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Progress on an open source computer-assisted structure elucidation suite (SENECA)

  • Stefan Kuhn
  • Christoph Steinbeck
Open Access
Poster presentation

Keywords

Genetic Algorithm Structure Generator Simulated Annealing Open Source Large Space 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

We suggested and developed various components for Computer-Assisted Structure Elucidation (CASE) over the years [1, 2]. Our current goal is to integrate these into an easy to use and efficient platform for end users, called SENECA. This is based on Bioclipse [3], an integrated software suite for chemo- and bioinformatics providing plugins for file handling and visualisation of compounds and spectra.

The SENECA feature currently comprises the following components and algorithms:

• A deterministic structure generator suitable for small chemical spaces.

• Simulated Annealing and Genetic Algorithm for random structure walks in large spaces.

Simulation of 13C NMR spectra for ranking results.

SENECA is a Bioclipse feature, available via the update site at http://www.ebi.ac.uk/steinbeck-srv/speclipse/net.bioclipse.seneca-updatesite/.

References

  1. 1.
    Steinbeck C, Krause S, Kuhn S: NMRShiftDB - Constructing a free chemical information system with open-source components. Journal of Chemical Information and Computer Sciences. 2003, 43: 1733-1739.Google Scholar
  2. 2.
    Kuhn S, Egert B, Neumann S, Steinbeck C: Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction. BMC Bioinformatics. 2008, 9: 400-. 10.1186/1471-2105-9-400.CrossRefGoogle Scholar
  3. 3.
    Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, et al: Bioclipse: An open source workbench for chemo- and bioinformatics. BMC Bioinformatics. 2007, 8: 59-10.1186/1471-2105-8-59.CrossRefGoogle Scholar

Copyright information

© Stefan and Christoph; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd.

Authors and Affiliations

  • Stefan Kuhn
    • 1
  • Christoph Steinbeck
    • 1
  1. 1.Wellcome Trust Genome CampusHinxton, CambridgeUK

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