Identifying and supporting SIB Resources
Every four years, the Institute’s External Scientific Advisory Board (SAB) provides recommendations on the portfolio of SIB-supported Resources. By taking into account competitive criteria – such as the impact and scientific return on investment of candidate resources – together with SIB’s global portfolio management and strategic orientation, the SAB identifies best-in-class resources, and provides guidelines for their continuous development. Based on these recommendations, the Board of Directors decides the allocation of funding and the SIB Management team then assists the groups developing the resources in implementing their action plan. Since 2018 a 'This email address is being protected from spambots. You need JavaScript enabled to view it.' initiative is dedicated to our resources' developers, in order to help them to grow their user base and share their know-how with the community (more information for our members).
Click on the resource name to find out more about the resource and to access the corresponding webpage - or go to Expasy to access all resources by SIB Groups
ASAP
Automated single-cell analysis portal
- Type: Software tool
- Description: Collaborative web portal aimed at democratizing single-cell omics data analyses for researchers. The entire single-cell analysis pipeline is available in ASAP, allowing users to choose from a panel of tools and guiding them through tutorials.
Bgee
Gene expression expertise
Marc Robinson-Rechavi group, contact person: This email address is being protected from spambots. You need JavaScript enabled to view it.
- Type: Knowledgebase with expert curation and software tool
- Description: Gene expression data including all types of transcriptomes, allowing retrieval and comparison of expression patterns between animals, human, model organisms and diverse species of evolutionary or agronomical relevance.
Cellosaurus
The cell lines knowledge resource
- Type: Knowledgebase with expert curation
- Description: Attempts to describe all cell lines used in biomedical research, including immortalized cell lines, naturally immortal cell lines (stem cell lines), finite life cell lines when those are distributed and widely used, vertebrate cell lines with an emphasis on human, mouse and rat cell lines, and invertebrate (insect and tick) cell lines.
Press coverage: «Toutes les espèces animales multicellulaires peuvent générer des lignées» - Le Temps
Cellosaurus is an ELIXIR Core Data Resource
Glyco@Expasy
Zooming in on web-based glycoinformatics resources
- Type: Tools and knowledgebases with expert curation
- Description: Web portal of glycoinformatics resources developed within an international network of glycoscientists to popularize the use of bioinformatics in glycobiology and to emphasize the relationship between glycobiology and protein-oriented bioinformatics resources.
Nextstrain
Real-time tracking of pathogen evolution
- Type: Software tool
- Description: Open-source project to harness the scientific and public health potential of pathogen genome data (e.g. SARS-CoV-2, influenza, ebola) by providing continually-updated view of publicly available data alongside powerful analysis and visualization tools.
Rhea
Knowledgebase of biochemical reactions
- Type: Knowledgebase with expert curation
- Description: Rhea is an expert curated knowledgebase of enzyme and transport reactions which uses the chemical ontology ChEBI to represent reaction participants. Rhea is the standard for enzyme and transporter annotation in UniProtKB and is used to build SwissLipids and MetaNetX.
Rhea is an ELIXIR Core Data Resource and a Global Core Biodata Resource
STRING
Protein-protein Interaction Networks and Functional Enrichment Analysis
Christian von Mering group, contact person: Damian Szklarczyk
- Type: Knowledgebase and software tool
- Description: Resource for known and predicted protein-protein interactions, including direct (physical) and indirect (functional) associations derived from various sources, such as genomic context, high-throughput experiments, (conserved) co-expression and the literature.
STRING is an ELIXIR Core Data Resource and a Global Core Biodata Resource
SwissDrugDesign
Widening access to computer-aided drug design
Olivier Michielin & Vincent Zoete group
- Type: Software tools
- Description: Web portal of computer-aided drug design tools, from molecular docking (SwissDock) to pharmacokinetics and druglikeness (SwissADME), through virtual screening (SwissSimilarity), lead optimization (SwissBioisostere) and target prediction of small molecules (SwissTargetPrediction).
SwissLipids
A knowledge resource for lipids
- Type: Knowledgebase
- Description: Information about lipids, including lipid structures, metabolism and interactions, providing a framework for the integration of lipid and lipidomics data with biological knowledge and models.
SWISS-MODEL
Protein structure homology-modelling
Torsten Schwede group, contact persons: This email address is being protected from spambots. You need JavaScript enabled to view it.
- Type: Software tool and repository
- Description: Automated protein structure homology-modelling platform for generating 3D models of a protein using a comparative approach, and database of annotated models for key reference proteomes based on UniProtKB.
SwissOrthology
One-stop shop for orthologs
Christophe Dessimoz and Evgeny Zdobnov & Evgenia Kriventseva groups
- Type: Phylogenomic databases and software tools
- Description: Web portal of resources to infer orthologs, i.e. corresponding genes across different species, a key aspect to predicting gene function or reconstructing species trees. It includes OrthoDB, BUSCO as well as OMA and the Quest for Orthologs benchmark service.
SwissRegulon Portal
Tools and data for regulatory genomics
- Type: Software tools and knowledgebases
- Description: Web portal for regulatory genomics, including genome-wide annotations of regulatory sites and motifs, the web server ISMARA for automated inference of regulatory networks and CRUNCH for automated analysis of ChIP-seq data, and REALPHY for reconstructing phylogenies from raw sequence data.
UniProtKB/Swiss-Prot
Protein knowledgebase
- Type: Knowledgebase with expert curation
- Description: Hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants.
Read about the latest news using this resource
UniProt is an ELIXIR Core Data Resource and a Global Core Biodata Resource
V-Pipe
Viral genomics pipeline
- Type: Software tool
- Description: Pipeline integrating various open-source software packages for assessing viral genetic diversity from next-generation sequencing data.