Find open-source science resources

Interactive browser for the complete Human Phenotype Ontology (~19,800 terms), with a graph-based term explorer and a clinical profile analyzer for phenotype similarity, differential diagnosis, and gene prioritization.

Aggregate results from bioinformatics analyses across many samples into a single report.

AI-powered note linking and research graph navigation

compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.

Web application and service for visualizing small- to medium-scale models of gene regulatory networks. It automatically lays out either an unweighted or weighted network graph based on an Excel input spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows. It is best-suited for visualizing networks of fewer than 35 nodes and 70 edges and has general applicability.

Auto-generates clean, customizable academic CVs from open research data (OpenAlex, ORCID, Crossref, DataCite, Open Editors Plus). A single canonical CV object drives every output format (HTML, PDF, DOCX, LaTeX, Markdown); citations render through CSL; and the account holder is matched by persistent identifier (ORCID / OpenAlex ID) rather than name string. Free for individuals, open-source, and FAIR by design.

A static web application presents an interactive knowledge graph of single-cell long-read RNA sequencing literature synthesized from seven source papers. Users navigate mind-tree, network graph, guided learning-path, and Sankey views linking platforms, protocols, methods, and software. A benchmark tab provides 34 question-answer pairs with category and difficulty filters, exportable as JSON or CSV for LLM and agent evaluation.

Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.

Multi-PDF conversation, retrieval, and citation in Zotero with commercial/local models (Ollama), MCP support

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community

Interactive explorer for single-cell transcriptomics data enabling visualization of UMAP/t-SNE embeddings, differential expression analysis, and cross-dataset comparison through a fast web-based interface; widely adopted for exploring atlas-scale single-cell datasets and integrating with AI/ML analysis workflows (773+ stars, MIT License)

FlowVision is offline flow cytometry analysis software for Windows and macOS. It supports FCS 2.0, 3.0, 3.1 and 3.2 file formats, polygon/rectangle/ellipse/quadrant gating with auto-fit (snap to cluster), spillover compensation, biexponential and hyperlog scales, MFI statistics (median, geometric mean, CV%), multi-file batch analysis with per-file gate overrides, and hierarchical gating. Spectral unmixing supports linear, NNLS, and Poisson-weighted least squares algorithms, with autofluorescence extraction and spillover spreading matrix. UMAP dimensionality reduction with reproducible seed and landmark mode for high-parameter panels. Imports FlowJo .wsp (compensation matrix) and exports gates to FlowJo .wsp and Gating-ML 2.0 (ISAC open standard) for interoperability with FlowJo, R/flowWorkspace/CytoML, and FCS Express.

JavaScript genome browser that is highly customizable via plugins and track customizations.

SMILES-Mapper is a small web app that allows students to easily visualize how SMILES & InChI strings are created together with other mol-block file formats such as .mol and .sdf files.

Open source web framework for small molecule analysis based on Django.

JavaScript library that can be used to generate interactive and highly customizable web-based genome browsers.

Embeddable genome viewer. Integration data from a wide variety of sources, and can load data directly from popular genomics file formats including bigWig, BAM, and VCF.

JavaScript library for drawing canvas-based gene diagrams.

D3 JavaScript based genome viewer. Constructs SVGs.