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This package provides functions for the analysis of data generated by the multiplex substrate profiling by mass spectrometry for proteases (MSP-MS) method. Data exported from upstream proteomics software is accepted as input and subsequently processed for analysis. Tools for statistical analysis, visualization, and interpretation of the data are provided.

Biocaml aims to be a high-performance user-friendly library for Bioinformatics.

Foundation model for universal cell segmentation achieving state-of-the-art performance across bacteria, tissue, yeast, cell culture, and diverse imaging modalities (brightfield, fluorescence, phase), with pip-installable inference and Napari plugin (vanvalenlab/Caltech, bioRxiv 2024)

Another list focuses on Python stuff related to Chemistry.

HOSO is an ontology of informational entities and processes related to healthcare organizations and services.

SIMD C library for global, semi-global, and local pairwise sequence alignments

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)

GRIDSS: the Genomic Rearrangement IDentification Software Suite.

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)

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

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

The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.

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).

A VCF Parser for Python.

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.

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]

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.

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