Difference between revisions of "Main Page"

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{{DISPLAYTITLE:''Dynamo''}}
 
 
<strong>Wiki is  under construction!!!</strong>
 
  
  
 
''Dynamo'' is a software environment for subtomogram averaging of cryo-EM data.
 
''Dynamo'' is a software environment for subtomogram averaging of cryo-EM data.
  
Our goal is to provide a reliable tool for all kind of users: newcomers needing a mild learning curve, advanced users with lots of data to process as fast as possible, and developers that need a flexible framework to test new ideas and algorithms.
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This wiki [[Getting started|guides new ''Dynamo'' users]] all the way from tomograms to averages and classes. In a full workflow, you would  organize tomograms in [[Catalogue | catalogues]], use them to  [[Particle picking|pick particles]] and create [[Subtomogram alignment|alignment]] and [[Classification |classification projects]] to be run on different [[computing environments]].
 
 
 
 
This wiki guides ''Dynamo'' users all the way from tomograms to averages and classes. In a full workflow, you would  organize tomograms in [[Catalogue | catalogues]], use them to  [[Particle picking|pick particles]], then create [[Subtomogram alignment|alignment projects]], or even [[Classification | classification projects]].
 
 
 
You don't need to perform the full workflow with ''Dynamo''. ''Dynamo'' is very modular, and with a basic understanding of the [[formats]] of each of those stages, you can jump to the module that carries the analysis part of your interest.
 
 
 
 
 
For downloads of the software, please use our older website [http://www.dynamo-em.org] instead. This will require logging in.
 
  
Please cite this paper if ''Dynamo'' is useful in your research:
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Please cite these papers if ''Dynamo'' is useful in your research:
[http://www.ncbi.nlm.nih.gov/pubmed/22245546|''Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.''] Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H., J Struct Biol. 2012 Jan 8.
 
  
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* [http://www.sciencedirect.com/science/article/pii/S1047847711003650|''Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.''] Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H., J Struct Biol. 2012.
  
== About this wiki==
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* [http://www.sciencedirect.com/science/article/pii/S1047847716301113| ''Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms''] Castaño-Díez D, Kudryashev M,  Stahlberg H., in J Struct Biol. 2017 Feb; 197(2):135-144
  
Whenever you see the mark T.B.I. : ''to be implemented''. If you see this mark on any described functionality, this means that this is probably not in your ''Dynamo'' version, but is under development on our side. If the described functionality might be of interest for you, this might be a good moment to contact us to describe how you would use it, so that we can try to design the tool in a compatible way.
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* [https://doi.org/10.1107/S2059798317003369''The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services''] Castaño-Díez D. in Acta Crystallographica Section D: Structural Biology 73 (6).

Latest revision as of 16:10, 17 May 2017


Dynamo is a software environment for subtomogram averaging of cryo-EM data.

This wiki guides new Dynamo users all the way from tomograms to averages and classes. In a full workflow, you would organize tomograms in catalogues, use them to pick particles and create alignment and classification projects to be run on different computing environments.

Please cite these papers if Dynamo is useful in your research: