GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components.

Frederique Lisacek,Hugo López-Fernández,Daniel Glez-Peña,Rosalía Laza,Reyes Pavón,Florentino Fdez-Riverola,Miguel Reboiro-Jato

doi:10.1371/journal.pone.0204474

Abstract

Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these applications via their Graphical User Interfaces (GUI) is a key factor for their final success and real utility for researchers. Despite the existence of different packages and applications focused on advanced data visualization, there is a lack of specific libraries providing pertinent GUI components able to help scientific bioinformatics software developers. To that end, this paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development. Within GC4S, developers of new applications can focus on the specific GUI requirements of their projects, relying on GC4S for generalities and abstractions. GC4S is free software distributed under the terms of GNU Lesser General Public License and both source code and documentation are publicly available at http://www.sing-group.org/gc4s

Highlights

The importance of bioinformatics and computational biology in research today is leading to the development of a growing number of complex bioinformatics tools and software packages
All the approaches discussed above highlight how the usability of different types of bioinformatics applications can be improved by adopting well-established practices in usability and software engineering
We provided an overview of the GC4S library and presented three real-world use cases to illustrate its capabilities and usefulness

Summary

Introduction

The importance of bioinformatics and computational biology in research today is leading to the development of a growing number of complex bioinformatics tools and software packages. GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components create the gradient are set programmatically in this example This component has the mouse wheel zooming feature enabled by default, but it can be programmatically disabled. Based on this core component, it is provided the MultipleSequenceAlignmentViewerControl component that presents a MultipleSequenceAlignmentViewerPanel along with a toolbar with different options for the end-users of the visualization. These options are: (i) selecting the tracks model and renderer that are being shown, (ii) changing the viewer configuration through a GUI dialog, and (iii) exporting the view as image or HTML document. The CardsPanel component provides this functionality and it is used in SEDA to display different configuration panels to the user, depending on the selection previously made in a combo box (Fig 17)

Discussion and lessons learned

Conclusions