Service list

ASAP (Automated Single-cell Analysis Portal) is a web-based, collaborative portal aimed at democratizing single-cell omics data analyses and to render it more accessible to researchers. ASAP does not require any installation and enables standardized analyses that can be run in minutes by any user without requiring significant computing power. The entire single-cell analysis pipeline is available in ASAP, allowing users to choose from a panel of tools, and guiding them through tutorials.

Database to retrieve and compare gene expression patterns between animal species. 

The BioMedIT Network establishes a coordinated nationwide network of secure infrastructures to support computational biomedical research and clinical bioinformatics. Built on the centers of expertise established at partner universities (regional nodes), this network is managed by the Personalized Health Informatics Group, a group of the SIB Swiss Institute for Bioinformatics. 

BUSCO provides quantitative measures for the assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.

Continuous automated benchmarking of computational protein structure prediction methods (and model quality estimation techniques). CAMEO assessment is based on blind predictions for weekly pre-released targets from PDB. 

A knowledge resource on cell lines.

CLASTR, the Cellosaurus STR similarity search tool enables users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication and detecting potential contamination and misidentification cases.

ENZYME is a repository of information on enzyme nomenclature based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). ENZYME describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.

An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Pointers to positions in nucleotide sequence entries provide access to promoter sequences. 

SIB's resource portal with access to all major tools and databases provided by different SIB groups and external partners. Specific query features allow interacting with many resources at the same time. 

Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help the research communities to make and keep data Findable, Accessible, Interoperable and Reusable (FAIR). The FAIR Cookbook guides researchers and data stewards of the Life Science domain in their FAIRification journey and provides policy makers and trainers with practical examples to recommend in their guidance and use in their educational material. As a UK-LU joint Node Service, we will continue the development the FAIR Cookbook as well as collaborate towards its sustainability.

This is a joint Node Service between ELIXIR Luxembourg and ELIXIR UK.

Glyco@Expasy centralizes web-based glycoinformatics resources developed within an international network of glycoscientists. The philosophy is that it should be {glycoscientist AND protein scientist}–friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. Glyco@Expasy was designed with glycoscientists to meet the growing needs of the community for glycoinformatics.

GlyConnect is a platform integrating several sources of information to characterise the molecular actors of glycosylation, mainly glycoproteins and N- and O-linked glycans. The purpose of GlyConnect is to bring out in a single resource the relationships between glycans, the proteins that carry them, the enzymes that synthesise or degrade them and the proteins that bind them.

HAMAP is a system for the classification and functional annotation of protein sequences. It consists of a collection of expert curated family profiles for protein classification and associated rules for protein annotation. 

Integrated Proteogenomics DataBases an open source database that provides integrated annotations, predictions and a six-frame translation for one respective genome sequence in an easily usable format, both as a search DB (FASTA format) with informative identifiers and a GFF file that integrates all annotations and identifiers.

Models genome-wide expression data in terms of genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample- dependent activities, and their genome-wide targets. 

MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments - namely MNXref - and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

The MHC Motif Atlas helps visualize, analyse, and compare the different binding specificities of thousands of class I and class II MHC molecules, and includes binding motifs, peptide length distributions, motifs of phosphorylated ligands, multiple specificities, or links to X-ray crystallography structures.

The archive for structural models which are not based on experimental data and complements the PDB archive for experimental structures and PDB- Dev for integrative structures. Any type of macromolecular structure which would otherwise be suitable for the PDB but whose coordinates are not based on experimental data can be deposited in ModelArchive. This includes single chains or complexes consisting of proteins, RNA, DNA, or carbohydrates including small molecules bound to them.

The mOTUs tool uses phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) to profile microorganisms at species-level resolution when using metagenomic data as input. Since the MGs represent housekeeping genes, mOTUs can also be used to profile transcriptionally active community members when using metatranscriptomic data as input. Furthermore, MG-based SNV profiling provides an efficient alternative to using whole genome sequences to compare microbial strain populations.

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. 

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.

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. 

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. 

The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. 

PROSITE consists of entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. PROSITE is a key element of the UniProt annotation pipeline “UniRule”. 

REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites are available for download after the analysis is finished.

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. 

sciCORE provides a high-performance computing infrastructure, large-scale storage resources, scientific software and databases, server infrastructures and user support. It also provides expertise to scientific research groups.

The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies.  (https://pubmed.ncbi.nlm.nih.gov/32379317/)