Service list

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/)

SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions. This information is extracted from public documents and package inserts. SIDER makes available side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations. It currently covers associations between 5,868 side effects and 1,430 drugs. Part of the Human Omics Analysis Toolbox. 

SIENA has been developed for the automated assembly and preprocessing of protein binding site ensembles.

The SIGnaling Network Open Resource annotates signaling information from the literature as binary causative relationships.

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

Data Analysis service for ribosomal RNA

Web application to compare multiple protein structural motifs.

slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing identification of biological drivers of cell-to-cell variability and model confounding factors.

SMART (Simple Modular Architecture Research Tool) is a web resource providing simple identification and extensive annotation of protein domains via sequence homology searches. It contains manually curated models for more than 1,200 protein domains. In its ‘Genomic’ mode, it annotates proteins from completely sequenced genomes of 2,031 species as a basis for their functional annotation. It provides flexible tools to visually explore protein domain architectures across sequences and organisms. Part of the Human Omics Analysis Toolbox. 

SNPmasker is a program to mask all SNPs in given sequence using information of dbSNP. Additionally it is possible to mask all non-unique words using GenomeMasker module.

Prediction of single point protein mutations likely to be involved in disease.

Structural and physico-chemical interpretation of QSAR models

A database of RNA-binding splicing regulatory proteins reporting functional domains, protein and chemical interactors and expression data.

The Swiss Pathogen Surveillance Platform (SPSP) is a secure One-health online platform that enables near real-time sharing under controlled access of pathogen sequencing data and their associated clinical/epidemiological metadata.

SQANTI3 is the first module of the [Functional IsoTranscriptomics (FIT)](https://tappas.org/) framework, which also includes IsoAnnot and tappAS.

Nextflow pipeline for splicing quantitative trait loci (sQTL) mapping based on sQTLseekeR2, performing the following analysis steps:

1. Index the genotype file
2. Preprocess the transcript expression data
3. Test for association between splicing ratios (a multivariate phenotype) and genetic variants in cis (nominal pass)
4. Obtain an empirical P-value for each phenotype (permutation pass, optional)
5. Control for multiple testing.

Analysis workflow for plant sRNA sequencing data.

Software for Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation.

 SSAM-lite is a lightweight, browser-based implementation of the SSAM framework. It provides the functionality of SSAMs most popular and widely used features in a graphical user interface with a few functions added for convenience and ease of use. It can be run on a modest laptop.

A validated reference peptide database for targeted proteomics. (Formerly QSDB)

Either as a cooperation or consultancy service.

• Cineca
• INFN
• GARR

STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. 

StructureProfiler is a tool to screen structures based on selection criteria typically used upon dataset assembly for structure-based design methods.

SulfAtlas is a knowledge-based database which (i) helps to better annotate sulfatases in (meta)genomic data and notably to improve the prediction of substrate specificities; (ii) guides the experimental biologists to select target sulfatases which remain to be characterized in term of function and structure. The data contained in SulfAtlas is curated by experts, based on our phylogeny-based classification system and on literature.

SweeD is a high-performance computing software that detects the site of the beneficial mutation, using the Site Frequency Spectrum. It can analyze whole genome data of thousands of individuals in a few hours.

Database of protein expression time series for specific experiments on streptomyces, caulobacter, neiseria.

SWISS-MODEL Repository is a continuously updated database of annotated protein structure homology models generated by the fully automated SWISS-MODEL modelling pipeline. 

SWISS-MODEL is a fully automated service for protein structure homology modelling. It provides a personal web based workspace for interactive modelling, storing project data and visualizing results online. 

SwissBioPics is a freely available library of interactive biological images for visualizing subcellular location data. It includes cell types from all kingdoms of life - from muscle, neuronal and epithelial cells of animals to rods, cocci, clubs, spirals, and other more exotic forms of bacteria and archaea.