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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…

Workflows are among the most commonly used tools in a variety of execution environments. Many of them target a specific environment; few of them make it possible to execute an entire workflow in different environments, e.g. Kubernetes and…

Simulation-driven development of intelligent machines benefits from artificial terrains with controllable, well-defined characteristics. However, most existing tools for terrain generation focus on artist-driven workflows and visual…

We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data…

Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…

In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that…

Interactive systems are commonly prototyped as web applications. This approach enables studies with functional prototypes on a large scale. However, setting up these studies can be complex due to implementing experiment procedures,…

Keeping up with research and finding related work is still a time-consuming task for academics. Researchers sift through thousands of studies to identify a few relevant ones. Automation techniques can help by increasing the efficiency and…

Clinicians often face workflow problems that are perceived as either too bespoke or low stakes to attract commercial attention. Historically, most do not have the technical knowledge to address these problems, but the recent emergence of…

Visual programming has the potential of providing novice programmers with a low-code experience to build customized processing pipelines. Existing systems typically require users to build pipelines from scratch, implying that novice users…

In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance.…

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…

We present an application, Superplot, for calculating and plotting statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space, produced by e.g. MultiNest. A simple graphical interface…

Hybrid systems are increasingly used in critical applications such as medical devices, infrastructure systems, and autonomous vehicles. Lince is an academic tool for specifying and simulating such systems using a C-like language with…

Process Execution Engines are a vital part of Business Process Management (BPM) and Manufacturing Orchestration Management (MOM), as they allow the business or manufacturing logic (expressed in a graphical notation such as BPMN) to be…

We describe a novel, interdisciplinary, computational methods course that uses Python and associated numerical and visualization libraries to enable students to implement simulations for a number of different course modules. Problems in…

Scientific codes are increasingly being used in compositional settings, especially problem solving environments (PSEs). Typical compositional modeling frameworks require significant buy-in, in the form of commitment to a particular style of…

Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science. Research software is often developed by scientists with limited…

Statistical models serve as the cornerstone for hypothesis testing in empirical studies. This paper introduces a new cross-platform Python-based package designed to utilise different likelihood prescriptions via a flexible plug-in system.…

Software Product Line Engineering enables systematic reuse across families of related software intensive systems. This survey synthesises key SPLE foundations, lifecycle concepts, adoption models, tooling and AI era challenges. Based on a…