bio.tools

Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences.

Important

bio.tools will be shortly shut down for maintenance on Monday, Nov 25 in the morning. We apologize for any inconvenience.

Communities in bio.tools

Explore communities in bio.tools and see what resources are used by different scientific communities.

Experts from scientific communities are key in identifying what are the methods and software resources used in their research activities. We rely upon scientific communities to improve the terminology and description of resources in different domains of the Life Sciences. This includes the communities being fostered by ELIXIR, and any other group of scientists with an interest to help out.

We strongly encourage everyone to take part in the community effort and contribute. Email us for more info.

Communities and domains

In bio.tools we try, with the help of the community, to create content domains or "slices" relevant to a specific community, research area or task (e.g. Proteomics, Rare diseases, COVID-19).

Explore and search bio.tools domains and manage your own domains. Read more about bio.tools domains here.

bio.tools COVID-19 related tools

See the bio.tools https://covid-19.bio.tools domain for a list of COVID-19 related tools.

If you believe any tools are missing, please feel free to update the list as specified in the instructions at https://covid-19.bio.tools.

You can also browse tools by EDAM concepts from the Virology and vaccine design section below.

What is bio.tools?

The use of bioinformatics is ubiquitous within the life sciences. In bio.tools, we are striving to provide a comprehensive registry of software and databases, facilitating researchers from across the spectrum of biological and biomedical science to find, understand, utilise and cite the resources they need in their day-to-day work.

Everything from simple command-line tools and online services, through to databases and complex, multi-functional analysis workflows is included. Resources are described in a rigorous semantics and syntax, providing end-users with the convenience of concise, consistent and therefore comparable information.

Each bio.tools entry is assigned a human-readable, unique identifier based on the resource name, e.g. biotools:signalp. These identifiers provide a persistent reference to our "Tool Cards" of essential information, as well as a means to trace resources and integrate bio.tools data with other resources.

All the bio.tools data and technical components are available under open license and we warmly welcome you to get involved. bio.tools development is supported by ELIXIR - the European infrastructure for life science information.

bio.tools is supported by ELIXIR through the ELIXIR-EXCELERATE grant, which is funded by the European Union Horizon 2020 program under grant agreement 676559.

Open Data

bio.tools content is freely available to all under CC BY 4.0 license - you are free to share and adapt the data, so long as you give credit and don’t restrict the freedom of others.

Open Source

bio.tools source code is freely available to all under GPL-3.0 - you are free to share and adapt our software, but you must ensure it remains free for all its users.

Built by You

We depend on the goodwill and enthusiasm of our 1000+ (and growing!) contributors - if you develop or provide tools and online services, please add them after signing-up.

Tool IDs

All bio.tools entries are assigned a human-friendly unique identifier, e.g. biotools:signalp. Once verified, a bio.tools ID provides a stable way to trace resources and integrate bio.tools data with other projects.

Standard Semantics

The scientific function of bio.tools resources can be precisely annotated in defined terms from the EDAM ontology, including common topics, operations, types of data and data formats.

Standard Syntax

bio.tools resource descriptions adhere to a rigorous syntax defined by biotoolsSchema, which provides regular expressions, controlled vocabularies and other syntax rules for 50 key attributes.

Community-driven

We rely upon scientific communities to improve the terminology and description of resources in different domains of the life sciences - we welcome your help with this work in progress.

Backed by ELIXIR

bio.tools is anchored within ELIXIR, the European Infrastructure for Biological Information. bio.tools will remain free, open and maintained in the long term.

Tools Platform

bio.tools is an integral part of the ELIXIR Tools Platform, enabling the development, description, discovery, re-use, deployment and benchmarking of software tools and workflows.

API

Our Web API provides an easy way to access the bio.tools data, allowing precise or alternatively flexible queries over all fields. Please see the API reference and API Usage Guide.

Documentation

Check out the docs for bio.tools, biotoolsSchema and the EDAM ontology - report any problems or make suggestions via GitHub.

Support

Whether you are a user of bio.tools, a developer who wants to add their tools, or a scientist who wants integrate our data with your own; help is at hand. Head over to GitHub or mail us directly.

Browse resources by popular terms

Explore bio.tools by the most popular bioinformatics concepts, or view all tools.

Concepts are defined in the EDAM ontology which you can browse at OLS, BioPortal or in the EDAM Browser.

Genetics

Resources for the study of genes and heredity in living organisms. They provide analytical approaches for studying gene structure, genetic variation, the regulation of gene expression and the relationships between organism genotype and phenotype.

Genetics Gene expression Gene regulation Gene expression profiling Transcription factors and regulatory sites Functional, regulatory and non-coding RNA Genetic variation DNA polymorphism Genotyping Genotype and phenotype Population genetics Gene functional annotation Gene and protein families Gene prediction Enrichment analysis Genome visualisation

Proteins

Resources for protein sequence analysis, protein visualization, and the prediction, modelling and analysis of protein structure. They provide analytical approaches to interpret and explore protein sequence and structure data, and to understand protein function and mechanism of action.

Protein sequence analysis Protein structure analysis Protein folds and structural domains Gene and protein families Protein structural motifs and surfaces Protein sites, features and motifs Transcription factors and regulatory sites Protein interactions Protein modelling Protein fold recognition Protein structure prediction Protein secondary structure prediction Protein binding site prediction Protein property calculation Protein subcellular localisation prediction Protein folding, stability and design

Nucleic acids

Resources for the processing and analysis of nucleic acid sequence, structural and other data. They provide analytical methods to interpret and explore nucleic acid sequence and structural data in context of gene structure, genetic variation, and the regulation of gene expression.

DNA RNA Genetic mapping Read mapping Functional, regulatory and non-coding RNA Methylation analysis DNA polymorphism SNP detection Nucleic acid sequence analysis Nucleic acid sites, features and motifs Nucleic acid feature detection Transcription factor binding site prediction Transcription factors and regulatory sites Transcriptional regulatory element prediction Nucleic acid structure analysis RNA secondary structure prediction

Sequence analysis

Resources for the processing and analysis of molecular sequences including sequence editing and visualisation, molecular sequence databases, binding sites, alignments and motifs in nucleic acid and protein sequences.

Sequence sites, features and motifs Sequence similarity search Sequence alignment Sequence motif recognition Sequence annotation Sequence visualisation Nucleic acid sequence analysis Nucleic acid feature detection Transcription factors and regulatory sites Protein sequence analysis Protein feature detection Sequence assembly Mapping Genome annotation PCR primer design Phylogenetics

Structure analysis

Resources for the processing and analysis of molecular structure data including the prediction and modelling of protein structure and interactions between nucleic acids, proteins and small molecules.

Structure analysis Molecular modelling Molecular docking Molecular dynamics Structure prediction Structure visualisation Protein structure analysis Protein folds and structural domains Protein structural motifs and surfaces Protein modelling Protein model validation Protein structure prediction Protein secondary structure prediction Nucleic acid structure analysis RNA secondary structure prediction Small molecules

Omics

Resources for the processing and analysis of the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.

Genomics Functional genomics Comparative genomics Population genomics Phylogenomics Metagenomics Transcriptomics Epigenomics Proteomics Structural genomics Metabolomics Pharmacogenomics

Virology and vaccine design

Resources which may be applicable to rational vaccine strategies for the design of novel immunogens capable of inducing long-term protective immunity.

Virology Virulence prediction Virtual screening Peptide immunogenicity prediction Epitope mapping DNA vaccine design Protein structure prediction Side chain modelling Backbone modelling Ligand-binding site prediction Protein-ligand docking Immunoinformatics Subcellular localisation prediction Immunoproteins and antigens Transmembrane protein prediction Molecular dynamics Molecular docking Public health and epidemiology Infectious disease Pathology

Other

Other popular concepts.

Sequencing Sequencing quality control Sequence assembly Genome annotation Systems biology Cell biology Molecular interactions, pathways and networks Pathway or network prediction Pathway or network visualisation Phylogeny Pathology Oncology Formatting Machine learning Image analysis Spectral analysis