ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

PLoS One. 2016 Feb 16;11(2):e0149263. doi: 10.1371/journal.pone.0149263. eCollection 2016.


Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ceramides / metabolism
  • Computational Biology / methods*
  • Gene Expression*
  • Humans
  • Internet*
  • Kinetics
  • Models, Biological
  • NF-kappa B / metabolism
  • Signal Transduction
  • Software*
  • Statistics as Topic*
  • Systems Biology / methods*
  • Transcription Factors / metabolism


  • Ceramides
  • NF-kappa B
  • Transcription Factors

Grant support

The research leading to this work was funded by the Innovative Medicine Initiative Joint Undertaking (IMI JU) under grant agreement nr. 115001 (MARCAR project) and a Marie Curie International Outgoing Fellowship within the EU 7th Framework Program for Research and Technological Development (project AMBiCon, 332020). The authors acknowledge support by the German Research Foundation (DFG) and the Open Access Publishing Fund of the University of Tuebingen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.