Basel Dynamo Workshop 2018

The Basel Dynamo workshop will take place from August the 28th to August the 31st in the Biozentrum of the University of Basel.

The workshop provides 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.

Registration

A link for registration will be published here from the first of May. 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 fee of 350 CHF (700 CHF for industry), which covers meals during the workshop.

Accommodation

The registration fee does not include accommodation. Participants are asked to do their own accommodation arrangements.

Program

Venue

The course will take place in the room U1075 of the Pharmazentrum in Basel.

Duration of the course

The course will start at 11:00 on the 28th of August. Last presentation will be at 12h00 on the 31st of August. After that, the participants will be welcome to keep on working (on their won data or course materials) in the computing room with the supervision of the course instructors till 17h00, when the workshop will officially end.

Contents

The final program schedule will be updated here by mid August. 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, Biozentrum, University of Basel, Switzerland.

Alex Noble, National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, NY, USA

Henning Stahlberg, C-CINA Center for Cellular Imaging and NanoAnalytics (C-CINA) , University of Basel, Switzerland.

Administration

Karen Bergmann, C-CINA, University of Basel, Switzerland.

Instructors

Daniel Castaño-Díez, BioEM Lab, University of Basel, Switzerland.

Alex Noble, New York Structural Biology Center.

Paula Pérez-Navarro, C-CINA, University of Basel, Switzerland.

Stefano Scaramuzza, C-CINA, University of Basel, Switzerland.

further instructors to be announced

Sponsors

SNF

Biozentrum of the University of Basel.

CSCS the Swiss Center for Scientific Computing.