Difference between revisions of "Dynamo Workshop CIC bioGUNE 2020"
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| − | The | + | The Bilbao ''Dynamo'' workshop 2020 will take place from April the 29th to April the 30th at 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. | + | The workshop provides an introductory 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. |
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== Registration fee== | == Registration fee== | ||
| − | Participants will be asked to confirm their registration with the payment of a fee of | + | Participants will be asked to confirm their registration with the payment of a fee of 100 EUR (500 EUR for industry), which covers registration and meals during the workshop. |
== Accommodation == | == 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. | + | Please note that the travel and lodging are '''not''' covered in the workshop registration fee and participants will have to arrange it by themselves. |
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= Program = | = Program = | ||
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== Venue == | == Venue == | ||
| − | The workshop will take place in the | + | The workshop will take place in the computing room of the CIC-Biogune. |
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== Duration of the course == | == Duration of the course == | ||
| − | The course will start at 9: | + | The course will start at 9:00 on the 29th of April. Last presentation will be at 17h00 on the 30th of April. |
==Computing facilities== | ==Computing facilities== | ||
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= Organization= | = Organization= | ||
==Organizers== | ==Organizers== | ||
| − | + | *Daniel Castaño-Díez, BioEM lab, University of Basel, Switzerland. | |
*Aitor Hierro, CIC-Biogune, Bilbao, Spain. | *Aitor Hierro, CIC-Biogune, Bilbao, Spain. | ||
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*Adriana Rojas, CIC-Biogune, Bilbao, Spain. | *Adriana Rojas, CIC-Biogune, Bilbao, Spain. | ||
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==Instructors== | ==Instructors== | ||
| − | + | *Soledad Baños, CIC-Biogune, Bilbao, Spain. | |
| + | *Alister Burt, ILL, Grenoble, France. | ||
*Daniel Castaño-Díez, BioEM Lab, University of Basel, Switzerland. | *Daniel Castaño-Díez, BioEM Lab, University of Basel, Switzerland. | ||
| − | * | + | * Carlos López, CIC-Biogune, Bilbao, Spain |
| + | * Isaac Santos, CIC-BIogune, Bilbao, Spain | ||
*Stefano Scaramuzza, C-CINA, University of Basel, Switzerland. | *Stefano Scaramuzza, C-CINA, University of Basel, Switzerland. | ||
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==Sponsors== | ==Sponsors== | ||
*[http://www.snf.ch FNS/SNF] CIC-Biogune. | *[http://www.snf.ch FNS/SNF] CIC-Biogune. | ||
*[http://www.snf.ch FNS/SNF] Swiss National Science Foundation. | *[http://www.snf.ch FNS/SNF] Swiss National Science Foundation. | ||
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Revision as of 14:08, 24 January 2020
The Bilbao Dynamo workshop 2020 will take place from April the 29th to April the 30th at the Biozentrum of the University of Basel.
The workshop provides an introductory 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.
Contents
Registration
Use this form for registration in the waiting list. 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 a fee of 100 EUR (500 EUR 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.
Program
The exact time schedule can be consulted will be published here.
Venue
The workshop will take place in the computing room of the CIC-Biogune.
Duration of the course
The course will start at 9:00 on the 29th of April. Last presentation will be at 17h00 on the 30th of April.
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, University of Basel, Switzerland.
- Aitor Hierro, CIC-Biogune, Bilbao, Spain.
- Adriana Rojas, CIC-Biogune, Bilbao, Spain.
Instructors
- Soledad Baños, CIC-Biogune, Bilbao, Spain.
- Alister Burt, ILL, Grenoble, France.
- Daniel Castaño-Díez, BioEM Lab, University of Basel, Switzerland.
- Carlos López, CIC-Biogune, Bilbao, Spain
- Isaac Santos, CIC-BIogune, Bilbao, Spain
- Stefano Scaramuzza, C-CINA, University of Basel, Switzerland.
