SNA--a toolbox for the stoichiometric analysis of metabolic networks

BACKGROUND: Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem. RESULTS: SNA is a interactive, high performance toolbox for analysing the possible steady state behaviour of metabolic networks by computing the generating and elementary vectors of their flux and conversions cones. It also supports analysing the steady states by linear programming. The toolbox is implemented mainly in Mathematica and returns numerically exact results. It is available under an open source license from: http://bioinformatics.org/project/?group_id=546. CONCLUSION: Thanks to its performance and modular design, SNA is demonstrably useful in analysing genome scale metabolic networks. Further, the integration into Mathematica provides a very flexible environment for the subsequent analysis and interpretation of the results.

Loss estimation for landslides in mountain areas – An integrated toolbox for vulnerability assessment and damage documentation

Global environmental change includes changes in a wide range of global scale phenomena, which are expected to affect a number of physical processes, as well as the vulnerability of the communities that will experience their impact. Decision-makers are in need of tools that will enable them to assess the loss of such processes under different future scenarios and to design risk reduction strategies. In this paper, a tool is presented that can be used by a range of end-users (e.g. local authorities, decision makers, etc.) for the assessment of the monetary loss from future landslide events, with a particular focus on torrential processes. The toolbox includes three functions: a) enhancement of the post-event damage data collection process, b) assessment of monetary loss of future events and c) continuous updating and improvement of an existing vulnerability curve by adding data of recent events. All functions of the tool are demonstrated through examples of its application.

«Toolbox Assessment» - ein hochschuldidaktischer Service im virtuellen Raum

Zeitgemäße Hochschullehre verlangt nach zeitgemäßen Prüfungsformen. Mit «Assessment», wie es hier verstanden wird, ist jedoch nicht nur die abschließende Lernerfolgskontrolle gemeint. Im Ideal der kompetenzorientierten Hochschullehre erhalten die Studierenden auch auf dem Weg zur angestrebten Handlungskompetenz immer wieder Gelegenheit zur Standortbestimmung. Eine Benotung ist dabei nicht zwingend, informierendes Feedback jedoch schon. Mit der «Toolbox Assessment» erhalten Lehrende dazu nun ein attraktives Hilfsmittel buchstäblich in die Hand.

XMapTools: a MATLAB©-based program for electron microprobe X-ray image processing and geothermobarometry

XMapTools is a MATLAB©-based graphical user interface program for electron microprobe X-ray image processing, which can be used to estimate the pressure–temperature conditions of crystallization of minerals in metamorphic rocks. This program (available online at http://www.xmaptools.com) provides a method to standardize raw electron microprobe data and includes functions to calculate the oxide weight percent compositions for various minerals. A set of external functions is provided to calculate structural formulae from the standardized analyses as well as to estimate pressure–temperature conditions of crystallization, using empirical and semi-empirical thermobarometers from the literature. Two graphical user interface modules, Chem2D and Triplot3D, are used to plot mineral compositions into binary and ternary diagrams. As an example, the software is used to study a high-pressure Himalayan eclogite sample from the Stak massif in Pakistan. The high-pressure paragenesis consisting of omphacite and garnet has been retrogressed to a symplectitic assemblage of amphibole, plagioclase and clinopyroxene. Mineral compositions corresponding to ~165,000 analyses yield estimates for the eclogitic pressure–temperature retrograde path from 25 kbar to 9 kbar. Corresponding pressure–temperature maps were plotted and used to interpret the link between the equilibrium conditions of crystallization and the symplectitic microstructures. This example illustrates the usefulness of XMapTools for studying variations of the chemical composition of minerals and for retrieving information on metamorphic conditions on a microscale, towards computation of continuous pressure–temperature-and relative time path in zoned metamorphic minerals not affected by post-crystallization diffusion.

An automated method for mapping physical soil and water conservation structures on cultivated land using GIS and remote sensing techniques

An efficient and reliable automated model that can map physical Soil and Water Conservation (SWC) structures on cultivated land was developed using very high spatial resolution imagery obtained from Google Earth and ArcGIS, ERDAS IMAGINE, and SDC Morphology Toolbox for MATLAB and statistical techniques. The model was developed using the following procedures: (1) a high-pass spatial filter algorithm was applied to detect linear features, (2) morphological processing was used to remove unwanted linear features, (3) the raster format was vectorized, (4) the vectorized linear features were split per hectare (ha) and each line was then classified according to its compass direction, and (5) the sum of all vector lengths per class of direction per ha was calculated. Finally, the direction class with the greatest length was selected from each ha to predict the physical SWC structures. The model was calibrated and validated on the Ethiopian Highlands. The model correctly mapped 80% of the existing structures. The developed model was then tested at different sites with different topography. The results show that the developed model is feasible for automated mapping of physical SWC structures. Therefore, the model is useful for predicting and mapping physical SWC structures areas across diverse areas.