Dynamo workshop 2017

The workshop provides hands-on training in all practical aspects of sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: tomogram visualization and archiving, particle picking, 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 three-day course.

Registration

Use this link for registration. Please contact us directlyl if you don't receive a confirmation email in the next couple of days.

Accepted participants will be asked to confirm their registration by the payment of a fee of 270 CHF. This fee covers meals and dinners during the workshop, but not the lodgement. Participants are asked to do their own arrangements for accommodation.

Venue

The workshop will take place from the 23th to the 25th of August 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.

Travel and Lodging

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

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.

Access the computers through these guidelines

Program

The program can be downloaded here. We will cover:

• Creation of alignment projects.
• Creation of classification projects.
• Use of supercomputing devices.
• Management of complex tomography projects (Catalogues)
• Particle picking in different geometries: filaments, membranes, vesicles.

Materials: data and walkthroughs

The exact contents will be updated here .

Flash presentations

Participants are cordially asked to bring along a short presentation (around 3mins per participant) for the Flash Presentation session on Wednesday. Please send them beforehand or give them to us during the first day, as we need to set them on the same computer.

Andreas Engel
Roberto Melero
Luke Chao
Christian Zimmerli
Jitin Singla
Justin Ooi Seng Geap
Guntur Fibriansah
Hemanth Kumar Narayana Reddy 
Paul Korir
Andrew Michael Burns
Gabriela Condezo
Christoph Pratsch
Martin polak
Barnali Waugh
Oishik Banerji
Olivier Le Bihan
Vanessa Flegler
Wen Yang
Raven Shah
Adrian Hodel
William Close [*]
Yi-Wei Chang [*]
Yanquing Zhang [*] 
Raphaela Seeger [*]
Jack Turner [*] 
Zhexin Wang

External Speakers

Alex Noble, New York Structural Biology Center.

Florian Schur, EMBL, Heidelberg.

Dimitri Tegunov, Max-Planck Institute, Göttingen.

Organizers

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

Mikhail Kudryashev, MPI for Biophysics, Frankfurt.

Henning Stahlberg, 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.

Mikhail Kudryashev, MPI for Biophysics, Frankfurt.

Alex Noble, New York Structural Biology Center.

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

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

Sponsors

Biozentrum of the University of Basel.

CSCS the Swiss Center for Scientific Computing.