22 papers · ranked by Valyu relevance
Nathan R. Kern, Soohyung Park, Yiwei Cao, Wonpil Im
As high-performance computing provides the ability to generate and analyze ever larger simulation trajectories, the challenges in learning, applying, and sharing the best analytical practices become more salient. Extracting reproducible scientific insights from simulation requires a thorough understanding of many…
Zekun Ren, Hongzhao Tan, Jiaen Yee, Kedar Hippalgaonkar
Physical Unified Device Architecture (PUDA) is an AI-native hardware harness for self-driving laboratories (SDLs). Rather than building a human-centered graphical user interface (GUI) orchestration layer, PUDA creates a command-line runtime environment that lets agents observe, orient, decide, and act over experiments…
Alexander Alsalihi, Robert M. Flight, Hunter N. B. Moseley
The recount3 online resource provides tens of thousands of uniformly processed RNA-seq samples across human and mouse from major sequencing repositories like the Sequence Read Archive. While access to these datasets has traditionally been centered in the R/Bioconductor ecosystem, the growing prominence of Python in…
Haoyang Su, Ying Wen
Command line interface (CLI) agents are emerging as a practical paradigm for agent-computer interaction over evolving filesystems, executable command line programs, and online execution feedback. Recent work has used reinforcement learning (RL) to learn these interaction abilities from verifiable task feedback, yet few…
Shiraishi, Momoko, Cao, Yinzhi + 2 more
—Command-line interface (CLI) fuzzing tests programs by mutating both command-line options and input file contents, thus enabling discovery of vulnerabilities that only manifest under specific option-input combinations. Prior works of CLI fuzzing face the challenges of generating semanticsrich option strings and input…
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…
Augusto Borges, Jerónimo R. Miranda-Rodríguez, Alberto S. Ceccarelli, Guilherme Ventura + 3 more
Title: Summary Stress inference offers a rapid computational approach for estimating the mechanical state of a tissue without requiring invasive experiments. Here, we present a protocol for inferring mechanical stresses in tissues using ForSys, an open-source Python tool. We describe steps for preparing the Python…
Lucie Khamvongsa-Charbonnier, Robert Aboukhalil, Hélène Chiapello, Thomas Denecker + 6 more
As the generation of data in the life and health sciences expands rapidly, there is a growing need for professionals and students in these fields to master core bioinformatics skills, particularly those relating to Unix-like systems, most commonly used in bioinformatics. This paper introduces two key contributions to…
Olivia W Lang, Benjamin Beer, Dean Zhang, Courtney LeSon + 3 more
The growing diversity of genomic and epigenomic assays has driven a parallel expansion in data formats, analysis workflows, and figure-generation tools. However, tools for analyzing data and assembling publication-quality figures are often specialized to a specific assay, dramatically limiting their interoperability…
Jia Ding, Yun Peng, Ruochen Wei, Boquan Wang + 3 more
The development of BLIT follows a clear technical trajectory ([vbag088-F1]): it begins with the implementation of a core R6-based command engine for shell command translation and pipeline chaining. Building upon this foundation, the project employs bibliometric analysis to identify and prioritize high-impact…
Murat Cokol, Lubomir Chorbadjiev, Yoon-ha Lee, Minal Jamsandekar + 3 more
Interpretation of genomic variants, positions, and regions depends on reliable annotation—adding evidence such as predicted effect, conservation, population frequency, and gene-level context—yet the underlying resources are numerous, versioned, and assembly-specific. We present the Genomic Annotation Infrastructure…
Tapan Kumar Mondal, Abhijeet Roy, U B Angadi, Abhishek Mazumder
Identification of Quantitative Trait Loci from DNA sequence data is a multistep process, which is difficult for the plant breeders. To make the QTL identification breeders friendly, we developed QTLIT, a tool comprised of popular R packages and open sources software under a single umbrella for QTL analysis that enables…
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
We present an open source collection of scripts and programs for the setup, management and evaluation of calculations with the Vienna ab-initio simulation package (VASP), called utils4VASP. It contains 20 independent Python scripts and Fortran programs, all with a unified and intuitive handling concept based on command…
Authors not listed
The analysis of molecular dynamics (MD) simulations is a critical but fragmented process, often requiring researchers to chain together multiple software tools and write bespoke scripts for routine structural and dynamic analyses. This workflow complexity creates a significant barrier to efficiency, standardization…
Manuel Alonso-Carracedo, Ruben Fernandez-Boullon, Pedro Celard, Francisco J. Rodriguez-Martinez + 1 more
As computing education expands beyond traditional programming into operational domains such as systems administration and command-line environments, existing pedagogical frameworks struggle to capture a dimension that is critical in these contexts: the real-world consequences of learner actions. Existing cognitive…
Le Zhang, Daniela Cassol, Brendan Gongol, Thomas Girke
Workflow management systems (WMS) are essential for creating and automating multi-step data analyses and ensuring the reproducibility of biological insights. Although numerous WMS solutions exist, few provide deep integration of command-line software with the R and Bioconductor ecosystems, where a substantial portion…
Andrea Telatin
NBI-Slurm is a Perl package that provides a simplified, user-friendly interface for submitting and managing jobs on SLURM high-performance computing (HPC) clusters. It offers both a library of Perl modules for programmatic job management and a suite of command-line tools designed to reduce the cognitive overhead of…
Authors not listed
Here, we present MolPic, an open-source Python-based software that can be used to generate high-resolution, publication-quality molecular figures directly from compound names or SMILES strings. MolPic supports single-molecule rendering, batch processing, and automated multi-panel 2D figure generation, which are…
Dong-Jun Lee, Tae-Ho Lee, Taesoo Kwon, Raman Singh
The analysis of large-scale next-generation sequencing (NGS) data requires substantial computational power, often necessitating the use of high-performance computing (HPC) environments. However, the command-line interfaces for these resources create a significant barrier for many researchers. To bridge this gap, we…
Bo Wen, Kai Li, Michael Riffle, Michael J. MacCoss + 2 more
De novo peptide sequencing detects peptides directly from tandem mass spectra without a protein sequence database, and deep learning has substantially advanced its performance. Casanovo, one such widely used model, is distributed as a Python command-line program. Consequently, installation, GPU and dependency…
Bo Wen, Kai Li, Michael Riffle, Michael J. MacCoss + 2 more
De novo peptide sequencing detects peptides directly from tandem mass spectra without a protein sequence database, and deep learning has substantially advanced its performance. Casanovo, one such widely used model, is distributed as a Python command-line program. Consequently, installation, GPU and dependency…