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Cloud computing provides a great opportunity for scientists, as it enables large-scale experiments that cannot are too long to run on local desktop machines. Cloud-based computations can be highly parallel, long running and data-intensive,…
Software ecosystems are collections of projects that are developed and evolve together in the same environment. Existing literature investigates software ecosystems as isolated entities whose boundaries do not overlap and assumes they are…
Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become…
Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities…
Effective treatment of cancer requires early diagnosis which involves the patient's awareness of the early signs and symptoms, leading to a consultation with a health provider, who would then promptly refer the patient for confirmation of…
Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Enumerated threat agent lists have long driven biodefense priorities. The global SARS-CoV-2 pandemic demonstrated the limitations of searching for known threat agents as compared to a more agnostic approach. Recent technological advances…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
Twenty-five years ago the desktop computer started becoming ubiquitous in the scientific lab. Researchers were delighted with its ability to both control instrumentation and acquire data on a single system, but they were not completely…
Scientific workflow has become essential in software engineering because it provides a structured approach to designing, executing, and analyzing scientific experiments. Software developers and researchers have developed hundreds of…
Given the ever-increasing advances of digital microfluidic biochips and their application in a wide range of areas including bio-chemistry experiments, diagnostics, and monitoring purposes like air and water quality control and etc.,…
Production operation of large distributed computing infrastructures (DCI) still requires a lot of human intervention to reach acceptable quality of service. This may be achievable for scientific communities with solid IT support, but it…
Software defect detection is a critical task in software engineering. However, no prior studies have specifically addressed defect detection in bioinformatics software. Given that the performance of defect detection tasks is primarily…
GitHub Copilot is transforming software development by automating tasks and boosting productivity through AI driven code generation. In this paper, we conduct a literature survey to synthesize insights on Copilot's impact on productivity…
Nature is often used to inspire solutions for complex engineering problems, but achieving its full potential is challenging due to difficulties in discovering relevant analogies and synthesizing from them. Here, we present an end-to-end…
One of the ultimate goals of software engineering is to leave virtual spaces and move real things. We take one step toward supporting users with this goal by connecting a type-based synthesis algorithm, (CL)S, and its IDE to a logistics lab…
Development of fast methods to conduct in silico experiments using computational models of cellular signaling is a promising approach toward advances in personalized medicine. However, software-based cellular network simulation has…
While there has been substantial empirical work identifying factors that influence the contribution to, and use of open source software, we have as yet little theory that identifies the key constructs and relationships that would allow us…
Patch reviewing is critical for software development, especially in distributed open-source development, which highly depends on voluntary work, such as Linux. This paper studies the past 10 years of patch reviews of the Linux memory…