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Archived Comments for: Molecular structure input on the web

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  1. References for the CDK, Blue Obelisk, and Bioclipse.

    Egon Willighagen, Uppsala University

    3 February 2010

    It is also gratifying to see the
    advent of open source movement in cheminformatics on the Internet, as advocated for
    example by the Blue Obelisk Group (40) and witnessed by collaborative projects like
    Chemistry Development Kit CDK (41), Jmol (42), Bioclipse (43) and several others.

    I like to point to reader to the following papers regarding references 40, 41, en 43.

    Blue Obelisk (ref 40 in the paper)
    R. Guha, M. T. Howard, G. R. Hutchison, P. Murray-Rust, H. Rzepa, C. Steinbeck, J. Wegner, E. L. Willighagen, 'The Blue Obelisk-interoperability in chemical informatics.', Journal of Chemical Information and Modeling, Vol. 46, No. 3. (2006), pp. 991-998. (doi:10.1021/ci050400b)

    Chemistry Development Kit (ref 41)
    C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann, E. Willighagen, 'The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.', J Chem Inf Comput Sci, Vol. 43, No. 2. (2003), pp. 493-500. (doi:10.1021/ci025584y)

    Bioclipse (ref 43)
    Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Masak, Gilleain Torrance, Johannes Wagener, Egon Willighagen, Christoph Steinbeck, Jarl Wikberg, 'Bioclipse 2: A scriptable integration platform for the life sciences Export', BMC Bioinformatics, Vol. 10, No. 1. (2009), 397. (doi:10.1186/1471-2105-10-397)

    Competing interests

    I am author on these papers.