title: ballaxy: web services for structural bioinformatics.
abstract: BACKGROUND
  Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together.
  
  
  RESULTS
  In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.
  
  
  METHODS
  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL.
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Anna Katharina
authors.initials: AK
authors.lastname: Hildebrandt
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Stöckel
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Nina M
authors.initials: NM
authors.lastname: Fischer
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Luis
authors.initials: L
authors.lastname: de la Garza
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Krüger
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Nickels
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Röttig
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Charlotta
authors.initials: C
authors.lastname: Schärfe
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Schumann
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Thiel
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Lenhof
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
authors.affiliation: Center for Bioinformatics, Saarland University, 66041 Saarbrücken, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72607 Tübingen and Chair for Software-Engineering and Bioinformatics, Institute for Informatics, Johannes-Gutenberg-University Mainz, 55128 Mainz, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hildebrandt
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface; D057188:Workflow