Difference between revisions of "Dynamo workshop 2017"
| (37 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | |||
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. | 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== | ==Registration== | ||
| − | + | ||
| + | '''The event is closed.''' | ||
| + | |||
| + | <!-- Use [https://www.surveymonkey.com/r/CQYTVF3 this link for registration]. Please [mailto:daniel.castano@unibas.ch 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== | ==Venue== | ||
The workshop will take place from the 23th to the 25th of August in the [http://www.biozentrum.unibas.ch Biozentrum] of the University of Basel. | The workshop will take place from the 23th to the 25th of August in the [http://www.biozentrum.unibas.ch Biozentrum] of the University of Basel. | ||
| − | Practical lectures | + | 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) | * Lunch vouchers are valid in the canteen of the Hospital (close to the Biozentrum) | ||
| − | * Interested participants can visit the CINA | + | * Interested participants can visit the CINA facilities on Friday afternoon. |
==Travel and Lodging== | ==Travel and Lodging== | ||
| Line 26: | Line 29: | ||
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. | 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 [[Computers Basel 2017 | '''through these guidelines''' ]] | |
| − | |||
==Program== | ==Program== | ||
| − | The program | + | The program can be downloaded [http://{{SERVERNAME}}/w/doc/workshops/2017/Dynamo_programm_2017.pdf here]. We will cover: |
* Creation of alignment projects. | * Creation of alignment projects. | ||
* Creation of classification projects. | * Creation of classification projects. | ||
| Line 38: | Line 40: | ||
===Materials: data and walkthroughs === | ===Materials: data and walkthroughs === | ||
| − | The exact contents | + | The exact contents will be updated [[Materials Basel 2017 | '''here''' ]]. |
==Flash presentations== | ==Flash presentations== | ||
| − | Participants are | + | 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. |
| + | |||
| + | <nowiki>Yi-Wei Chang | ||
| + | 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 | ||
| + | Jack Turner | ||
| + | Yanquing Zhang [*] | ||
| + | Raphaela Seeger [*] | ||
| + | Zhexin Wang [*] </nowiki> | ||
| − | + | ==External Speakers== | |
| + | Alex Noble, New York Structural Biology Center. | ||
| + | |||
| + | Florian Schur, EMBL, Heidelberg. | ||
| + | |||
| + | Dimitri Tegunov, Max-Planck Institute, Göttingen. | ||
==Organizers== | ==Organizers== | ||
| Line 64: | Line 97: | ||
Mikhail Kudryashev, MPI for Biophysics, Frankfurt. | 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. | Stefano Scaramuzza, C-CINA, University of Basel, Switzerland. | ||
| − | |||
==Sponsors== | ==Sponsors== | ||
Latest revision as of 09:05, 27 August 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.
Contents
Registration
The event is closed.
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.
Yi-Wei Chang 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 Jack Turner Yanquing Zhang [*] Raphaela Seeger [*] 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.
