title: ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.
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/.
authors.affiliation: Department of Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Römer
authors.affiliation: Department of Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Eichner
authors.affiliation: Department of Computer Science, University of Tübingen, Tübingen, Germany.|Department of Bioengineering, University of California, San Diego, San Diego, California, United States of America.
authors.forename: Andreas
authors.initials: A
authors.lastname: Dräger
authors.affiliation: Department of Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Clemens
authors.initials: C
authors.lastname: Wrzodek
authors.affiliation: Department of Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Finja
authors.initials: F
authors.lastname: Wrzodek
authors.affiliation: Department of Computer Science, University of Tübingen, Tübingen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Zell
mesh_terms: D002518:Ceramides / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D015870:Gene Expression; D006801:Humans; D020407:Internet; D007700:Kinetics; D008954:Models, Biological; D016328:NF-kappa B / Q000378:metabolism; D015398:Signal Transduction; D012984:Software; D013223:Statistics as Topic; D049490:Systems Biology / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002518:Ceramides; D016328:NF-kappa B; D014157:Transcription Factors