26 papers · ranked by Valyu relevance
Saketh Ram Kasibatla, Kiran Medleri Hiremath, Raven Rothkopf, Sorin Lerner + 2 more
—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 otherwise exposed on the computer, but requires users to recall textual syntax and…
Sofien Gannouni, Kais Belwafi, Mohammad Reshood Al-Sulmi, Meshal Dawood Al-Farhood + 5 more
'Meshal Dawood Al-Farhood' 'Omar Ali Al-Obaid' 'Abdullah Mohammed Al-Awadh' 'Hatim Aboalsamh' 'Abdelfettah Belghith' 'Saugat Bhattacharyya'] There are many applications controlled by the brain signals to bridge the gap in the digital divide between the disabled and the non-disabled people. The deployment of novel…
Andres Veidenberg, Ari Löytynoja
Motivation: Bioinformatics software often lacks graphical user interfaces (GUIs), which can limit its adoption by non-technical members of the scientific community. Web interfaces are a common alternative for building cross-platform GUIs, but their potential is underutilized: web interfaces for command-line tools…
Mayank Agarwal, Jorge J. Barroso, Tathagata Chakraborti, Eli M. Dow + 4 more
'Eli M. Dow' 'Kshitij P. Fadnis' 'Borja Godoy' 'Madhavan Pallan' 'Kartik Talamadupula'] This paper 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…
Dario Beraldi, John Hancock
The visualization of next generation sequencing data is a fundamental part of genomics enabling the analyst to assess the quality of the results and generate hypotheses. Accordingly, several programs for browsing genomic data are widely popular amongst the genomics community, for example, IGV () or Artemis () are…
Torsten Seemann
Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I…
Florian Rupprecht, Jason Kai, Biraj Shrestha, Steven Giavasis + 4 more
In numerous scientific domains, established tools have often been developed with complex command-line interfaces. Such is the case for brain imaging and bioinformatics, making the use of powerful legacy tools in modern workflow paradigms challenging. We present (i) Styx, a compiler for generating language-native…
Florian Rupprecht, Jason Kai, Biraj Shrestha, Steven Giavasis + 4 more
'Ting Xu' 'Tristan Glatard' 'Michael P Milham' 'Gregory Kiar'] In numerous scientific domains, established tools have often been developed with complex command-line interfaces. Such is the case for brain imaging and bioinformatics, making the use of powerful legacy tools in modern workflow paradigms challenging. We…
Serghei Mangul, Lana S. Martin, Alexander Hoffmann, Matteo Pellegrini + 1 more
Researchers in the biomedical sciences increasingly rely on applications that lack a graphical interface and require inputting code that, such as UNIX. Scientists who are not trained in computer science face an enormous challenge in analyzing the high-throughput data their research groups generate. We present a…
Diomidis Spinellis
—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 language prompts into executable commands for various Linux command-line tools.…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Artem Voronkov, Leonardo A. Martucci, Stefan Lindskog
A graphical user interface (GUI) represents the most common option for interacting with computer systems. However, according to the literature system administrators often favor command line interfaces (CLIs). The goal of our work is to investigate which interfaces system administrators prefer, and which they actually…
Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas + 7 more
Background Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with…
Umakant Mishra
| 1. Introduction 1 | | | --- | --- | | 2. Inventions on Command buttons 2 | | | 2.1 Method for adding a graphical user interface to a command line application | | | (5617527) 2 | | | 2.2 Closely integrated key icons in a graphical interface (5694562) 3 | | | 2.3 GUI pushbutton with multi-function mini-button (5736985)…
Yann Spöri, Jean-François Flot
Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript and Python. Although Haxe is…
Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi + 6 more
'Vijini Mallawaarachchi' 'Bhavya Papudeshi' 'Scott A. Handley' 'C. Titus Brown' 'Nathan S. Watson-Haigh' 'Robert A. Edwards' 'Scott Markel'] Introduction As bioinformatics analyses increase in size and complexity, workflow managers are becoming more popular for building pipelines [1-3]. Workflow managers, such as…
Marta Pasquini, Marco Stenta
Background. The increasing amount of chemical reaction data makes traditional ways to navigate its corpus less effective, while the demand for novel approaches and instruments is rising. Recent data science and machine learning techniques support the development of new ways to extract value from the available reaction…
Jaakko S Tyrmi
STAPLER is a command line program intended for creating, managing and parallelizing bioinformatics workflows. Considerable emphasis has been placed on the ease of adoption and use by effortless installation, simple definition of workflows and quick-start tutorials. Custom workflows can be defined in an easy, modular…
Monika Vogler, Jonas Busk, Hamidreza Hajiyani, Peter Bjørn Jørgensen + 9 more
The future of materials science is borderless, cooperative, and distributed across the globe. This necessitates flexible, reconfigurable software defined research workflows, which we herein demonstrate by integrating multiple disciplines and modalities. Our brokering approach to research orchestration exposes entire…
Fabio Cumbo, Jayadev Joshi, Daniel Blankenberg
Background – The integration of command-line tools into the Galaxy platform is crucial for making complex computational methods accessible to a broader audience and ensuring reproducible research. However, the manual development of tool wrappers (i.e., the XML files that define the user interface and execution logic in…
Tycho Kirchner, Konstantin Riege, Steve Hoffmann
The Linux shell is arguably one of the most important computational tools across various scientific disciplines. Its high flexibility makes it the platform of choice for many file operations and smaller scripting tasks. Also, many stand-alone programs are called from the Linux shell - typically followed by multiple…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
Xian Yu, Zhenxian Zheng, Lei Chen, Zilan Qin + 3 more
Large language model (LLM) agents increasingly automate bioinformatics analyses, but most existing bioinformatics tools were built for standalone use by human experts. An agent driving such a tool must reason about its installation, configuration, and execution from documentation for human, spending many turns, tokens…
Authors not listed
Predicting sites of metabolism (SOMs), i.e., the atom positions in a molecule where metabolic reactions are initiated, is an important component of the computational development pipeline for pharmaceuticals, agrochemicals, and cosmetics. Among the available SOM prediction models, FAME 3, published in 2019, stands out…
Himaghna Bhattacharjee, Jackson Burns, Dionisios Vlachos
The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery…
Himaghna Bhattacharjee, Jackson Burns, Dionisios Vlachos
The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery…