A goal of multiomics experiments is to understand how mechanistic molecular biology is altered between conditions, typically a control group and experimental groups. Oftentimes, this involves studying...

Untargeted LC–MS metabolomics generates large, noisy datasets that demand complex, parameter-intensive workflows across multiple software tools. While over 5000 metabolomics datasets are available in ...

This tutorial offers a step-by-step guide for analytical chemists to train machine learning models for MS-based metabolomics. It covers data preparation, feature engineering, model selection, evaluati...

The rise of data-driven science has made research data management (RDM) essential, yet implementing it remains complex due to diverse disciplinary needs, limited tailored guidance, and gaps in trainin...

The Bioconductor Code of Conduct Committee updates, disseminates, upholds and enforces the Code of Conduct (http://bioconductor.org/about/code-of-conduct/) across all platforms of the Bioconductor…

Supplementary materials that accompany scientific articles enhance transparency, reproducibility and scientific impact. This study presents FAIR-SMART, a tool that enables computational access to thes...

Mass spectrometry-based lipidomics and metabolomics generate large, complex datasets requiring effective analysis. Here, authors review key statistical and visualization methods alongside widely used R and Python tools, and provide a GitBook with step-by-step code for accessible, reproducible data analysis.

Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption ...

Release Notes for Cytoscape

Over the past decades, mass spectrometry has served as a fundamental technique for molecular identification in the field of metabolomics, widely applied to the analysis and characterization of biomole...

The construction of multicellular mechanistic models in systems biology typically requires months of literature research, programming expertise, and deep knowledge of specialized computational tools. ...

Knowledge graph construction has become an essential domain for the future of biomedical research. But current approaches demand a high amount of redundant labor. These redundancies are the result of ...

Bioconductor packages are currently annotated using the biocViews controlled vocabulary (Carey et al., 2024), structured as a graph with nearly 500 terms, of which 175 are meant for software annotatio...

AbstractSummary. Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predi

Mass spectrometry (MS)-based proteomics data analysis is composed of many stages from quality control, data cleaning, and normalization to statistical and functional analysis, without forgetting multiple visualization steps. All of these need to be reported next to published results to make them fully understandable and reusable for the community. Although this seems straightforward, exhaustively reporting all aspects of an analysis workflow can be tedious and error prone. This letter reports good practices when describing data analysis of MS-based proteomics data and discusses why and how the community should put efforts into more transparently reporting data analysis workflows.

The exponential growth of untargeted metabolomics data, now reaching billions of mass spectra in public repositories, benefits from reannotation strategies for data reuse. While tandem mass spectromet...

第30回ののゲストは、UCSD（カリフォルニア大学サンディエゴ校）に約20年間勤務されたソフトウェア開発者の大野圭一朗さんです。大野さんは、同大学の医学部の研究室で専属の開発者として、生物学分野におけるネッ…

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A model context protocol (MCP) server for the EBI Ontology Lookup Service (OLS) - seandavi/ols-mcp-server