Find open-source science resources
A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.
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228 of 6,592 resources
Showing 201–228
Diffusion model for scalable protein structure design with multi-motif scaffolding capabilities, achieving state-of-the-art designability, diversity, and novelty through SE(3)-equivariant attention and massive data augmentation (AlQuraishi Lab, 2024)
structural variant calling and genotyping with existing tools, but,smoothly.
DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects.
Automated data visualization with minimal code
Parse scientific papers to structured fields (title/author/sections/references)
A collection of research papers for AI-based protein design.
Neural differential equations in PyTorch
Scalable gVCF merging and joint variant calling for population sequencing projects
Generative model for programmable protein design using diffusion modeling, equivariant graph neural networks, and conditional random fields to efficiently sample diverse all-atom structures; supports conditional generation via composable conditioners for substructure, symmetry, shape, and neural-network predictions; validated crystallographically (Generate Biomedicines, Nature 2023)
Large-scale PDF/LaTeX/JATS parsing to standardized JSON for millions of papers
Google DeepMind's AlphaFold-derived classifier for proteome-wide missense variant effect prediction, providing pathogenicity scores for all ~71M possible human missense variants and classifying 89% with 90% precision; pre-computed predictions are integrated into Ensembl VEP and UCSC Genome Browser to support clinical variant interpretation (Science 2023)
Extract figures, tables, captions, and section titles from scholarly PDFs
This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.
First system to make novel, verifiable scientific discoveries by pairing LLMs with evolutionary search, solving open problems in combinatorics (cap set problem) and discovering faster matrix multiplication algorithms
DGL-LifeSci is a [DGL](https://www.dgl.ai/)-based package for various applications in life science with graph neural network.
Large language model for science
PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.
Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.
R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.
JavaScript library that can be used to generate interactive and highly customizable web-based genome browsers.
BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.
An ontology encoding the Common Information Model (CIM) schema
SWAN ontology consists in a collection of ontologies used to create, manage and share scientific knowledge bases.
Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows
An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species. The original structure of the histopathology ontology was designed ab initio when the [INHAND](http://www.goreni.org/) manuscripts were not available. However, the ontology has been repetitively reviewed and updated to align with the subsequently published INHAND manuscripts. During this process cross references to INHAND lesion identifiers were added to the ontology. [from GitHub]
Selventa legacy chemical namespace used with the Biological Expression Language