Find open-source science resources

Open-source PDF parser for AI-ready data, converting PDFs into Markdown/JSON/HTML/Tagged PDF with layout analysis and reading-order detection; ranks #1 overall on extraction benchmarks with deterministic bounding boxes and hybrid AI mode (26K+ stars, Apache 2.0)

Vitro is a full stack framework for building semantic web applications. It is not domain specific.

A quality control tool for high throughput sequence data.

Machine learning software for extracting structured metadata from scholarly documents

Chemical 2D structure editor application/applet based on the [Chemistry Development Kit](https://sourceforge.net/projects/cdk/).

Concatenation software for the fast assembly of multi-gene datasets with character set and codon information.

Open-source bioimage analysis platform for digital pathology and research, featuring AI-powered cell detection, tissue classification, and whole-slide image analysis with extensible scripting and plugin architecture (1.3K+ stars, actively maintained)

Java-based browser. Fast, efficient, scalable visualization tool for genomics data and annotations. Handles a large variety of formats.

Java framework for processing biological data.

Open Parser for Systematic IUPAC nomenclature

Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump

Genetic variant annotation and effect prediction toolbox.

GRIDSS: the Genomic Rearrangement IDentification Software Suite.

Parse scientific papers to structured fields (title/author/sections/references)

Customizable pipeline for differential expression analysis with an intuitive GUI.

Variant Discovery in High-Throughput Sequencing Data.

Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments.

Natural Product-likeness calculator v-2.1 : calculates natural product-likeness of small molecules based on open-data of natural products.