Cite

If you use our work for your research and publications result from that, we would kindly ask you to cite us. If you use only BALL please cite the following article:

  • A. Hildebrandt, A. K. Dehof, A. Rurainski, A. Bertsch, M. Schumann, N. C. Toussaint, A. Moll, D. Stöckel, S. Nickels, S. C. Mueller, H. Lenhof, and O. Kohlbacher, "BALL--biochemical algorithms library 1.3.," Bmc bioinformatics, vol. 11, iss. 1, p. 531, 2010.
    [Bibtex]
    @article{Hildebrandt2010,
    abstract = {The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements.},
    author = {Hildebrandt, Andreas and Dehof, Anna Katharina and Rurainski, Alexander and Bertsch, Andreas and Schumann, Marcel and Toussaint, Nora C and Moll, Andreas and St\"{o}ckel, Daniel and Nickels, Stefan and Mueller, Sabine C and Lenhof, Hans-Peter and Kohlbacher, Oliver},
    file = {:Users/thiel/Library/Application Support/Mendeley Desktop/Downloaded/Hildebrandt et al. - 2010 - BALL--biochemical algorithms library 1.3.pdf:pdf},
    issn = {1471-2105},
    journal = {BMC bioinformatics},
    keywords = {Algorithms,BALL,Computational Biology,Computational Biology: methods,Databases, Factual,Software},
    mendeley-tags = {BALL},
    month = jan,
    number = {1},
    pages = {531},
    title = {{BALL--biochemical algorithms library 1.3.}},
    url = {http://www.biomedcentral.com/1471-2105/11/531},
    volume = {11},
    year = {2010}
    }

If you use BALLView please additionally cite:

  • [DOI] A. Moll, A. Hildebrandt, H. Lenhof, and O. Kohlbacher, "BALLView: a tool for research and education in molecular modeling.," Bioinformatics (oxford, england), vol. 22, iss. 3, pp. 365-6, 2006.
    [Bibtex]
    @article{Moll2006,
    abstract = {We present BALLView, a molecular viewer and modeling tool. It combines state-of-the-art visualization capabilities with powerful modeling functionality including implementations of force field methods and continuum electrostatics models. BALLView is a versatile and extensible tool for research in structural bioinformatics and molecular modeling. Furthermore, the convenient and intuitive graphical user interface offers novice users direct access to the full functionality, rendering it ideal for teaching. Through an interface to the object-oriented scripting language Python it is easily extensible.},
    author = {Moll, Andreas and Hildebrandt, Andreas and Lenhof, Hans-Peter and Kohlbacher, Oliver},
    doi = {10.1093/bioinformatics/bti818},
    file = {:Users/thiel/Library/Application Support/Mendeley Desktop/Downloaded/Moll et al. - 2006 - BALLView a tool for research and education in molecular modeling.pdf:pdf},
    issn = {1367-4803},
    journal = {Bioinformatics (Oxford, England)},
    keywords = {BALL,Computer Graphics,Computer Simulation,Computer-Assisted Instruction,Computer-Assisted Instruction: methods,Models, Molecular,Molecular Biology,Molecular Biology: education,Molecular Biology: methods,Research Design,Software,User-Computer Interface},
    mendeley-tags = {BALL},
    month = {feb},
    number = {3},
    pages = {365--6},
    pmid = {16332707},
    title = {{BALLView: a tool for research and education in molecular modeling.}},
    url = {http://bioinformatics.oxfordjournals.org/content/22/3/365.abstract},
    volume = {22},
    year = {2006}
    }

If you use ballaxy please additionally cite:

  • A. K. Hildebrandt, D. Stöckel, N. Fischer, L. de la Garza Trevino, J. Krüger, S. Nickels, M. Röttig, C. Schärfe, M. Schumann, P. Thiel, H. Lenhof, O. Kohlbacher, and A. Hildebrandt, "Ballaxy: web services for structural bioinformatics," Bioinformatics, vol. 31, iss. 1, pp. 121-2, 2015.
    [Bibtex]
    @Article{BALLaxyBioinfo,
    author = {Hildebrandt, Anna Katharina and Stöckel, Daniel and Fischer, Nina and de la Garza Trevino, Luis and Krüger, Jens and Nickels, Stefan and Röttig, Marc and Schärfe, Charlotta and Schumann, Marcel and Thiel, Philipp and Lenhof, Hans-Peter and Kohlbacher, Oliver and Hildebrandt, Andreas},
    title = {ballaxy: web services for structural bioinformatics},
    year = {2015},
    abstract = {MOTIVATION: 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 (Hildebrandt et al., 2010) due to 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 frontend 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. AVAILABILITY: 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. Ballaxy is licensed under the terms of the GPL.},
    journal = {Bioinformatics},
    volume = {31},
    number = {1},
    pages = {121-2},
    url = {http://dx.doi.org/10.1093/bioinformatics/btu574},
    pmid = {25183489}
    }