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The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…

We present a workflow and associated toolkit to automate the creation of graphical user interfaces (GUI) for executables run from command line interfaces (CLI). The workflow consists of three phases, namely (Step 1) the plugin design, (Step…

AI assistants can now carry out tasks for users by directly interacting with website UIs. Current semantic parsing and slot-filling techniques cannot flexibly adapt to many different websites without being constantly re-trained. We propose…

Although birthed in the era of teletypes, the command line shell survived the graphical interface revolution of the 1980's and lives on in modern desktop operating systems. The command line provides access to powerful functionality not…

Developers and data scientists often struggle to write command-line inputs, even though graphical interfaces or tools like ChatGPT can assist. The solution? "ai-cli," an open-source system inspired by GitHub Copilot that converts natural…

In this paper we describe EasyInterface, an open-source toolkit for rapid development of web-based graphical user interfaces (GUIs). This toolkit addresses the need of researchers to make their research prototype tools available to the…

We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to i) spend less time on data management and processing, ii)…

Context. Software development pipelines are used for automating essential parts of software engineering processes, such as build automation and continuous integration testing. In particular, interactive pipelines, which process events in a…

Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…

Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…

The emergent dynamics of complex gene regulatory networks govern various cellular processes. However, understanding these dynamics is challenging due to the difficulty of parameterizing the computational models for these networks,…

Companies developing Web applications have faced an increasing demand for high-quality products with low cost and production time ever smaller. However, developing such applications is still considered a time-consuming and error-prone task,…

The emergence of R, a freely available data analysis environment, brought to the researcher in any science field a set of well-concerted instruments of immense power and low cost. In botany and zoology, these instruments could be used, for…

Modern biomedical applications often involve time-series data, from high-throughput phenotyping of model organisms, through to individual disease diagnosis and treatment using biomedical data streams. Data and tools for time-series analysis…

The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…

To address the difficulty of creating online collaborative evolutionary systems, this paper presents a new prototype library called Worldwide Infrastructure for Neuroevolution (WIN) and its accompanying site WIN Online (http://winark.org/).…

This whitepaper reports on Project CLAI (Command Line AI), which aims to bring the power of AI to the command line interface (CLI). The CLAI platform sets up the CLI as a new environment for AI researchers to conquer by surfacing the…

The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…

Branch is a web application that provides users with no programming with the ability to interact directly with large biomedical datasets. The interaction is mediated through a collaborative graphical user interface for building and…

We present clinguin, a system for ASP-driven user interface design. Clinguin streamlines the development of user interfaces for ASP developers by letting them build interactive prototypes directly in ASP, eliminating the need for separate…