Related papers: A field guide to cultivating computational biology
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
While data science has emerged as a contentious new scientific field, enormous debates and discussions have been made on it why we need data science and what makes it as a science. In reviewing hundreds of pieces of literature which include…
This paper draws attention to the potential of computational methods in reworking data generated in past qualitative studies. While qualitative inquiries often produce rich data through rigorous and resource-intensive processes, much of…
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a biological system is a key element of precision medicine. Indeed it allows to tailor diagnostic, prognostic and treatment choice to individual…
Discovery of new knowledge is increasingly data-driven, predicated on a team's ability to collaboratively create, find, analyze, retrieve, and share pertinent datasets over the duration of an investigation. This is especially true in the…
With the advancement of high-throughput biotechnologies, we increasingly accumulate biomedical data about diseases, especially cancer. There is a need for computational models and methods to sift through, integrate, and extract new…
This article sets out our perspective on how to begin the journey of decolonising computational fields, such as data and cognitive sciences. We see this struggle as requiring two basic steps: a) realisation that the present-day system has…
The gradual accumulation of damage and dysregulation during the aging of living organisms can be quantified. Even so, the aging process is complex and has multiple interacting physiological scales -- from the molecular to cellular to whole…
The current disparity in computational knowledge is a critical hindrance to the diversity and success of the field. Recommendations are outlined for policies and funding models to enable the growth and retention of a new generation of…
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,…
Computational scientists are facing a new era where the old ways of developing and reusing code have to be left behind and a few daring steps are to be made towards new horizons. The present work analyzes the needs that drive this change,…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and…
Undergraduate research experiences hold many potential benefits. Students can learn about new areas opening up previously unknown paths in academia and industry. The hands-on experience often provides a deeper understanding of what science,…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base construction and protein structure determination all benefit from human input. In…
The reproduction and replication of novel results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the issues closely revolve around the…
In the world of Information Technology, new computing paradigms, driven by requirements of different classes of problems and applications, emerge rapidly. These new computing paradigms pose many new research challenges. Researchers from…
The number of biomedical research articles published has doubled in the past 20 years. Search engine based systems naturally center around searching, but researchers may not have a clear goal in mind, or the goal may be expressed in a query…
Data is a precious resource in today's society, and is generated at an unprecedented and constantly growing pace. The need to store, analyze, and make data promptly available to a multitude of users introduces formidable challenges in…