Scaffold Hunter

Scaffold Hunter is a Java-based open source tool for the visual analysis of data sets with a focus on data from the life sciences, aiming at an intuitive access to large and complex data sets. The tool offers a variety of views, e.g. graph, dendrogram, and plot view, as well as analysis methods, e.g. for clustering and classification. Scaffold Hunter has its origin in drug discovery, which is still one of the main application areas, and is evolved into a reusable open source platform for a wider range of applications. The tool offers flexible plugin and data integration mechanisms to allow adaption to new fields and data sets, e.g. from medical image retrieval. Scaffold Hunter is used worldwide in research, both academic and commercial, and for teaching at the Technical University of Dortmund, Germany, and the University of Sydney, Australia.

Please visit our Sourceforge project site for further information or follow one of the direct links to specific subpages:

• Download Scaffold Hunter
• Download sample data sets
• News
• Wiki
• FAQ
• Tutorials
• Browse source code

Screenshots

Publications

• Scaffold Hunter: A comprehensive visual analytics framework for drug discovery
  Till Schäfer, Nils Kriege, Lina Humbeck, Karsten Klein, Oliver Koch, Petra Mutzel
  Journal of Cheminformatics, 2017, 9:28 (Bibtex)

• Visual Analysis of Biological Activity Data with Scaffold Hunter
  Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer
  Molecular Informatics, WILEY-VCH Verlag, 2013, 32, 964-975 (Bibtex)

• Scaffold Hunter: Facilitating Drug Discovery by Visual Analysis of Chemical Space
  Karsten Klein, Nils Kriege, Petra Mutzel
  Computer Vision, Imaging and Computer Graphics. Theory and Application, 2013, 359, 176-192 (Bibtex)

• Interactive exploration of chemical space with Scaffold Hunter
  Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I. Oprea, Petra Mutzel, Herbert Waldmann
  Nature Chemical Biology, 2009, 5, 581-583 (Bibtex)

Development

Chair 11: Workgroup Algorithm Engineering Department of Computer Science TU Dortmund

Computer Science 1: Computational Analytics Group Institute for Computer Science University of Bonn

Medicinal Chemistry: Workgroup Koch Faculty of Chemistry and Chemical Biology TU Dortmund

MArVL: Monash Adaptive Visualisation Lab Faculty of Information Technology Monash University

History

The Scaffold Hunter project was initiated by Karsten Klein, Petra Mutzel (both Chair 11: Workgroup Algorithm Engineering, TU Dortmund at the time of initiation, now University of Konstanz and University of Bonn), and Stefan Wetzel (Chemical Biology, MPI for Molecular Physiology Dortmund), a first version of Scaffold Hunter was implemented by the student project group PG504 at TU Dortmund under their supervision. For version 2.x, many parts of it were improved, extended, and rewritten by the student project group PG552 under the supervision of Carsten Gutwenger, Nils Kriege, and Karsten Klein at TU Dortmund.
We would like to thank the members of PG504, Anke Arndt, Vanessa Bembenek, Ambia Ben Ahmed, Philipp Büdenbender, Nils Kriege, Adalbert Gorecki, Sergej Rakov, Michael Rex, Gebhard Schrader, Henning Wagner, André Wiesniewski, and Cengizhan Yücel, and the members of PG552, Bernhard Dick, Thorsten Flügel, Henning Garus, Michael Hesse, Philipp Kopp, Philipp Lewe, Dominic Sacré, Till Schäfer, and Thomas Schmitz, for their contribution and enthusiasm in creating the prototype application. The final reports of PG504 and PG552 can be retrieved here and here, respectively.
Parts of the software have been developed within the programs Google Summer of Code 2013 and 2014 by Jeroen Lappenschaar, Andrey Zhylka and Werner Sturm. The research assistants Nils Kriege, Till Schäfer, Sven Schrinner and Philipp Mewes have contributed to the development of Scaffold Hunter in the last years.