Related papers: Sustainable Software Development for Next-Gen Sequ…
Developing software to undertake complex, compute-intensive scientific processes requires a challenging combination of both specialist domain knowledge and software development skills to convert this knowledge into efficient code. As…
Like other engineering disciplines, software engineering should also have principles to guide the construction of sustainable computer applications. Tangible properties include a) unlimited scalability, b) maximal reproducibility, and c)…
Data generation is a key issue in big data benchmarking that aims to generate application-specific data sets to meet the 4V requirements of big data. Specifically, big data generators need to generate scalable data (Volume) of different…
The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to…
As quantum computers advance, the complexity of the software they can execute increases as well. To ensure this software is efficient, maintainable, reusable, and cost-effective -key qualities of any industry-grade software-mature software…
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
Achieving the UN Sustainable Development Goals (SDGs) demands adequate levels of awareness and actions to address sustainability challenges. Software systems will play an important role in moving towards these targets. Sustainability skills…
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable…
Concurrent advances across fields such as organoid technology, Microelectrode Arrays (MEAs), neuromorphic computing, and machine learning have given rise to a groundbreaking research paradigm: Synthetic Biological Intelligence (SBI). SBI…
Software has the potential to be a key driver in fostering sustainability. Despite this potential, it is not clear if and how the software industry integrates consideration of sustainability into its common software development processes.…
The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic…
Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant…
In Search Based Software Engineering, Genetic Programming has been used for bug fixing, performance improvement and parallelisation of programs through the modification of source code. Where an evolutionary computation algorithm, such as…
Programming is ubiquitous in applied biostatistics; adopting software engineering skills will help biostatisticians do a better job. To explain this, we start by highlighting key challenges for software development and application in…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Novel compute systems are an emerging research topic, aiming towards building next-generation compute platforms. For these systems to thrive, they need to be provided as research infrastructure to allow acceptance and usage by a large…
Generative AI (GenAI) has recently emerged as a groundbreaking force in Software Engineering, capable of generating code, identifying bugs, recommending fixes, and supporting quality assurance. While its use in coding tasks shows…