standardized workflows (i) carlos oscar sorzano techn. director i 2 pc natl. center biotechnology...

Standardized Workflows (I)

Carlos Oscar SorzanoTechn. Director I2PC

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

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

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.

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

A wokflow ontology

Who needs workflows?

What can be achieved?

• Consensuated Workflow Ontology?

• Interchange points (workflow I/O)?Workflow

Interchange Points

Interchange Points needan interchange standard

Specific proposal in the discussion

An interchange standard needsan automatic check of compliance

Conclusions

• Consensuated Workflow Ontology?

• Interchange points (workflow I/O)?

Workflow +