Webservices hosted at sciCORE

Web interfaces can proviode 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 Protein Model Portal is developped in colaboration with the RCSB PDB as a module of the structural biology knowledgebase, and integrates information on experimental structures and theoretical models from different resources. PMP  (PMP is supported by a sub-grant to Rutgers University from the National Institute of General Medical Sciences of the National Institutes of Health.)
Developed at SIB & University of Basel. Group Torsten Schwede.
CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. Our platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.
Developed at SIB & University of Basel. Group Mihaela Zavolan.

 

Locally hosted services

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

 

Galaxy is an open source, web-based platform for data intensive biomedical research developed at Penn State University and Johns Hopkins University. It provides an easy way to perform, reproduce, and share complete analyses.
LabKey is an open source biomedical data management system. LabKey is compliant with the Swiss law on human research (Human Research Act, HRA).
openBIS is an open, distributed system for managing biological information. The main goal is to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized e.g. for High Content Screening, Proteomics, Deep Sequencing, and Metabolomics. openBIS has been developed by the CISD group at winthin the SystemsX.ch SyBIT project.