Römer, Michael and Eichner, Johannes and Dräger, Andreas and Wrzodek, Clemens and Wrzodek, Finja and Zell, Andreas

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

PLoS ONE vol. 11 (2016), no. 2, Public Library of Science, pp. e0149263


Abstract

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.


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BibTeX

@article{Roemer2016a,
  author = {R\"omer, Michael and Eichner, Johannes and Dr\"ager, Andreas and
    Wrzodek, Clemens and Wrzodek, Finja and Zell, Andreas},
  title = {{ZBIT Bioinformatics Toolbox: a Web-Platform for Systems Biology
    and Expression Data Analysis}},
  year = {2016},
  month = feb,
  number = {2},
  volume = {11},
  pages = {e0149263},
  journal = {PLoS ONE},
  publisher = {Public Library of Science},
  abstract = {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 \url{https://webservices.cs.uni-tuebingen.de}.},
  doi = {10.1371/journal.pone.0149263},
  keywords = {Transcription factors, Bioinformatics, DNA-binding proteins, Genome analysis, Systems biology, Software tools, Carcinogens, User interfaces},
  url = {http://dx.doi.org/10.1371%2Fjournal.pone.0149263},
}