Santos, CIC-BIogune, Bilbao, Spain
  • Stefano Scaramuzza, C-CINA, University of Basel, Switzerland.


Sponsors