Workflow systems

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Workflows (or other artefacts) do not have to be in a particular format to be uploaded to myExperiment. The Workflows tab summarises the content in myExperiment - you can see the different workflow systems that currently have content on the site.

myExperiment has specific additional support for some of these systems:

This page describes how to add additional types of content.

Registering Workflow Systems in myExperiment

There are three main methods of uploading a workflow, each with differing levels of code support required from the workflow system author and in the assistance given to the end users during the upload process.

1. Register a workflow system via the website and upload the workflow.

This is the simplest method of creating a new content type, but provides the least support to end users uploading workflows.

When uploading a workflow to myExperiment, you choose "Enter custom metadata" and select "Other" in the "Workflow Type" drop down menu. You are then able to provide a title for the kind of workflow you are about to upload. myExperiment is unable to know anything about the workflow system and so during the workflow upload process you then have the option of providing the basic metadata and a preview image for myExperiment to show.

2. Upload a workflow via the REST API

This is similar to (1) except that instead of uploading the workflow via the web interface, the workflow system uses the REST API to provide a direct upload facility. During the upload, the workflow system software can provide the basic metadata and a preview image alongside the actual workflow file. This is explained in the online API documentation.

3. Write a "workflow processor"

This option requires writing code (possibly with support from the development team) that will run on the myExperiment servers so that the web site can automatically extract data from the workflow file. When a workflow is uploaded, it is automatically presented to each workflow processor until one accepts it. The processor is then able to provide basic metadata, workflow previews and offer a decomposition of the workflow for both the REST API and a structured breakdown which is visible in the workflow page. Some workflow systems, such as Taverna, BioExtract and Trident, already use this feature and therefore provide examples.

Note that myExperiment is also able to execute workflows: it can be configured to send workflows to a remote workflow system with a server-based enactor. Taverna 1 workflows can be executed in this way and Taverna 2 will also be supported when the Taverna 2 server becomes available. Other systems can be added using this mechanism. At present this capability is largely used by the myExperiment development team and additional user interface development is likely to be needed for users to run workflows from arbitrary systems.