Standardized Workflows (I) Carlos Oscar Sorzano Techn. Director I 2 PC Natl. Center Biotechnology (CSIC)

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Standardized Workflows (II) Carlos Oscar Sorzano Techn. Director I 2 PC Natl. Center Biotechnology (CSIC)

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Presentation transcript:

Standardized Workflows (I) Carlos Oscar Sorzano Techn. Director I 2 PC Natl. Center Biotechnology (CSIC)

What is a workflow? Workflow Input image Output image Workflow

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.

What is a workflow instance? Low pass filter in Xmipp with transition band Set Of 2D Images Low pass freq Transition bandwidth Low pass filter in Xmipp with Gaussian shape Set Of 2D Images Freq. Sigma

Can we generalize? Preprocessing 2D Set Of 2D Images Workflow Workflow instance Normalization 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.

A wokflow ontology We can define a workflow hierarchy.

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.

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.

A wokflow ontology

Who needs workflows?

What can be achieved? Consensuated Workflow Ontology? Interchange points (workflow I/O)? Workflow

Interchange Points

Interchange Points need an interchange standard Specific proposal in the discussion

An interchange standard needs an automatic check of compliance

Conclusions Consensuated Workflow Ontology? Interchange points (workflow I/O)? Workflow +