Service list
Name of service | Description | Related links* |
---|---|---|
Network Analyzer |
A tool to visualize the output from the database for annotation, visualization and integrated discovery DAVID in order to reveal overlapping biological connections for a list of relevant genes. |
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Nextflow |
Enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. |
bio.tools |
neXtProt |
An innovative knowledge platform dedicated to human proteins. It contains a wealth of data on all the human proteins that are produced by the 20'000 protein- coding genes found in the human genome. |
bio.toolsFAIRsharing |
Nextstrain |
Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response. This resource supports COVID-19 / SARS-CoV-2 research. |
bio.tools |
NLP4BIA tools |
Textmining tools |
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Norine |
Norine has been and remains the unique resource dedicated to nonribosomal peptides (NRPs). It contains a database complemented with analysis tools (structure comparison, inference of monomer structure from chemical structure, mass spectrum analysis, NRP annotation for submission to the database). NRPs are secondary metabolites produced by bacteria and fungi and display a diverse spectrum of biological activity. |
bio.tools |
Ocean Gene Atlas |
The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences. |
bio.tools |
OLIDA |
Curated database of oligogenic diseases and genetic variants causing these diseases. The successor of DIDA, a similar database for digenic diseases |
bio.tools |
OMA |
OMA identifies orthologs among 2000 genomes from all domains of life. Other distinctive characteristics are the high quality of its inferences, the feature-rich web interface, and frequent update schedule of two releases per year. |
bio.toolsFAIRsharing |
Omics Discovery Index (OmicsDI) |
The Omics Discovery Index provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics). It indexes metadata from more than 20 omics resources across four continents. |
bio.toolsFAIRsharing |
OmniPath |
A database of causal protein-protein interactions, transcriptional and post-transcriptional regulation, enzyme-PTM interactions, protein complexes, annotations (function, disease roles, expression, localization, structure) and intercellular communication. Integrates data from more than 100 resources. |
bio.tools |
OMPdb |
OMPdb is a database of beta-barrel outer membrane proteins from Gram-negative bacteria. |
bio.tools |
Ontology for Nutritional Studies |
Terms that are commonly encountered while conducting, reporting, storing, harmonizing, integrating, and describing nutritional studies. ONS builds upon a subset of the Ontology for Biomedical Investigations (OBI), reuses already formalized information by importing terms already defined in other ontologies, and defines de novo key classes/terms to tailor concept to the nutritional field |
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OpenConext |
Open source software underlying the technology for SURF's single sign-on and facilitating national and international online collaboration in education and research. |
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OpenEBench |
OpenEBench (https://openebench.bsc.es) is the ELIXIR benchmarking and technical monitoring platform for bioinformatics tools, web servers and workflows. |
bio.tools |
OpenMS |
Mass Spec. analysis platform (See also Topp, LFQProfiler & RNPxl, MetaboProfiler) |
bio.tools |
OpenPepXL |
OpenMS tool for the study of Protein-Protein interactions. |
bio.tools |
Orange |
Open source software environment for development of biomedical data mining applications and data analysis workflows. |
bio.tools |
Orange4WS |
A service‐oriented environment for data mining, integrating web services as workflow components |
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Orione |
A Galaxy instance customized for data-intensive computational analyses in microbiology and metagenomics. |
bio.tools |
Orphadata |
Orphadata provides the scientific community with comprehensive, quality data sets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats. |
bio.toolsFAIRsharing |
Orphanet |
Orphanet is the reference resource for information and data on rare diseases and orphan drugs. Orphanet derives from its knowledge base an ontology of rare diseases, information on rare diseases and data on rare diseases. |
bio.toolsFAIRsharing |
OrthoDB |
OrthoDB is a comprehensive catalog of evolutionary and functional annotations of orthologs, covering over 22 million genes from over 5000 species of animals, fungi, plants, archaea, bacteria, and viruses. |
bio.toolsFAIRsharing |
ORVAL |
(Oligogenic Resource for Variant Analysis) is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). |
bio.tools |
OTP |
OTP = "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing. The application provides support in all steps of this process, including data transfer from temporary to final storage, execution of data quality monitoring programs, alignment of reads to the reference genome and variant calling. It allows full automatization, extended project administration, and full processing control for operators. |
bio.tools |
PanDrugs |
PanDrugs is a method to prioritize anticancer drug treatments according to individual genomic data. PanDrugs current version integrates data from 24 primary sources and supports 56297 drug-target associations obtained from 4804 genes and 9092 unique compounds |
bio.tools |
PANGAEA |
A service for the publishing, archiving and re-using data. |
bio.tools |
ParameciumDB |
ParameciumDB is a community model organism database for the ciliate Paramecium. The web site gives access to genomes of many Paramecium species and their annotations. ParameciumDB also integrates genome-wide datasets (DNA-seq, RNA-seq, ChIP-seq) provided by the community. This portal is used to query, retrieve, visualize and compare the most up-to-date public data. |
bio.tools |
Pasta |
Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences; |
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PatSearch |
To searches user submitted sequences for any combination of Position Weight Matrices (PWMs), primary sequence patterns and structural motifs. |
bio.tools |