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Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma

In contrast to bioinformatics, open-source software is not as widely used in the pharmaceutical industry for molecular modeling and cheminformatics. Typical reasons given for this include problems with code quality, stability, and long-term support for the software (somehow this is less of a concern with bioinformatics software... kind of makes one think). Recently, our group has started making heavy use of an open-source cheminformatics toolkit RDKit [1] in our production environment. Importantly, we are not just acting as consumers of open-source software -- we are active members of the open-source community and have support from management to contribute code back to the project.

In this presentation we will provide a brief overview of the RDKit itself and then present a number of case studies of how we have made use of this open-source platform. Examples will include using the toolkit for method development [2, 3], integration with proprietary tools, and some recent (and upcoming) contributions to the open-souce community, including a database cartridge for fast and flexible similarity searching in the open-source PostgreSQL database [4], and adding support for the RDKit within the open-source pipelining platform Knime [5]. We will finish with a discussion of some practical aspects of working on and with open-source tools in a large research organization.

References

  1. 1.

    RDKit: open-source cheminformatics. http://www.rdkit.org,

  2. 2.

    Vulpetti A, Hommel U, Landrum G, Lewis R, Dalvit C: Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine. J. Am Chem. Soc. 2009, 131: 12949-12959. 10.1021/ja905207t.

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    Vulpetti A, Landrum G, Ruedisser S, Erbel P, Dalvit C: 19F NMR Chemical Shift Prediction with Fluorine Fingerprint Descriptor. J. of Fluorine Chem. 2010, 131: 570-577. 10.1016/j.jfluchem.2009.12.024.

    CAS  Article  Google Scholar 

  4. 4.

    PostgreSQL : http://www.postgresql.org,

  5. 5.

    KNIME : http://www.knime.org,

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Correspondence to Gregory Landrum.

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Landrum, G., Lewis, R., Palmer, A. et al. Making sure there's a "give" associated with the "take": producing and using open-source software in big pharma. J Cheminform 3, O3 (2011). https://doi.org/10.1186/1758-2946-3-S1-O3

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Keywords

  • Molecular Modeling
  • Research Organization
  • Practical Aspect
  • Production Environment
  • Large Research