- Proteins & Proteomes

- Database

UniProtKB/Swiss-Prot

Protein knowledgebase

- Systems Biology

- Software tool

OMAMO

OMAMO allows the user to find the best simple model organism

- Transcriptomics
- Evolution & Phylogeny
- Systems Biology

- Database
- Software tool

SwissRegulon Portal

Tools and data for regulatory genomics

- Genes & Genomes
- Systems Biology

- Software tool

CREMA

Cis-Regulatory Element Motif Activities

- Transcriptomics
- Systems Biology

- Software tool

CRUNCH

Automated pipeline for ChIP-seq data analysis

- Proteins & Proteomes

- Database

UniProt SPARQL endpoint

SPARQL access to UniProt and related data

- Transcriptomics

- Database

PolyAsite

Database of curated RNA polyadenylation sites

- Genomics

- Database
- Software tool

EPD

Eukaryotic Promoter Database

- Transcriptomics

- Database
- Software tool

ASAP

Web-based, cooperative portal for single-cell data analyses

- Systems Biology

- Database

Cellosaurus

Knowledge resource on cell lines

- Systems Biology

- Database

Cellosaurus SPARQL endpoint

SPARQL access to Cellosaurus

- Transcriptomics
- Evolution biology

- Database
- Software tool

Bgee

Gene expression expertise

- Transcriptomics
- Evolution biology

- Database

Bgee SPARQL endpoint

SPARQL access to the Bgee gene expression database

- Proteins & Proteomes
- Systems Biology

- Database
- Software tool

STRING

Protein-protein interaction networks and enrichment analysis

- Proteins & Proteomes

- Database

UniProtKB

Protein sequence database

- Evolution & Phylogeny

- Database
- Software tool

OMA

Orthology inference among complete genomes

- Evolution & Phylogeny

- Database

OMA SPARQL endpoint

SPARQL access to the OMA Orthology database

- Evolution & Phylogeny

- Database

OrthoDB

Ortholog evolutionary and functional annotations

- Evolution & Phylogeny

- Database

OrthoDB SPARQL endpoint

SPARQL access to the OrthoDB catalog of orthologs

- Proteins & Proteomes
- Structural Biology

- Database

SWISS-MODEL Repository

Protein structure homology models

- Proteins & Proteomes
- Glycomics

- Database

GlyConnect

Integrated data platform to study glycosylation

- Proteins & Proteomes
- Glycomics

- Database

UniLectin

Structural and functional classification of lectins

- Transcriptomics
- Systems Biology

- Database

SwissRegulon

Database of genome-wide annotations of regulatory sites

- Proteins & Proteomes
- Glycomics

- Database

MatrixDB

Extracellular proteins and polysaccharides interactions

- Proteins & Proteomes

- Database
- Software tool

PaxDb

Protein abundance across several organisms

- Genes & Genomes
- Evolution & Phylogeny

- Database
- Software tool

SwissOrthology

One-stop shop for orthologs

- Structural Biology

- Database

ModelArchive

Repository of predicted macromolecular structure models

- Transcriptomics

- Software tool

miRmap

Prediction of microRNA target repression strength

- Genomics
- Evolution biology

- Database

Selectome

Database of positive selection

- Proteins & Proteomes
- Metabolomics

- Database
- Software tool

MetaNetX

Metabolic network repository & analysis

- Proteins & Proteomes
- Metabolomics

- Database

MetaNetX SPARQL endpoint

SPARQL access to MetaNetX

- Proteins & Proteomes

- Database

ABCD

Database of chemically defined antibodies

- Transcriptomics

- Software tool

TagScan

Genome-wide sequence tag scanner

- Transcriptomics

- Database
- Software tool

Fly Cell Atlas

Single-cell transcriptomes of the entire adult Drosophila

- Transcriptomics
- Proteins & Proteomes
- Systems Biology

- Software tool

NOODAI

Multi-omics data analysis and integration

- Genes & Genomes
- Proteins & Proteomes

- Software tool

MetaGraph

Petabase-scale sequence search

- Proteins & Proteomes
- Evolution & Phylogeny

- Database
- Software tool

Orthology Benchmarking

Quest for Orthologs benchmarking service

- Evolution & Phylogeny

- Software tool

FastOMA

Orthology inference at scale

- Genomics
- Evolution & Phylogeny

- Software tool

Nextclade

Clade assignment and quality control for viral genomes

- Genomics
- Population genetics

- Software tool

V-pipe

Viral genomic variant detection pipeline

- Evolution & Phylogeny

- Software tool

raxmlGUI

raxmlGUI 2.0 is a graphical user interface to RAxML

- Proteins & Proteomes
- Structural analysis

- Software tool

SWISS-MODEL Workspace

Fully automated protein structure homology-modeling server

- Proteins & Proteomes

- Database
- Software tool

HAMAP

UniProtKB family classification and annotation

- Genes & Genomes
- Evolution & Phylogeny

- Software tool

REALPHY

Inference of phylogenetic trees from genome data

- Genomics
- Population genetics

- Software tool

V-pipe SARS-CoV-2

V-pipe pipeline for SARS-CoV-2 sequencing data

- Genomics
- Evolution biology

- Software tool

Nextstrain

Real-time tracking of pathogen evolution

- Genomics

- Software tool

ShoRAH

Analysis of NGS data

- Structural analysis

- Software tool

OpenStructure

Molecular modelling and visualisation environment

- Metagenomics

- Software tool

LEMMI

Continuous benchmarking of methods for metagenomics

- Structural analysis

- Software tool

SwissParam

Topology and parameters for small molecules

- Proteins & Proteomes
- Structural Biology

- Database
- Software tool

CAMEO

Weekly automated benchmarking of protein structure modelling

- Transcriptomics
- Systems Biology

- Software tool

ISMARA

Webservice for gene expression and epigenetic data analysis

- Genomics
- Systems Biology

- Software tool

Phylogibbs

Regulatory sites in a collection of DNA sequences

- Transcriptomics
- Systems Biology

- Software tool

DWT-online

Dinucleotide Weight Tensor toolbox and visualisation service

- Proteins & Proteomes

- Software tool

MSight

Mass Spectrometry Imager

- Proteins & Proteomes

- Software tool

MELANIE

2-D PAGE analysis

- Proteins & Proteomes

- Software tool

HAMAP-Scan

Scanning of protein sequences against HAMAP families

- Proteins & Proteomes

- Database

HAMAP SPARQL endpoint

SPARQL access to the HAMAP annotation rules

- Proteins & Proteomes

- Software tool

prolfqua

R package for protein differential expression analysis

- Transcriptomics

- Database

Glittr

Git repositories with bioinformatics training material

- Transcriptomics

- Software tool

QuasR

Quantification and analysis of Short Reads

- Transcriptomics
- Systems Biology

- Software tool

Bonsai

Analysis of single cell RNA-seq data

- Metagenomics

- Software tool

MAGFlow/BIgMAG

Metagenome metrics and taxonomical annotation visualization

- Genomics

- Software tool

Loculus

Infrastructure for managing pathogen genomic data

- Proteins & Proteomes

- Database
- Software tool

neXtProt

Human protein knowledgebase

- Glycomics

- Software tool

HMO-Glycologue

Simulator of Human Milk Oligosaccharide synthesis

- Systems Biology

- Software tool

CLASTR

Cellosaurus STR similarity search tool

- Proteins & Proteomes
- Structural analysis

- Software tool

SwissTargetPrediction

Target prediction for bioactive small molecules

- Genes & Genomes
- Systems Biology

- Database

cancercelllines.org

Genomic variants in human cancer cell lines

- Genomics
- Systems Biology

- Database

arrayMAP

Curated array data repository for cancer genomics

- Proteins & Proteomes
- Glycomics

- Database

SugarBind

Pathogen Sugar-Binding Database

- Genomics

- Database
- Software tool

SNP2TFBS

Regulatory SNPs affecting TF binding site affinity

- Genes & Genomes
- Systems Biology

- Database

Progenetix

Genomic profiles of cancer samples with focus on CNV

- Structural Biology
- Glycomics

- Database

UniCarb-DB

Glycan structures and associated mass spectrometry data

- Text mining & Machine learning

- Software tool

Variomes

Search engine to support the curation of genomic variants

- Transcriptomics

- Database
- Software tool

Human Cell Atlas

Mapping the human body at the cellular level

- Proteins & Proteomes
- Text mining & Machine learning

- Database

MHC Motif Atlas

- Systems Biology

- Database

SPHN Metadata Catalog

Central access point for FAIR health datasets in Switzerland

- Systems Biology

- Database

SPHN SPARQL endpoint

SPARQL access to the SPHN data

- Metagenomics
- Systems Biology

- Database

HuMSub Catalog

Human gut microbiota subspecies catalog

- Genomics
- Evolution biology

- Software tool

CT-CBN

Estimate conjunctive Bayesian networks

- Genomics
- Evolution biology

- Software tool

GenSpectrum

Real-time pathogen genomic sequence analysis

- Genomics
- Population genetics

- Software tool

fastsimcoal

Fast sequential Markov coalescent simulation of genomic data

Foldtree

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