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The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemo- and Bioinformatics. Its architecture and capabilities as well as the development as an open-source project by a team of international collaborators from academic and industrial institutions is described. The CDK provides methods for many common tasks in(More)
BACKGROUND There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more(More)
BACKGROUND Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks. RESULTS Bioclipse is a free, open source workbench with advanced features for the life sciences. Version(More)
The process of designing and implementing NMRShiftDB, an open-source, open-content database for chemical structures and their NMR data based solely on free software is described. NMRShiftDB is available to the community on http://www.nmrshiftdb.org. It allows for open submission and retrieval of data sets by its user community. The software and the content(More)
CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be(More)
BACKGROUND Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known.(More)
Unfortunately, the original version of this supplement [1] contained errors in two of the abstracts; P037 and P127. Please see details below. In P037, the image presented as Figure eight is incorrect. The correct figure is shown below (Fig. 1). permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to(More)
Metabolomics studies the occurrence and change of concentrations of small molecular weight chemical compounds (metabolites) in organisms, organs, tissues, cells and ultimately cell compartments in the context of environmental changes, disease or other boundary conditions. It does this by means of spectroscopic and chro-matographic techniques and by(More)
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(More)
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