Find open-source science resources

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

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.

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

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.

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community

AI-powered note linking and research graph navigation

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

MiRA (Multilayer Interactive Rendering Application) is a free, browser-based, installation-free tool for interactive visualisation of multilayer networks in ecology and biology. While developed with biology in mind, MiRA can render any multilayer network. Available as a standalone web app and also fully integrated into the emln R package.

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)

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

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.

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.

The Open Neuroscience Graph (openneuroscience.org) is an open-access, curated knowledge graph that maps the open science ecosystem in neuroscience as a browsable digital garden. Built from an Obsidian vault and published as a static website using Quartz, the project replaces traditional linear presentation with a networked structure of interlinked Markdown notes. Bidirectional links, full-text search, and an integrated graph visualization allow users to navigate thematic relationships dynamically rather than sequentially. The complete source material is openly available to sustain, replicate and extend the resource, includding all Markdown content, media attachments, Quartz configuration files, and site customizations. Researchers, educators, and open-science practitioners may explore the site directly, download the vault for offline use in Obsidian, or fork the material to build new, derivative knowledge bases. PID=https://doi.org/10.5281/zenodo.20181900

Molecular Biology Tools is a free browser-based collection of molecular biology utilities for routine sequence analysis, primer design, Sanger sequencing primer planning, cloning setup, and wet-lab calculations. The site includes tools for PCR primer design, Sanger primer design and primer walking, primer binding checks, restriction site analysis, reverse complement generation, ORF and protein translation, codon optimization, ligation calculations, molarity calculations, dilution calculations, and multi-solute solution recipe preparation. The tools run in the browser and are intended for quick experimental planning, without requiring logins or uploading sequences to the server.