Full-coverage spatial distribution of epibenthic communities in the south-eastern North Sea in relation to habitat characteristics and fishing effort.

Full-coverage spatial data of occurrence and a detailed description of habitat requirements of epibenthic communities are needed in many conservation and management contexts. In the North Sea the focus has so far been on small benthic infauna, whereas structure and ecosystem functions of larger epifaunal communities have been largely ignored. This study provides a comprehensive analysis of epibenthic community structure in the south-eastern North Sea, including a detailed inventory of species, diversity and spatially contiguous distribution of communities. Data from nearly 400 stations were compiled for the study, enabling us to describe epibenthic community structure at unprecedented spatial resolution. Eight distinct epibenthic communities were found in the south-eastern North Sea by using multivariate analysis. Distribution modelling with eight environmental variables (bottom temperature and salinity, temperature differences between summer and winter, mud content of sediments, maximum bottom shear stress, stratification, water depth and annual primary production) and one human pressure (fishing effort) was used to extrapolate probable spatial distributions and to identify associated habitat characteristics of the communities in the south-eastern North Sea. Three large epibenthic communities "Coast", "Oysterground" and "Tail End" reflect a gradual habitat change from the coast towards offshore regions, expressed in gradients of bottom salinity, seasonal temperature differences and stratification as the dominant environmental factors. Five smaller communities ("Amrum Bank", "Frisian Front", "Deeps", "Dogger Bank" and "Dogger Slope") outline specific habitats in the south-eastern North Sea. The "Dogger Slope" community has not been recognized before, but has a predicted spatial extent of 7118 km2. Due to the high occurrence of long-lived, sessile species such as sponges this community is very sensitive to demersal fishing.

BALL-SNPgp-from genetic variants toward computational diagnostics.

UNLABELLED: In medical research, it is crucial to understand the functional consequences of genetic alterations, for example, non-synonymous single nucleotide variants (nsSNVs). NsSNVs are known to be causative for several human diseases. However, the genetic basis of complex disorders such as diabetes or cancer comprises multiple factors. Methods to analyze putative synergetic effects of multiple such factors, however, are limited. Here, we concentrate on nsSNVs and present BALL-SNPgp, a tool for structural and functional characterization of nsSNVs, which is aimed to improve pathogenicity assessment in computational diagnostics. Based on annotated SNV data, BALL-SNPgp creates a three-dimensional visualization of the encoded protein, collects available information from different resources concerning disease relevance and other functional annotations, performs cluster analysis, predicts putative binding pockets and provides data on known interaction sites. AVAILABILITY AND IMPLEMENTATION: BALL-SNPgp is based on the comprehensive C ++ framework Biochemical Algorithms Library (BALL) and its visualization front-end BALLView. Our tool is available at www.ccb.uni-saarland.de/BALL-SNPgp CONTACT: ballsnp@milaman.cs.uni-saarland.de.

BALL--biochemical algorithms library 1.3.

BACKGROUND: The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers. In the ten years since its original publication, BALL has seen a substantial increase in functionality and numerous other improvements. RESULTS: Here, we discuss BALL's current functionality and highlight the key additions and improvements: support for additional file formats, molecular edit-functionality, new molecular mechanics force fields, novel energy minimization techniques, docking algorithms, and support for cheminformatics. CONCLUSIONS: BALL is available for all major operating systems, including Linux, Windows, and MacOS X. It is available free of charge under the Lesser GNU Public License (LPGL). Parts of the code are distributed under the GNU Public License (GPL). BALL is available as source code and binary packages from the project web site at http://www.ball-project.org. Recently, it has been accepted into the debian project; integration into further distributions is currently pursued.

BALLView: a tool for research and education in molecular modeling.

We present BALLView, a molecular viewer and modeling tool. It combines state-of-the-art visualization capabilities with powerful modeling functionality including implementations of force field methods and continuum electrostatics models. BALLView is a versatile and extensible tool for research in structural bioinformatics and molecular modeling. Furthermore, the convenient and intuitive graphical user interface offers novice users direct access to the full functionality, rendering it ideal for teaching. Through an interface to the object-oriented scripting language Python it is easily extensible.

BALLView: an object-oriented molecular visualization and modeling framework.

We present BALLView, an extensible tool for visualizing and modeling bio-molecular structures. It provides a variety of different models for bio-molecular visualization, e.g. ball-and-stick models, molecular surfaces, or ribbon models. In contrast to most existing visualization tools, BALLView also offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as publication quality images or as movies. Even unexperienced users have direct access to this functionality through an intuitive graphical user interface, which makes BALLView particularly useful for teaching. For more advanced users, BALLView is extensible in different ways. Owing to its framework design, extension on the level of C per thousand+ per thousand per thousand+ code is very convenient. In addition, an interface to the scripting language Python allows the interactive rapid prototyping of new methods. BALLView is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors). It is available free of charge under the GNU Public License (GPL) from our website http://www.ballview.org.