title: FRED 2: an immunoinformatics framework for Python.
abstract: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications.
  
  
  
  FRED 2 is available at http://fred-2.github.io
  
  
  
  schubert@informatik.uni-tuebingen.de
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Schubert
authors.affiliation: Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany.
authors.forename: Mathias
authors.initials: M
authors.lastname: Walzer
authors.affiliation: Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany.
authors.forename: Hans-Philipp
authors.initials: HP
authors.lastname: Brachvogel
authors.affiliation: Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany.
authors.forename: András
authors.initials: A
authors.lastname: Szolek
authors.affiliation: Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany.
authors.forename: Christopher
authors.initials: C
authors.lastname: Mohr
authors.affiliation: Center for Bioinformatics, University of Tübingen, Tübingen 72076, Germany Department of Computer Science, Applied Bioinformatics, Tübingen 72076, Germany Quantitative Biology Center, Tübingen 72076, Germany Faculty of Medicine, University of Tübingen, Tübingen 72076, Germany Max Planck Institute for Developmental Biology, Biomolecular Interactions, Tübingen 72076, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry*; D006801:Humans; D016247:Information Storage and Retrieval; D012984:Software; D014612:Vaccines / Q000737:chemistry / Q000276:immunology
chemical_list: D018984:Epitopes, T-Lymphocyte; D014612:Vaccines