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).
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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 Derio, 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.
 
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 150 EUR (500 EUR for industry), which covers  registration and meals during the workshop.
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No fee will be charged.
  
 
== Accommodation ==
 
== 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.
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Please note that the travel and lodging are '''not''' covered by the workshop. Participants will have to arrange it by themselves.
  
 
= Program =
 
= Program =
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==Computing facilities==
 
==Computing facilities==
  
Participants will be provided with an individual workstation and with a temporary account on a remote supercomputing system.  
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Participants will be provided with an individual laptop.  
 
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  [[Installation|install]] the current versions of the code.   
 
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  [[Installation|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.
 
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.
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= Organization=
 
= Organization=
 
==Organizers==
 
==Organizers==
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*Nicola Abrescia, CIC-Biogune, Bilbao, Spain.
 
*Daniel Castaño-Díez, BioEM lab, University of Basel, Switzerland.  
 
*Daniel Castaño-Díez, BioEM lab, University of Basel, Switzerland.  
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*Marcelo Guerin, CIC-Biogune, Bilbao, Spain.
 
*Aitor Hierro, CIC-Biogune, Bilbao, Spain.
 
*Aitor Hierro, CIC-Biogune, Bilbao, Spain.
 
*Adriana Rojas, CIC-Biogune, Bilbao, Spain.
 
*Adriana Rojas, CIC-Biogune, Bilbao, Spain.
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*Mikel Valle, CIC-Biogune, Bilbao, Spain.
  
 
==Instructors==
 
==Instructors==

Revision as of 16:55, 28 January 2020

The Bilbao Dynamo workshop 2020 will take place from April the 29th to April the 30th at the CIC-Biogune center in Derio, 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

Registration will be opened till 28th of February, and limited to 30 participants. 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

No fee will be charged.

Accommodation

Please note that the travel and lodging are not covered by the workshop. 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 laptop. 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

  • Nicola Abrescia, CIC-Biogune, Bilbao, Spain.
  • Daniel Castaño-Díez, BioEM lab, University of Basel, Switzerland.
  • Marcelo Guerin, CIC-Biogune, Bilbao, Spain.
  • Aitor Hierro, CIC-Biogune, Bilbao, Spain.
  • Adriana Rojas, CIC-Biogune, Bilbao, Spain.
  • Mikel Valle, 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