scholarly journals Improving bioinformatics software quality through incorporation of software engineering practices

2022 ◽  
Vol 8 ◽  
pp. e839
Author(s):  
Adeeb Noor
Keyword(s):  
Software Engineering ◽  
Software Development ◽  
Software Quality ◽  
Formal Education ◽  
Scientific Software ◽  
Cultural Changes ◽  
Bioinformatics Software ◽  
Software Engineers ◽  
Engineering Practices

Background Bioinformatics software is developed for collecting, analyzing, integrating, and interpreting life science datasets that are often enormous. Bioinformatics engineers often lack the software engineering skills necessary for developing robust, maintainable, reusable software. This study presents review and discussion of the findings and efforts made to improve the quality of bioinformatics software. Methodology A systematic review was conducted of related literature that identifies core software engineering concepts for improving bioinformatics software development: requirements gathering, documentation, testing, and integration. The findings are presented with the aim of illuminating trends within the research that could lead to viable solutions to the struggles faced by bioinformatics engineers when developing scientific software. Results The findings suggest that bioinformatics engineers could significantly benefit from the incorporation of software engineering principles into their development efforts. This leads to suggestion of both cultural changes within bioinformatics research communities as well as adoption of software engineering disciplines into the formal education of bioinformatics engineers. Open management of scientific bioinformatics development projects can result in improved software quality through collaboration amongst both bioinformatics engineers and software engineers. Conclusions While strides have been made both in identification and solution of issues of particular import to bioinformatics software development, there is still room for improvement in terms of shifts in both the formal education of bioinformatics engineers as well as the culture and approaches of managing scientific bioinformatics research and development efforts.

scholarly journals Software engineering practices for scientific software development: A systematic mapping study

2021 ◽  
Vol 172 ◽  
pp. 110848
Author(s):  
Elvira-Maria Arvanitou ◽  
Apostolos Ampatzoglou ◽  
Alexander Chatzigeorgiou ◽  
Jeffrey C. Carver
Keyword(s):  
Software Engineering ◽  
Software Development ◽  
Systematic Mapping Study ◽  
Mapping Study ◽  
Scientific Software ◽  
Systematic Mapping ◽  
Engineering Practices

scholarly journals Recent advances in biomedical simulations: a manifesto for model engineering

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 261 ◽  
Author(s):  
Joseph L. Hellerstein ◽  
Stanley Gu ◽  
Kiri Choi ◽  
Herbert M. Sauro
Keyword(s):  
Software Engineering ◽  
Simulation Models ◽  
Version Control ◽  
Research Directions ◽  
Control Error ◽  
Cellular Processes ◽  
Software Engineers ◽  
Engineering Practices ◽  
Software Engineering Tools

Biomedical simulations are widely used to understand disease, engineer cells, and model cellular processes. In this article, we explore how to improve the quality of biomedical simulations by developing simulation models using tools and practices employed in software engineering. We refer to this direction as model engineering. Not all techniques used by software engineers are directly applicable to model engineering, and so some adaptations are required. That said, we believe that simulation models can benefit from software engineering practices for requirements, design, and construction as well as from software engineering tools for version control, error checking, and testing. Here we survey current efforts to improve simulation quality and discuss promising research directions for model engineering.

An Analysis of Process Characteristics for Developing Scientific Software

2011 ◽  
Vol 23 (4) ◽  
pp. 64-79 ◽  
Author(s):  
Diane Kelly
Keyword(s):  
Software Engineering ◽  
Software Development ◽  
Professional Training ◽  
Scientific Software ◽  
Development Environment ◽  
Engineering Development ◽  
Development Processes ◽  
Agile Software ◽  
Development Methods ◽  
Software Development Methods

The development of scientific software is usually carried out by a scientist who has little professional training as a software developer. Concerns exist that such development produces low-quality products, leading to low-quality science. These concerns have led to recommendations and the imposition of software engineering development processes and standards on the scientists. This paper utilizes different frameworks to investigate and map characteristics of the scientific software development environment to the assumptions made in plan-driven software development methods and agile software development methods. This mapping exposes a mismatch between the needs and goals of scientific software development and the assumptions and goals of well-known software engineering development processes.

scholarly journals Towards Specific Software Engineering Practices for Early-Stage Startups

2020 ◽  
pp. 18-22
Author(s):  
Jorge Melegati ◽  
Rafael Chanin ◽  
Afonso Sales ◽  
Rafael Prikladnicki
Keyword(s):  
Software Engineering ◽  
Software Development ◽  
Early Stage ◽  
Position Paper ◽  
Market Driven ◽  
Engineering Practices ◽  
Software Development Practices

Abstract In this position paper, our goal is to argue the need for specific software development practices to early-stage startups. In order to reach this goal, we discuss the consequences of innovative and market-driven contexts, which are two of the key elements when describing software startups. We also argue that these practices could be applied to innovative initiatives within established companies since they share similar characteristics and challenges as those from startups.

Boosting the Competitiveness of Organizations With the Use of Software Engineering

2021 ◽  
pp. 198-216
Author(s):  
Mirna Muñoz
Keyword(s):  
Software Engineering ◽  
Software Development ◽  
Software Quality ◽  
Development Process ◽  
Research Work ◽  
Software Development Process ◽  
The Core ◽  
Development Organizations ◽  
Technological Base ◽  
The One

Software has become the core of organizations in different domains because the capacity of their products, systems, and services have an increasing dependence on software. This fact highlights the research challenges to be covered by computer science, especially in the software engineering (SE) area. On the one way, SE is in charge of covering all the aspects related to the software development process from the early stages of software development until its maintenance and therefore is closely related to the software quality. On the other hand, SE is in charge of providing engineers able to provide technological-base solutions to solve industrial problems. This chapter provides a research work path focused on helping software development organizations to change to a continuous software improvement culture impacting both their software development process highlighting the human factor training needs. Results show that the implementation of best practices could be easily implemented if adequate support is provided.

scholarly journals Coordinate Free Programming of Computational Fluid Dynamics Problems

2000 ◽  
Vol 8 (4) ◽  
pp. 211-230 ◽  
Author(s):  
Philip W. Grant ◽  
Magne Haveraaen ◽  
Michael F. Webster
Keyword(s):  
Fluid Dynamics ◽  
Computational Fluid Dynamics ◽  
Software Engineering ◽  
Software Development ◽  
Coordinate Systems ◽  
Scientific Applications ◽  
Software Modules ◽  
The Difference ◽  
Engineering Practices ◽  
Dynamics Problems

It has long been acknowledged that the development of scientific applications is in need of better software engineering practices. Here we contrast the difference between conventional software development of CFD codes with a method based on coordinate free mathematics. The former approach leads to programs where different aspects, such as the discretisation technique and the coordinate systems, can get entangled with the solver algorithm. The latter approach yields programs that segregate these concerns into fully independent software modules. Such considerations are important for the construction of numerical codes for practical problems. The two approaches are illustrated on the coating problem: the simulation of coating a wire with a polymer.

Ethics in Software Engineering

2009 ◽  
pp. 2795-2802
Author(s):  
Pankaj Kamthan
Keyword(s):  
Software Engineering ◽  
Software Quality ◽  
Public Interest ◽  
Code Of Ethics ◽  
Future Research ◽  
Bottom Line ◽  
Daily Lives ◽  
Human Value ◽  
Legal Implications ◽  
Software Engineers

As software becomes pervasive in our daily lives, its values from a purely human perspective are brought to light. Ethical conduct is one such human value. There are various reasons for discussing the issue of ethics within a software engineering context. By participating in a software development process, software engineers can influence the final product, namely the software itself, in different ways including those that may be contrary to public interest. In other words, they could engage in an unethical behavior, inadvertently or deliberately. This could lead to personal harm, and potentially result in loss of confidence in software and loss of trust in organizations that own them. This can adversely affect the acceptance of software as a useful product, question the credibility of software engineering as a profession, lead to legal implications, and impact the bottom line of the software industry at-large. This article is organized as follows. We first outline the background necessary for later discussion. This is followed by a proposal for a quality-based framework for addressing ethics, and software quality treatment of a software engineering code of ethics. Next, avenues and directions for future research are outlined, and finally, concluding remarks are given.

Software Engineering and Software Quality Management

2014 ◽  
Vol 926-930 ◽  
pp. 2642-2645
Author(s):  
Wen Hong Liu ◽  
Chun Yan Wang ◽  
Li Ge
Keyword(s):  
Software Engineering ◽  
Quality Management ◽  
Software Quality ◽  
Software Reliability ◽  
Rapid Development ◽  
High Quality ◽  
Software Products ◽  
Software Quality Management ◽  
Management Method

As the rapid development of social informatization, software reliability and security are highly required. Only applying high-quality software products can increase work efficiency. Quality is the life of software. How to enhance the quality of software products and how to use effective quality management method is an urgent need. This paper discuss the key point of software engineering and software quality management, and this is the basis of software quality ensurance model.

Teaching Agile Software Development Quality Assurance

2009 ◽  
pp. 2700-2713
Author(s):  
Orit Hazzan ◽  
Yael Dubinsky
Keyword(s):  
Quality Assurance ◽  
Software Engineering ◽  
Software Development ◽  
Software Quality ◽  
Agile Software Development ◽  
Specific Teaching ◽  
Quality Issues ◽  
Agile Software ◽  
Software Development Environments ◽  
The Way

This chapter presents a teaching framework for agile quality—that is, the way quality issues are perceived in agile software development environments. The teaching framework consists of nine principles, the actual implementation of which is varied and should be adjusted for different specific teaching environments. This chapter outlines the principles and addresses their contribution to learners’ understanding of agile quality. In addition, we highlight some of the differences between agile software development and plan-driven software development in general, and with respect to software quality in particular. This chapter provides a framework to be used by software engineering instructors who wish to base students learning on students’ experiences of the different aspects involved in software development environments.

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