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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…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Advances in science are being sought in newly available opportunities to collect massive quantities of data about complex systems. While key advances are being made in detailed mapping of systems, how to relate this data to solving many of…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
High performance computing (HPC) devices is no longer exclusive for academic, R&D, or military purposes. The use of HPC device such as supercomputer now growing rapidly as some new area arise such as big data, and computer simulation. It…
The traditional foundation of science lies on the cornerstones of theory and experiment. Theory is used to explain experiment, which in turn guides the development of theory. Since the advent of computers and the development of…
The rapid evolution of intelligent electronic devices makes information technology, computer science and electronics strongly related to the teaching of natural sciences. Today almost everybody has a smart phone that can convert light,…
We present our ongoing work building a Raspberry Pi cluster consisting of 300 nodes. The unique characteristics of this single board computer pose several challenges, but also offer a number of interesting opportunities. On the one hand, a…
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"…
Microbiome studies have recently transitioned from experimental designs with a few hundred samples to designs spanning tens of thousands of samples. Modern studies such as the Earth Microbiome Project (EMP) afford the statistics crucial for…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
Freely and openly shared low-cost electronic applications, known as open electronics, have sparked a new open-source movement, with much un-tapped potential to advance scientific research. Initially designed to appeal to electronic…
Applications integrating analysis components require a programmable interface which defines statistical operations independently of any programming language. By separating concerns of scientific computing from application and implementation…
We have evolved an IT system that is ubiquitous and pervasive and integrated into most aspects of our lives. Many of us are working on 4th and 5th level refinements in efficiency and functionality. But, we stand on the shoulders of those…
With increased access to data and the advent of computers, the use of statistical tools and numerical simulations is becoming commonplace for ecologists. These approaches help improve our understanding of ecological phenomena and their…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
In this report, I describe the design and implementation of an inexpensive, eight node, 32 core, cluster of raspberry pi single board computers, as well as the performance of this cluster on two computational tasks, one that requires…