25 papers · ranked by Valyu relevance
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…
Charatvaraphan, Rujiphart, Chatchaiyadech, Bunradar + 12 more
Rujiphart Charatvaraphan\ , Bunradar Chatchaiyadech\ , Thitirat Sukijprasert\ , Chaiyong Ragkhitwetsagul\ , Morakot Choetkiertikul\ , Raula Gaikovina Kula† , Thanwadee Sunetnanta\ , Kenichi Matsumoto‡ \**Faculty of Information and Communication Technology, Mahidol University, Thailand †Graduate School of Information…
Mohayeminul Islam, Ajay Kumar Jha, May Mahmoud, Sarah Nadi
Library migration is the process of replacing a library with a similar one in a software project. Manual library migration is time consuming and error prone, as it requires developers to understand the Application Programming Interfaces (API) of both libraries, map equivalent APIs, and perform the necessary code…
Trina De, Vardan Andriasyan, Artur Yakimovich
Virological plaque assays are the primary method for quantifying infectious particles in a suspension, achieved by incubating a serial dilution of the virus with a monolayer of indicator cells. Existing software tools for quantification of plaque assay images lack modularity, show measurements disagreement or are…
K. Tsolakidis, Artu Breuer, S. Bender, Stavroula Margaritaki + 3 more
Advances in fluorescence microscopy have dramatically expanded the range of biological questions that can be addressed, enabling quantitative observations of molecular interactions and cellular dynamics with unprecedented spatial and temporal resolution. However, the growing complexity of imaging data has outpaced our…
Yoann Marquer, Domenico Bianculli, Lionel C. Briand
Python is one of the most popular programming languages; as such, projects written in Python involve an increasing number of diverse security vulnerabilities. However, existing state-of-the-art analysis tools for Python only support a few vulnerability types. Hence, there is a need to detect a large variety of…
Akira Tanaka, Yusuke Kawamoto
The reproducibility crisis in scientific research has received widespread recognition, thereby increasing the importance of meta-analyses that integrate statistical analyses from multiple studies. However, statistical methods often have ambiguous and implicit underlying assumptions, which can lead to their erroneous…
Endre Bakken Stovner, Max Ticó, Ester Muñoz del Campo, Joan Pallarès-Albanell + 3 more
Sequence interval algebra is key to modern bioinformatics. Pyranges v1 offers a Python Pandas-based interface to a comprehensive palette of Rust-powered operations (e.g., overlap, count, slice intervals), enabling the intuitive development of efficient pipelines for diverse sequence data, including gene annotations…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Ravi Pal, Akos Rudas, Tiffany Williams, Jeffrey N. Chiang + 2 more
This study presents an automatic feature extraction tool that first detects temporal location of landmarks within each cardiac cycle of ABP and PPG waveforms, including the systolic phase onset, systolic phase peak, dicrotic notch, and diastolic phase peak. Then, based on these landmarks, extracts 852 features per…
Saroja Somasundaram, Nelson J. Johansen, Trygve E. Bakken, Jeremy A. Miller
High-throughput chromatin accessibility assays such as ATAC-seq generate thousands of candidate regulatory elements (peaks), yet no standardized tool exists for assembling the diverse quantitative features needed to prioritize peaks for functional validation. Here we present PyPeakRankR, an open-source Python package…
Zimeng Wu, Octavian Voiculescu, Alessandro Mongera, Roberto Mayor + 2 more
Advances in microscopy and bioimage analysis are enabling unprecedented quantitative observation of dynamic biological systems. Smart microscopy closes the loop by feeding back image-derived information to control image acquisition on the fly, paving the way for increasingly autonomous and sophisticated experiments.…
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…
Jayadev Joshi, Fabio Cumbo, Daniel Blankenberg
R is widely used in statistical computing, data analysis, and bioinformatics. A key contributor to its success in bioinformatics and computational biology is the open-source project Bioconductor. As of its latest release (3.20), the Bioconductor community offers 2,289 software packages for biomedical research…
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…
Zhenzhen Ren, Xinpeng Zhang, Zhenxing Qian, Yan Gao + 3 more
The integration of external tools is pivotal for empowering Large Language Model (LLM) agents with real-world capabilities. However, training these agents through direct, continuous interaction with diverse tools is often prohibitively expensive, slow, and introduces additional development and maintenance overhead. To…
Mariano Ruz Jurado, David Rodriguez Morales, Lukas Zanders, Elijah Genetzakis + 3 more
Advances in omics technologies, particularly single-cell RNA sequencing (scRNA-seq), have provided an unbiased framework to study cellular heterogeneity, shifts in cell type composition, and the dynamics of cells in different organs and tissues (). The workflow for generating scRNA-seq data can be summarised into four…
Authors not listed
The materials-science literature is the richest reservoir of domain knowledge, yet converting its unstructured text—especially narrative passages and complex tables—into machine-readable data for analysis and ML model training remains challenging. To address this, we present KnowMat, an agentic, multi-stage pipeline…
Luna Xingyu Li, Carissa Bleker, Sylvain Soliman, Laurence Calzone + 13 more
Logical models are widely used to study regulatory and signaling systems, yet their reuse, annotation, and exchange across tools remain challenging. Although SBML Level 3 Qualitative Models (SBML-qual) provides a standard representation, its XML-based syntax is difficult to inspect and edit directly. Here we introduce…
Mohamed Salim Nasser Al Hinai, Zakira Naureen, Syed Abdullah Gilani
Since, Bioinformatic research is getting attraction that can be seen with sudden increase in development of tools as well as publications. However, there are challenges in bioinformatics which are making the results difficult to obtain while facing reproducibility, scalability, and accessibility of computational…
Conrad Oakes, Vera Beilinson, Margaret J. McFall-Ngai, Lior Pachter
Bacteria are highly heterogeneous, even under controlled conditions, making single-cell RNA sequencing (scRNA-seq) essential for studying microbial diversity and symbiosis. Since its first application in 2015, bacterial scRNA-seq has expanded, but different assays depend on distinct, custom, inhouse pre-processing…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Authors not listed
Mass spectrometry (MS) generates large datasets that are stored in increasingly optimized and complex file types, demanding technical expertise to extract information rapidly and easily. We wondered whether a simple structured query language (SQL) database could hold raw MS data and allow for easily readable queries…
Jakob Schuster, Kathleen Zeglinski, Lucinda Xiao, Olivia Voulgaris + 5 more
The wide variety of protocols and applications for DNA and RNA sequencing makes flexible tools for read processing an important step in sequence analysis. Beyond trimming and demultiplexing, custom read-level processing is commonly required for data exploration, QC and analysis. Existing tools are often task-specific…
Antonios Saravanos, John Pazarzis, Stavros Zervoudakis, Dongnanzi Zheng
Python libraries often need to maintain a stable public API even as internal implementations evolve, gain new backends, or depend on heavy optional libraries. In Python, where internal objects are easy to inspect and import, users can come to rely on "reachable internals" that were never intended to be public, making…