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Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research…

The performance of brain-computer interfaces (BCIs) improves with the amount of available training data, the statistical distribution of this data, however, varies across subjects as well as across sessions within individual subjects,…

The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…

Ascertaining reproducibility of scientific experiments is receiving increased attention across disciplines. We argue that the necessary skills are important beyond pure scientific utility, and that they should be taught as part of software…

Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly…

The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…

Knowledge bases are prevalent in various domains and have been widely used in a large number of real applications such as applications in online encyclopedia, social media, biomedical fields, bibliographical networks. Due to their great…

The web does not only enable new forms of science, it also creates new possibilities to study science and new digital scholarship. This paper brings together multiple perspectives: from individual researchers seeking the best options to…

The need for high availability and performance in data management systems has been fueling a long running interest in database replication from both academia and industry. However, academic groups often attack replication problems in…

As researchers strive to narrow the gap between machine intelligence and human through the development of artificial intelligence technologies, it is imperative that we recognize the critical importance of trustworthiness in open-world,…

This work-in-progress research paper explores the effectiveness of tutorials in interdisciplinary learning environments, specifically focusing on bioinformatics. Tutorials are typically designed for a single audience, but our study aims to…

Bioelectrical interfaces represent a significant evolution in the intersection of nanotechnology and biophysics, offering new strategies for probing and influencing cellular processes. These systems capitalize on the subtle but powerful…

Documentation is one of the most neglected activities in Software Engineering, although it is an important method of assuring quality and understanding. Bioinformatics software is generally written by researchers from fields other than…

Sharing artifacts -- such as trained models, pre-built indexes, and the code to use them -- aids in reproducibility efforts by allowing researchers to validate intermediate steps and improves the sustainability of research by allowing…

Machine learning strategies like multi-task learning, meta-learning, and transfer learning enable efficient adaptation of machine learning models to specific applications in healthcare, such as prediction of various diseases, by leveraging…

The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…

As an emerging interaction paradigm, physiological computing is increasingly being used to both measure and feed back information about our internal psychophysiological states. While most applications of physiological computing are designed…

Systematically developing high--quality reusable software components is a difficult task and requires careful design to find a proper balance between potential reuse, functionalities and ease of implementation. Extendibility is an important…

Information integration plays a pivotal role in biomedical studies by facilitating the combination and analysis of independent datasets from multiple studies, thereby uncovering valuable insights that might otherwise remain obscured due to…