Yildiz Ahmet, Dilaveroglu Erkan, Visne Ilhami, Günay Bilal, Sefer Emrah, Weinhausel Andreas, Rattay Frank, Goble Carole A, Pandey Ram Vinay, Kriegner Albert
Health & Environment Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria.
BMC Res Notes. 2014 Oct 20;7:740. doi: 10.1186/1756-0500-7-740.
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.
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.
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.
现有生物信息学工具和服务在功能、输入输出行为及用户界面方面的异质性，仍然是专家用户和非专家用户面临的瓶颈。为这些工具和服务提供通用接口的进展正引起研究人员的兴趣。然而，由于缺乏关于输入输出数据及参数的（元）信息，无法提供自动化和标准化的解决方案来帮助用户设置合适的参数。特别是在基于工作流的解决方案中，必须解决这些限制，以简化软件集成。
我们报告了一个Taverna Workbench插件：XworX BIFI（输入的精美界面），它是针对上述问题的解决方案。BIFI提供了一种图形用户界面（GUI）定义语言，用于布局用户界面并为Taverna工作流定义参数选项。BIFI还能够直接提交GUI定义文件（GDF），或从配置的存储库中发现合适的实例。在没有GDF的情况下，BIFI会生成一个默认界面。
Taverna Workbench是一款开源软件，能够在工作流中组合各种服务。然而，用户只能通过一个简单的用户界面为工作流提供输入数据，该界面仅提供一个文本区域以文本形式输入内容。工作流可能包含人类可读形式的元信息，如端口的描述文本和示例值。然而，并非所有工作流端口都有完善的文档记录或包含所有所需信息。BIFI为端口使用自定义用户界面组件，这些组件会向用户反馈用于服务执行的参数数据类型或结构，并实现客户端数据验证。此外，BIFI提供的用户界面允许用户交互式地构建工作流视图并与社区共享，从而显著提高了异构分布式服务消费的可用性。
