Basel Workshop 2019

The Basel Dynamo workshop will take place from August the 28th to August the 30th 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

Registration for this event is closed. All participants will be contacted by Monday, the 8th of July to be informed on the result of the application.

Registration fee

Participants will be asked to confirm their registration with the payment of a fee of 300 CHF (600 CHF 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. We recommend the following hostels:

• BaselBackPack - info@baselbackpack.com
• Youth Hostel Basel - basel@youthhostel.ch

Program

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

Venue

The workshop will take place in the Biozentrum of the University of Basel. Practical lectures will be held in the Room U1075, close to the Pharmazentrum entry in Klingelbergstrasse 70.

A map for the different events will be posted before the workshop:

• Lunch vouchers are valid in the canteen of the Hospital (close to the Biozentrum)
• Interested participants can visit the CINA facilities on Friday afternoon.

Duration of the course

The course will start at 9:30 on the 28th of August. Last presentation will be at 12h00 on the 30st 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.

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, 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.

• Lauren-Ann Metskas, Caltech, Pasadena, USA.

• Alex Noble, New York Structural Biology Center.

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

Sponsors

• FNS/SNF Swiss National Science Foundation.

• Biozentrum of the University of Basel.

• BioEM lab at the C-CINA center of the University of Basel.

• CSCS the Swiss Center for Scientific Computing.