Difference between revisions of "Basel Dynamo Workshop 2018"

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=Registration =
 
=Registration =
  
−
A link for registration will be published here on the first of May.
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Use  [https://www.surveymonkey.com/r/PQ22WVL this form] for registration into the '''waiting list'''. Please [mailto:daniel.castano@unibas.ch  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 350 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 =
 
= Program =
 +
 +
The exact time schedule can be consulted [http://{{SERVERNAME}}/w/doc/workshops/2018/Dynamo_programm_2018.pdf here]
 +
 +
== Venue  ==
 +
 +
The workshop will take place in the [http://www.biozentrum.unibas.ch 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 ==
 
== Duration of the course ==
−
The course will start at 14:00 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.  
+
The course will start at 10:30 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.
 +
 
 +
==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  [[Installation|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 ==
 
== Contents ==
−
The final program schedule will be updated here by mid August. As a general guideline, we will cover:
+
The course content can be found [[Materials Basel 2018| here]]. As a general guideline, we will cover:
  
 
* Alignment and reconstruction of tilt series.
 
* Alignment and reconstruction of tilt series.
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* Creation of 3d scenes.
 
* Creation of 3d scenes.
 
* Scripting in ''Dynamo'': gentle introduction to programming.
 
* 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.
 +
 +
* Joshua Hutchings, Birkbeck College, London, UK.
 +
 +
*Dustin Morado, MRC-LMB, Cambridge, UK.
 +
 +
*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==
 +
 +
*[http://www.snf.ch FNS/SNF]  Swiss National Science Foundation.
 +
 +
*[http://www.biozentrum.unibas.ch Biozentrum] of the University of Basel.
 +
 +
*[https://c-cina.unibas.ch/bioem BioEM lab]  at the  [https://c-cina.unibas.ch C-CINA center] of the University of Basel.
 +
 +
*[http://www.cscs.ch/index.html CSCS] the Swiss Center for Scientific Computing.

Latest revision as of 14:26, 27 August 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

Use this form for registration into 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 350 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 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 10:30 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.

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.
  • Joshua Hutchings, Birkbeck College, London, UK.
  • Dustin Morado, MRC-LMB, Cambridge, UK.
  • 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

  • FNS/SNF Swiss National Science Foundation.
  • CSCS the Swiss Center for Scientific Computing.
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