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.

Machine learning software for extracting structured metadata from scholarly documents

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 framework for processing biological data.

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

A quality control tool for high throughput sequence data.

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

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

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

Open Parser for Systematic IUPAC nomenclature

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.

VIP is a web portal for medical imaging applications. It allows users to access scientific applications as a service (directly through the web browser with no installation required), as well as distributed computing resources in a transparent manner. It exploits the resources available in the biomed virtual organization of the EGI e-infrastructure to offer an open service to researchers worldwide.

The MetaProteomeAnalyzer Cloud (MPA Cloud) is an intuitive, open-source tool for metaproteomics data analysis and interpretation, designed to analyse comprehensive metaproteomics data from tandem mass spectrometry experiments through a web interface.

Comparative genomics-driven translational research tool.

Novel machine learning-based method for prediction of ligand binding sites from protein structure.