Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm

Abstract

Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (“ Butterfly” paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions.

Ant-App-DB: a smart solution for monitoring arthropods activities, experimental data management and solar calculations without GPS in behavioral field studies

“…Ant-App-DB is a well-developed application, following the principles of three layered Butterfly 29,30 software development model towards scientific software engineering (SSE), integrating formal Unified Modelling Language (UML) 31,32 perspectives and incorporating Human Computer Interaction (HCI) design patterns.…”

The Lens of the Lab: Design Challenges in Scientific Software

“…Sometimes, developers decide for an "amethodological" approach (Kelly 2015). Methodologies tailored to SS have been outlined a number of times (Platz 1986;Pereira Junior 2007;Ahmed, Zeeshan, and Dandekar 2014), often emphasizing neglected (or difficult) aspects such as requirements, testing, and design (Cort et al 1985). As early as 1986, Platz (1986) observed the need to balance SE measures with creative freedom.…”

“…Recent approaches to SS development put interface design as a priority by valuing the interface designer's perspective (Mohammad 2010). The Butterfly development model, for instance, pays attention to interface design from early development stages, aiming at ease of use and learning by understanding user psychology, scientific domains, work environment, and HCI principles and patterns (Ahmed, Zeeshan, Dandekar 2014). The recent proposition for a "tool science" discipline, dedicated to SS development and teaching, recommends the improvement of usability through case study research, comparison of similar tools, and gamification.…”

“…Keefe also emphasizes the importance of tool evaluation from scientific domain experts; the need to prioritize accuracy over speed of use; and the presence of interaction requirements such as selection, navigation, and annotation. Ahmed, Zeeshan, and Dandekar (2014) argue that interface design should be guided by HCI principles of experimentation, contextualization, iteration, and empirical measurement. Their study proposes a comprehensive design process including the production of mockups, brainstorming, and prototyping informed by HCI design patterns (Ahmed, Zeeshan, and Dandekar 2014).…”

Untitled

“…3). I-ATAC is a platform designed by following software engineering principles for the sustainable bioinformatics software implementation (Ahmed et al, 2014). It is a Java based desktop application, which requires Java Runtime Environment and all integrated applications to be installed in data cluster (or local computer) as well as the reference genomes that will be used for the alignment.…”