Dynamo Workshop CIC bioGUNE 2020

From Dynamo
Jump to: navigation, search

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 in the Basque Country (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 for this workshop is closed. We are selecting the participants; in a few days we will contact all applicants (selected or not). Please contact us if you don't get a confirmation on the next days.

In view of the large number of applicants for this event, we will run a longer workshop in Basel later this year (August/September). Inscription for this ne event will be posted in the 3DEM and CCPEM lists .

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. Matlab licences will be provided for external users. 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.
  • Sean Connell, CIC bioGUNE, Bilbao, Spain.
  • Marcelo Guerin, CIC bioGUNE, Bilbao, Spain.
  • Aitor Hierro, CIC bioGUNE, Bilbao, Spain.
  • Adriana Rojas, CIC bioGUNE, Bilbao, Spain.
  • Iban Ubarretxena-Belandia, Biofisika-Basque Centre for Biophysics, 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