Volume 3 Supplement 1

6th German Conference on Chemoinformatics, GCC 2010

Open Access

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

  • Gregory Landrum1Email author,
  • Richard Lewis1,
  • Andrew Palmer2,
  • Nikolaus Stiefl1 and
  • Anna Vulpetti1
Journal of Cheminformatics20113(Suppl 1):O3

https://doi.org/10.1186/1758-2946-3-S1-O3

Published: 19 April 2011

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.

Authors’ Affiliations

(1)
Novartis Institutes for BioMedical Research
(2)
Novartis Institutes for BioMedical Research

References

  1. RDKit: open-source cheminformatics. http://www.rdkit.org,
  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.View ArticleGoogle Scholar
  3. 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.View ArticleGoogle Scholar
  4. PostgreSQL : http://www.postgresql.org,
  5. KNIME : http://www.knime.org,

Copyright

© Landrum et al; licensee BioMed Central Ltd. 2011

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.