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 

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ASAP

Automated single-cell analysis portal

Bart Deplancke group

  • 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.
  • Highlight: ASAP allows releasing datasets and versioned analyses up to millions of cells such as the Human Cell Atlas or the Fly Cell Atlas, that can be made directly available as public projects within the tool.

 

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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.
  • Highlight: Only resource to provide homologous gene expression comparisons between species.

 

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Cellosaurus

The cell lines knowledge resource

Amos Bairoch group

  • 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.
  • Highlight: An ELIXIR Core Data Resource and International Rare Diseases Research Consortium (IRDiRC) recognized resource.

 

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EPD

Eukaryotic Promoter Database

Philipp Bucher group, contact person: Giovanna Ambrosini

  • Type: Knowledgebase with expert curation and software tools
  • Description: Quality-controlled information on experimentally defined promoters of higher organisms, as well as web-based tools for promoter analysis.
  • Highlight: Over 190,000 promoters downloadable, analysable over a web interface and viewable in the UCSC genome browser.
 

 

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Glyco@Expasy

Zooming in on web-based glycoinformatics resources

Frédérique Lisacek group

  • 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.
  • Highlight: Designed to be glycoscientist and protein scientist friendly and to facilitate data exploration and support hypothesis building.
 

 

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neXtProt

Human protein knowledgebase

Amos Bairoch & Lydie Lane group

  • Type: Knowledgebase with expert curation and associated tools
  • Description: Information on human proteins such as function, involvement in diseases, mRNA/protein expression, protein/protein interactions, post-translational modifications, protein variations and their phenotypic effects.
  • Highlight: High data coverage through inte-gration of multiple sources. Advanced semantic search functionalities. Tools specifically designed for the proteomics community.
 

 

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Nextstrain

Real-time tracking of pathogen evolution

Richard Neher group

  • 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.
  • Highlight: The narratives feature is a method to support data-driven storytelling, which allows authoring of content displayed alongside a view into the data.
 

 

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Rhea

Knowledgebase of biochemical reactions

Alan Bridge group

  • 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.
  • Highlight: Rhea helps AI learn how enzymes function. An ELIXIR Core Data Resource.
 

 

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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.
  • Highlight: An ELIXIR Core Data Resource. STRING networks cover over 5,000 different organisms with over 25 million high-confidence links between proteins.

 

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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).
  • Highlight: Comprehensive and integrated web-based drug design environment.
 

 

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SwissLipids

A knowledge resource for lipids

Alan Bridge group

  • 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.
  • Highlight: Information on more than 590,000 lipid structures from over 640 lipid classes.
 

 

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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.
  • Highlight: Easy-to-use web-based platform processing over two million model requests per year, providing model information for experts and non-specialists.

 

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SwissOrthology

One-stop shop for orthologs

  • 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.
  • Highlight: World-leading orthology and comparative genomic resources.

 

 
Swiss Regulon

SwissRegulon Portal

Tools and data for regulatory genomics

Erik van Nimwegen group

  • 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.
  • Highlight: Allows users to upload raw microarray, RNA-seq or ChIP-seq data to automatically infer the core regulatory networks acting in their system of interest.

 

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UniProtKB/Swiss-Prot

Protein knowledgebase

Alan Bridge group

  • 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.
  • Highlight: Expert-curated part of UniProt, the most widely used protein information resource in the world, with over six million pageviews per month. An ELIXIR Core Data Resource.
 

 

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V-Pipe

Viral genomics pipeline

Niko Beerenwinkel group

  • Type: Software tool
  • Description: Pipeline integrating various open-source software packages for assessing viral genetic diversity from next-generation sequencing data.
  • Highlight: Enabling reliable and comparable viral genomics and epidemiological studies and facilitating clinical diagnostics of viruses.