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.

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

Introduction: alignment projects

Wednesday 7th of December (afternoon).

  • 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

Thursday 8th December (morning).

Classification

Thursday 8th December (afternoon).

Additional tools

Friday, 9th of September (morning)

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.