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Standardized Workflows (I)
Carlos Oscar SorzanoTechn. Director I2PC
Natl. Center Biotechnology (CSIC)
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What is a workflow?
Workflow
Input image
Output image
Workflow
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What is a workflow instance?
3D Reconstruction with reference volume in Xmipp
Set Of Images
Reconstructed volume
Common lines in EMAN
A workflow instance is a sequence of steps with some inputs and some outputs that implements a specific logical operation.
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What is a workflow instance?
Low pass filter in Xmipp with transition band
Set Of 2D Images
Set Of 2D Images
Low pass freq Transition bandwidth
Low pass filter in Xmipp with Gaussian shape
Set Of 2D Images
Set Of 2D Images
Freq. Sigma
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Can we generalize?
Preprocessing 2D
Set Of 2D Images
Set Of 2D Images
Workflow Workflow instanceNormalization
Cropping
…A workflow is an abstraction of a set of workflow instances (implementing the same logical action) covering the common set of inputs and outputs.
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A wokflow ontology
We can define a workflow hierarchy.
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Who needs workflows?• Individual packages to define their own “image processing” workflow.
Normally, the definition of the workflow is implicit or informal from a programmatic point of view.
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Who needs workflows?• Integrative platforms to connect pieces from different
packages. Normally, the definition of the workflow is explicit.
Integrative platforms are automating what users have been manually doing for a long time.
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A wokflow ontology
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A wokflow ontology
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Who needs workflows?
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What can be achieved?
• Consensuated Workflow Ontology?
• Interchange points (workflow I/O)?Workflow
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Interchange Points
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Interchange Points needan interchange standard
Specific proposal in the discussion
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An interchange standard needsan automatic check of compliance
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Conclusions
• Consensuated Workflow Ontology?
• Interchange points (workflow I/O)?
Workflow +