Find open-source science resources

NIST's open-source platform for data-driven atomistic materials design, integrating DFT datasets (JARVIS-DFT), machine learning property prediction (JARVIS-ML), and a comprehensive leaderboard for benchmarking materials AI methods across the periodic table (384+ stars)

Large-scale flow-based protein backbone generator utilizing hierarchical fold class labels for conditioning with a tailored scalable transformer architecture, enabling controllable de novo protein design (264+ stars)

DeepSeek's open-source large language model for formal theorem proving in Lean 4, integrating informal and formal mathematical reasoning through recursive subgoal decomposition and reinforcement learning powered by DeepSeek-V3, with open weights and ProverBench evaluation (2025)

Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business.

A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 40 publicly-available terminologies. (from repository)

In silico directed evolution framework using few-shot active learning to optimize protein activities, enabling rapid protein engineering with minimal experimental data (352+ stars, 2023)

Large language-and-vision assistant for biomedicine, instruction-tuned on GPT-4-generated biomedical multimodal instruction-following data to enable conversational visual question answering over radiology, pathology, and microscopy images, establishing open recipes for adapting general vision-language models to the biomedical domain (Microsoft Research & University of Washington, 2.2K+ stars)

GRIDSS: the Genomic Rearrangement IDentification Software Suite.

Systematic medical RAG toolkit for question answering over PubMed, StatPearls, textbooks, and Wikipedia, supporting multiple retrievers, domain LLMs, and follow-up-query workflows for benchmarked clinical/biomedical QA (ACL Findings 2024)

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.

General-purpose pathology foundation model pretrained on 100K+ diagnostic whole-slide images across 20 major tissue types, achieving state-of-the-art transfer learning across 30+ clinical tasks and serving as a universal feature extractor for digital pathology (Mahmood Lab, 722+ stars)

Vision-language pathology foundation model using contrastive learning on histopathology image-text pairs, enabling zero-shot classification, slide-level retrieval, and multimodal reasoning across diverse cancer types (Mahmood Lab, 494+ stars)

A database system designed to store, organize, and manage large-scale nucleotide sequencing read data (like PacBio reads) for the Dazzler genome assembler

A terminology for the skills necessary to make data FAIR and to keep it FAIR.

SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.

Universal chart comprehension and reasoning model

The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).

Circlator is a tool to circularize genome assemblies. It will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.

The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.

k-mer counting, filtering, and graph traversal.

NOVOPlasty - The organelle assembler and heteroplasmy caller. NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes..

A VCF Parser for Python.

Displaying sequence statistics for next-generation sequencing.

lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.

Educational resource on performing RNA-seq analysis in the cloud using Amazon AWS cloud services. Topics include preparing the data, preprocessing, differential expression, isoform discovery, data visualization, and interpretation.

A suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds. MOODS can also process high-order PWMs with dependencies between adjacent positions and sequence variants such as SNPs, insertions and deletions.

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

Learning nonlinear operators

AI for chemical reaction prediction and synthesis planning

FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities.

This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]

Finds SNP sites from a multi-FASTA alignment file.

The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.

Customizable pipeline for differential expression analysis with an intuitive GUI.

Flexible circular visualization of genome-associated data with BioPerl and SVG.

Horizon chart D3-based JavaScript library for DNA data.