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Researchers face a persistent barrier when applying computational algorithms with parameter configuration typically demanding programming skills, interfaces differing across environments, and settings rarely persisting between sessions.…
Linguine is a natural-language-inspired programming language that enables users to write programs in a fluent, controlled subset of English while preserving formal semantics. The language introduces anaphoric constructs, such as pronoun…
In the past few decades, the life sciences have experienced an unprecedented accumulation of data, ranging from genomic sequences and proteomic profiles to heavy-content imaging, clinical assays, and commercial biological products for…
Background: Increasingly, decision-making in healthcare relies on computer models, be it clinical prediction models at point of care or decision-analytic models at the policymaking level. Given the important role models play in both…
Recent advances in computing systems have led to a new digital era in which every area of life is nearly interrelated with information technology. However, with the trend towards large-scale IT systems, a new challenge has emerged. The…
Highly customized graphical user interfaces play a major role in today's software applications. There exist many technologies that support developing them. But these technologies demand writing a significant amount of unintuitive code to…
We create a Python GUI scripting interface working under Windows in addition to (UNIX/Linux). The GUI has been built around the Python open-source programming language. We use the Python's GUI library that so called Python Mega Widgets…
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of…
Data cleaning is naturally framed as probabilistic inference in a generative model of ground-truth data and likely errors, but the diversity of real-world error patterns and the hardness of inference make Bayesian approaches difficult to…
Software interfaces today generally fall at either end of a spectrum. On one end are programmable systems, which allow expert users (i.e. programmers) to write software artifacts that describe complex abstractions, but programs are…
Baseline is a platform for richly structured data supporting change in multiple dimensions: mutation over time, collaboration across space, and evolution through design changes. It is built upon Operational Differencing, a new technique for…
Small multiples are miniature representations of visual information used generically across many domains. Handling large numbers of small multiples imposes challenges on many analytic tasks like inspection, comparison, navigation, or…
Summary: Data management in clinical metabolomics studies is often inadequate. To improve this situation we created LabPipe to provide a guided, customisable approach to study-specific sample collection. It is driven through a local client…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
A timeline is presented which shows the stages involved in converting a bioinformatics software application from a set of standalone algorithms through to a simple web based tool then to a web based portal harnessing Grid technologies and…
Unlike static and rigid user interfaces, generative and malleable user interfaces offer the potential to respond to diverse users' goals and tasks. However, current approaches primarily rely on generating code, making it difficult for…
Accurate yet efficient Deep Neural Networks (DNNs) are in high demand, especially for applications that require their execution on constrained edge devices. Finding such DNNs in a reasonable time for new applications requires automated…
Scripting interfaces enable users to automate tasks and customize software workflows, but creating scripts traditionally requires programming expertise and familiarity with specific APIs, posing barriers for many users. While Large Language…
PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a…
We illustrate how purpose-specific, graphical modeling enables application experts with different levels of expertise to collaboratively design and then produce complex applications using their individual, purpose-specific modeling…