Webservices hosted at sciCORE

Web interfaces can provide easy and user friendly access to complex computational pipelines. sciCORE is hosting a number of well-established computational web based services which are developed by researchers at the University of Basel and are used both by local users as well as the international scientific community.

 
The SWISS-MODEL Workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. Each of the four steps -  identification of structural template(s), alignment of target sequence and template structure(s), model building, and model quality evaluation - requires specialized software and access to up-to-date protein sequence and structure databases. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. SWISS-MODEL is widely used for teaching and research - with more than 250'000 registered users worldwide. (SWISS-MODEL is supported by SIB)
Prof. Torsten Schwede - website SWISS-MODEL
 
The Continuous Automated Model EvaluatiOn (CAMEO) is a benchmarking service continuously evaluating the accuracy and reliability of protein structure prediction servers. CAMEO automatically assesses the servers on a weekly basis. Developed by the Computational Structural Biology Group at the Swiss Institute of Bioinformatics (SIB) and the Biozentrum of the University of Basel.
 
PolyASite is a portal developed by the Zavolan lab to curated polyadenylation (poly(A)) sites for several organisms (currently human, mouse and worm). As the alternative cleavage and polyadenylation (APA) of messenger RNAs has been implicated in changes in cell state related to proliferation, differentiation and diseases, PolyASite aims to serve as a reference resource in the study of APA in all of these contexts. The resource was curated from many data sets, obtained from many cell types and by different techniques designed to specifically capture RNA 3’ ends. PolyASite facilitates efficient finding, exploration and export of poly(A) sites, and includes estimates of the relative use of each site across all of the analyzed samples.
 
ISMARA - The Integrated System for Motif Actitivity Response Analysis is an online tool that models genome-wide expression or ChIP-seq data, in terms of computationally predicted regulatory sites for transcription factors (TFs) and micro-RNAs (miRNAs). The only input required for running ISMARA is either expression data (microarray CEL files or RNA-seq FASTQ and BED/BAM/SAM alignment files), or ChIP-seq data (FASTQ and BED/BAM/SAM alignment files), from a set of biological samples. Using the given gene expression or chromatin state data across a set of samples, ISMARA identifies the key transcription factors and miRNAs driving the observed expression/chromatin state changes, and makes detailed predictions regarding their regulatory roles. Results include, for each regulatory motif, inferred activities across the input samples, predicted genome-wide targets, enriched pathways and functional classes of genes, and direct interactions between regulators. All results are presented within interactive and easily navigable HTML pages. The full results are also available for download.

Locally hosted services

sciCORE is hosting several web based services and tools to support the local scientific user community, e.g.

 

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
For users with a sciCORE account, RStudio can be accessed here.
LabKey is an open source biomedical data management system. LabKey is compliant with the Swiss law on human research (Human Research Act, HRA).
REDcap is web application for building and managing online surveys and databases. It offers a free, easy-to-use, and secure method of flexible yet robust data collection.