New Software Tool (new + software_tool)

Distribution by Scientific Domains

Selected Abstracts

Digitization and geo-referencing of botanical distribution maps

Christian A. Schölzel
Aim In many fields of research, valuable information is stored in atlases and maps which are only available as printed media. Scientists who are interested in computational analysis often seek to digitize the data to make it accessible for numerical calculations. In this paper, an approach using the example of digitizing distribution maps taken from plant-taxonomic atlases is described. For this purpose, a software tool has been built for application in the Sonderforschungsbereich 350 `Interactions between and Modelling of Continental Geosystems' at the University of Bonn. Its functionality has to be simple in use and capable of transforming fields drawn on geographical maps into grid data even where the type of map projection is unknown. Location As an example, plant distributions over Europe and Asia have been digitized. Methods To achieve this aim through an objective statistical analysis, the local deterministic approximation has been used for geo-referencing. Results For this reason the development of a new software tool was required. Although there is a large market for related software from Geographical Information Systems (GIS), none of the available GIS-programs appeared to be capable of geo-referencing maps with unidentified projections. Rather than to give a product comparison, this paper aims on the methodology and mathematical formalism. Main conclusions The developed algorithm is a handy tool to capture data from maps based on obscure projections. Valuable historical maps, which are problematic for standard GIS-programs, can be made accessible for modern research work. [source]

Maximum pixel spectrum: a new tool for detecting and recovering rare, unanticipated features from spectrum image data cubes

Summary A new software tool, the maximum pixel spectrum, detects rare events within a spectrum image data cube, such as that generated with electron-excited energy-dispersive X-ray spectrometry in a scanning electron microscope. The maximum pixel spectrum is a member of a class of ,derived spectra' that are constructed from the spectrum image data cube. Similar to a conventional spectrum, a derived spectrum is a linear array of intensity vs. channel index that corresponds to photon energy. A derived spectrum has the principal characteristics of a real spectrum so that X-ray peaks can be recognized. A common example of a derived spectrum is the summation spectrum, which is a linear array in which the summation of all pixels within each energy plane gives the intensity value for that channel. The summation spectrum is sensitive to the dominant features of the data cube. The maximum pixel spectrum is constructed by selecting the maximum pixel value within each X-ray energy plane, ignoring the remaining pixels. Peaks corresponding to highly localized trace constituents or foreign contaminants, even those that are confined to one pixel of the image, can be seen at a glance when the maximum pixel spectrum is compared with the summation spectrum. [source]

microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets

Daniel Dieringer
Abstract In molecular ecology the analysis of large microsatellite data sets is becoming increasingly popular. Here we introduce a new software tool, which is specifically designed to facilitate the analysis of large microsatellite data sets. All common microsatellite summary statistics and distances can be calculated. Furthermore, the microsatellite analyser (msa) software offers an improved method to deal with inbred samples (such as Drosophila isofemale lines). Executables are available for Windows and Macintosh computers. [source]

Physiologically Based Modelling and Prediction of Drug Interactions

Frédéric Y. Bois
This article reviews briefly past developments in the area of physiologically based pharmacokinetic (PBPK) modelling of interactions. It also demonstrates a systems biology approach to the question, and the capabilities of new software tools to facilitate that development. Individual Systems Biology Markup Language models of metabolic pathways can now be automatically merged and coupled to a template PBPK pharmacokinetic model, using for example the GNU MCSim software. The global model generated is very efficient and able to simulate the interactions between a theoretically unlimited number of substances. Development time and the number of model parameter increase only linearly with the number of substances considered, even though the number of possible interactions increases exponentially. [source]