Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data.

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 expressed and what problems still exist.

Bioclipse: an open source workbench for chemo- and bioinformatics.

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 focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

Effect of hexavalent carcinogenic chromium on carp Cyprinus carpio immune cells.

Chromium is widely used in industrial processes, and is released into aquatic environments by electroplating, tannery and textile industries. Fishes in natural waters or in aquaculture facilities supplied with these waters are exposed to chromium waste and are presumed to be affected by deposits. Herein, we examine the effect of hexavalent chromium on carp Cyprinus carpio derived immune cells. In vitro exposure of carp leukocytes to hexavalent chromium induced cytotoxicity, decreased mitogen-induced lymphocyte activation and phagocyte functions at concentrations between 2 and 200 micromol Cr l(-1). Neutrophils responded to chromium challenge by changes in cell shape together with reduced nitric oxide and reactive oxygen production. This occurred at much lower concentrations than for the cytotoxic effects seen in leukocyte cultures derived from peripheral blood or pronephros. In a similar way, activation of carp lymphocytes by pokeweed mitogen was reduced in a dose-dependent manner, while cytotoxic effects on non-activated lymphocytes were observed at much higher doses of 200 micromol Cr l(-1). Altered lymphocyte and neutrophil functions are considered to be responsible for decreased resistance to pathogens observed in fishes under chronic chromium challenge.