Difference between revisions of "Main Page"

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<strong>Wiki is  under construction!!!</strong>
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{{DISPLAYTITLE:''Dynamo''}}
  
  
Hello there!
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''Dynamo'' is a software environment for subtomogram averaging of cryo-EM data.
  
The wiki-style ''Dynamo'' documentation is under construction.
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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]].
  
For downloads of the software, please use our current website [http://www.dynamo-em.org] instead.
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= Participate =
  
This wiki will guide ''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]].
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There is a [[https://groups.google.com/forum/#!forum/dynamo-for-cryo-electron-tomography/join forum in Google Groups]] where you can present your questions to developers and other users.
  
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.
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= Cite =
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Please cite these papers if ''Dynamo'' is useful in your research:
  
{{main|getting started|start here}}
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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
  
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).
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* [https://doi.org/10.3389/fmolb.2018.00082''Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package''] Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol. Biosci. 5:82.

Revision as of 14:59, 25 September 2019


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.

Participate

There is a [forum in Google Groups] where you can present your questions to developers and other users.

Cite

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