Find open-source science resources

Identifiers in the GTN correspond to training materials in various formats (markdown, slides, video). The users can apply learned concepts directly within the framework via galaxy workflows.

The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.

BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research.

Production-grade ETL for transforming complex documents into structured formats, with open-source API

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).

A representation of variables appearing in models in the environmental research space.

Cheminformatics toolkit

This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Ibuprofen small compound (3-letter code IBP, Drugbank code DB01050), a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid.

A vocabulary used in tandem with SHACL for representing node shapes

An Apache-based persistent URL (PURL) service

Phylo-Movies is an open-source React and Flask web application, also available as a desktop app, for inspecting ordered phylogenetic tree series. It computes and visualizes subtree-prune-and-regraft transition frames between consecutive trees, helping users see which taxa or subtrees move across sliding-window analyses, bootstrap replicates, and curated tree-series comparisons. The viewer includes timeline playback, tree comparison, MSA context, coloring, analytics, image export, and recording tools.

Library of descriptors to aid in the data-mining of materials properties, created by the Lawrence Berkeley National Laboratory.

Galaxy workflow for BlockClust pipeline.

This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.

Parallel Computing and Scientific Machine Learning: MIT 18.337J/6.338J course materials (1.9k+ stars)

It is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.

Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]

The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph.

Interactive browser for the complete Human Phenotype Ontology (~19,800 terms), with a graph-based term explorer and a clinical profile analyzer for phenotype similarity, differential diagnosis, and gene prioritization.

An international LGBTQ+ linked data vocabulary

This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Drew Dickerson Dodecamer sequence -CGCGAATTCGCG- (PDB code 1BNA). The trajectory used is a 500ns-long MD simulation taken from the BigNASim database (NAFlex_DDD_II entry).

DCAT-AP is a DCAT profile for sharing information about Catalogues containing Datasets and Data Services descriptions in Europe, under maintenance by the SEMIC action, Interoperable Europe. This Application Profile provides a minimal common basis within Europe to share Datasets and Data Services cross-border and cross-domain. [from homepage]

A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies).

Suite of tools to handle gene annotations in any GTF/GFF format.

An ontology demonstrating rich ontology for rubber extrusion.

Large-scale benchmark suite for protein fitness prediction and design, aggregating 200+ deep mutational scanning assays and clinical variant datasets across diverse protein families and taxa, with standardized zero-shot and supervised leaderboards for variant effect prediction, mutation effect prediction, and protein language model evaluation (OATML & Marks Lab, NeurIPS 2023 Spotlight, Datasets & Benchmarks)

The Generative Artificial Intelligence Delegation Taxonomy (GAIDeT) assigns identifiers to contributor roles as an extension to the Contributor Roles Taxonomy (CRediT) to support promoting transparency and accountability in academic publishing when AI contribtors are involved in research. It is operationalized in the [GAIDeT Declaration Generator](https://panbibliotekar.github.io/gaidet-declaration/), an interactive tool for researchers to disclose the delegation of tasks to generative AI (GAI) tools in accordance with the GAIDeT taxonomy.

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation, step by step, using the BioExcel Building Blocks (biobb).

This BioExcel Building Blocks library (BioBB) workflow provides a pipeline to setup DNA structures for the Ascona B-DNA Consortium (ABC) members. It follows the work started with the NAFlex tool to offer a single, reproducible pipeline for structure preparation, ensuring reproducibility and coherence between all the members of the consortium.

This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures using Coarse-Grained tools from the FlexServ server and analysing its molecular flexibility

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks (biobb).

This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).

This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures step by step, using the BioExcel Building Blocks library (biobb)

This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.

Webapp for generating conformers

CCSO is an educational ontology acting as a data model for concepts and entities within an academic setting, enabling also the annotation of potentially available resources. The ontology aims to conceptualize educational entities within Curriculum and Syllabus with appropriate coverage and quality, in order to support rich services on top for improving curriculum management and automatically enabling syllabus semantic processes. (from homepage)

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

HEPRO is an ontology of informational entities and processes related to health procedures and health activities.

An ontology of information entities about an individual

Easily get SRA download links and other information.

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.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks (biobb) REST API. The particular example used is the Lysozyme protein (PDB code 1AKI).