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BackgroundModern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.ResultsWe have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.ConclusionsopenBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.

The dynamical behavior of a harmonic chain in a spatially periodic potential ͑Frenkel-Kontorova model, discrete sine-Gordon equation͒ under the influence of an external force and a velocity proportional damping is investigated. We do this at zero temperature for long chains in a regime where inertia and damping as well as the nearest-neighbor interaction and the potential are of the same order. There are two types of regular sliding states: uniform sliding states, which are periodic solutions where all particles perform the same motion shifted in time; and nonuniform sliding states, which are quasiperiodic solutions where the system forms patterns of domains of different uniform sliding states. We discuss the properties of this kind of pattern formation, and derive equations of motion for the slowly varying average particle density and velocity. To observe these dynamical domains, we suggest experiments with a discrete ring of at least 50 Josephson junctions.

We calculate the eigenfrequencies of a rectangular cantilever of an atomic force microscope immersed in a fluid or a gas. To do so, the problem of combined elastomechanical and hydrodynamical equations is solved approximatively. The results are compared with experimentally obtained frequencies. For water the difference between experiment and theory is less than 4% if the ratio of the height of the cantilever to the width is less than 1/20 and if the corresponding eigenmode has at least four nodes.