About Workflows

The quantity and heterogeneity of data in the biodiversity sciences have given rise to many distributed resources. Typically, researchers wish to combine these resources into multi-step computational tasks for a range of analytical purposes. Workflows, made of modularised units that can be repeated, shared, reused and repurposed, offer a practical solution for this task.

Workflows are widely adopted as a practical way of carrying out in-silico analysis of relevant data and in-silico experimentation; for example, in bioinformatics and next-generation sequencing, in astronomy and physics, and in digitisation and digital preservation. The process of composing and executing complex sequences of digital data manipulations and modelling tasks allows both automation of routine tasks and pursuit of novel, large-scale analysis which, up until now, have been time-consuming to administer manually. Workflows represent a way of speeding up scientific advance when that advance is based on the manipulation of digital data (Gil, Deelman et al. 2007).

workflowdiagramcropped

A workflow in the Taverna Workbench
 

Design and construct
The Taverna Workbench provides a graphical environment where researchers can design and construct new analysis pipelines, or customise existing ones, before they are 
deployed and shared through the BioVeL Portal and myExperiment. New tools and services can be discovered through the BiodiversityCatalogue. Plug-and-play components simplify workflow construction. Workflow components are modularised units that are well-documented and designed to be used as steps in other workflows.

Run
Workflows are executed through the Taverna Server hidden behind the BioVeL Portal, a simple Web interface that provides access to a pool of ready-made workflows and allows you to manage, share and save workflow runs' results. You can monitor and interact with running workflows through the Portal, changing parameters and directing your analyses.

Share and discover
myExperiment is a social network and repository for users to publish, share, and discover workflows and workflow components. You can search and discover workflows from myExperiment through the Taverna workbench and the BioVeL portal. This means you have access to a large pool of existing methods to reuse or customise.

Example of creating a workflowdiagram1wfobst1vertical

Study on the ecological niche of the south-east Asian horseshoe crab, (Carcinoscorpius rotundicauda), an endangered species:
• Import south east Asian data from external library
• Apply succession of processing steps (made up of “services 1, 2, to X”), = “workflow”
• Result: ecological niche map

Showcase study 1: create a workflow*

Study on the ecological niche of the south east Asian horseshoe crab, an endangered species:
• Import south east Asian data from external library
• Apply succession of “services” = workflow
• Result: ecological niche map

Showcase study 2: re-use a workflow

Study on the ecological niche of the American horseshoe crab
• Import American data
• Re-use south east Asia crab study workflow
• Result: ecological niche map for American horseshoe crab
Compare the ecological niches of the south east Asian and American crabs.

diagram2wfobstafricavertical-18Potential study of the ecological niche of an African animal
• Import African data
• Re-use horseshoe crab study workflow
• Result: ecological niche map for African animal

 

 

 dolkhale3cropped

 

 

 

*Maps and horseshoe crab photo: courtesy Matthias Obst, University of Gothenburg, Sweden



FernTrees0127

biovel-video-screenshot

News

19 February 2015

At the final review of the project by the EC, one of the reviewers said: “Incredible work done with a community that is not unified. Remarkable work. It opens for new development in a near future. Hope for success. Good project. Happy that you have been financed three plus years ago.”

Read all about the project and its results in the Project Final Report or read the Executive Summary only.