BIFI: a Taverna plugin for a simplified and user-friendly workflow platform

Abstract

Background: Heterogeneity in the features, input-output behaviour and user interface for available bioinformatics tools and services is still a bottleneck for both expert and non-expert users. Advancement in providing common interfaces over such tools and services are gaining interest among researchers. However, the lack of (meta-) information about input-output data and parameter prevents to provide automated and standardized solutions, which can assist users in setting the appropriate parameters. These limitations must be resolved especially in the workflow-based solution in order to ease the integration of software.

Findings: We report a Taverna Workbench plugin: the XworX BIFI (Beautiful Interfaces for Inputs) implemented as a solution for the aforementioned issues. BIFI provides a Graphical User Interface (GUI) definition language used to layout the user interface and to define parameter options for Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF) directly or discover appropriate instances from a configured repository. In the absence of a GDF, BIFI generates a default interface.

Conclusion: The Taverna Workbench is an open source software providing the ability to combine various services within a workflow. Nevertheless, users can supply input data to the workflow via a simple user interface providing only a text area to enter the input in text form. The workflow may contain meta-information in human readable form such as description text for the port and an example value. However, not all workflow ports are documented so well or have all the required information.BIFI uses custom user interface components for ports which give users feedback on the parameter data type or structure to be used for service execution and enables client-side data validations. Moreover, BIFI offers user interfaces that allow users to interactively construct workflow views and share them with the community, thus significantly increasing usability of heterogeneous, distributed service consumption.

Figure 1

A simple Taverna workflow. The Graph of a simple workflow from The Taverna Workbench consisting of two workflow input ports, one processor and one workflow output port.

Figure 2

Taverna dialog for WIP. A screenshot of the Taverna workbench shows the input dialog to enter the data for WIPs. It provides only a text area to enter the input in text form.

Figure 3

An example port definition and generated UI. An outline of a port definition and the generated user interface component using it.

Figure 4

Comparison of example workflow 2 opened with and without using GDF. Example Workflow 2 consists of an R script with 5 input ports. BIFI is able to generate user interfaces for two of the ports automatically (right) if no GDF is found in the repository. But other ports can be mapped to more meaningful components with appropriate options (left) using GDF.

Figure 5

A simple workflow user interface by BIFI. A simple workflow user interface generated by BIFI. The GUI description file contains the default values and details about the workflow. With example values already set, the workflow is ready to run with a simple click.

Figure 6

The BIFI design component. The BIFI design component allows the user to modify the workflow view or change default values for the ports interactively.

Figure 7

Buttons of BIFI workflow user interface. BIFI provides tree buttons on top of WUI. Using the all parameters button users can enable all the ports in the workflow, not only defaults. To start execution using the BIFI Plugin inputs, users should use Run button provided by the BIFI Plugin. The Submit button shows the dialog to submit user interface options to the repository.

Figure 8

The first part of the workflow graph for Example Workflow 1. Some of the processor input ports have WIPs linked to them, some of them have not.

Figure 9

Mime-type to user interface mapping. Predictors determine which UI component to use for a specific port by using data from processors and predicting the corresponding data types (mime type). BIFI looks for the default UI for the given data type in the mapping table and creates it for the given port.

Figure 10

Comparison of WUIs of example Workflow 1 automatically built using wsdl-artifact provided by the Taverna Workbench and the BIFI Plugin. BIFI generated workflow user interface for setting input data for Example Workflow 1 (left) using Taverna wsdl-generic artifact and (right) using the extended BIFI wsdl-generic artifact.