Multiple scaling regimes in simple aging models

We investigate aging in glassy systems based on a simple model, where a point in configuration space performs thermally activated jumps between the minima of a random energy landscape. The model allows us to show explicitly a subaging behavior and multiple scaling regimes for the correlation function. Both the exponents characterizing the scaling of the different relaxation times with the waiting time and those characterizing the asymptotic decay of the scaling functions are obtained analytically by invoking a `partial equilibrium' concept.Comment: 4 pages, 3 figure

openBIS: a flexible framework for managing and analyzing complex data in biology research

<p>Abstract</p> <p>Background</p> <p>Modern 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.</p> <p>Results</p> <p>We 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.</p> <p>Conclusions</p> <p>openBIS 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.</p

NGS-pipe: a flexible, easily extendable, and highly configurable framework for NGS analysis

Next-generation sequencing is now an established method in genomics, and massive amounts of sequencing data are being generated on a regular basis. Analysis of the sequencing data is typically performed by lab-specific in-house solutions, but the agreement of results from different facilities is often small. General standards for quality control, reproducibility, and documentation are missing.; We developed NGS-pipe, a flexible, transparent, and easy-to-use framework for the design of pipelines to analyze whole-exome, whole-genome, and transcriptome sequencing data. NGS-pipe facilitates the harmonization of genomic data analysis by supporting quality control, documentation, reproducibility, parallelization, and easy adaptation to other NGS experiments. https://github.com/cbg-ethz/NGS-pipe [email protected]

Transport und Altern in glasartigen Systemen

Thema dieser Arbeit ist die Untersuchung der Gleichgewichts und Nichtgleichgewichts-Dynamik, die von thermisch aktivierten Sprungprozessen in ungeordneten Energielandschaften herrührt. Modelle, welche von der Sprungbewegung eines "Zustandspunktes" in einer ungeordneten komplexen Energielandschaft ausgehen, werden seit längerem zur Beschreibung der spezifischen Eigenschaften von glasartigen Materialien verwendet

Strategies and solutions to maintain and retain data from high content imaging, analysis, and screening assays

Data analysis and management in high content screening (HCS) has progressed significantly in the past 10 years. The analysis of the large volume of data generated in HCS experiments represents a significant challenge and is currently a bottleneck in many screening projects. In most screening laboratories, HCS has become a standard technology applied routinely to various applications from target identification to hit identification to lead optimization. An HCS data management and analysis infrastructure shared by several research groups can allow efficient use of existing IT resources and ensures company-wide standards for data quality and result generation. This chapter outlines typical HCS workflows and presents IT infrastructure requirements for multi-well plate-based HCS

Influence of hydrodynamic interactions on the dynamics of long-range interacting colloidal particles

We study the influence of hydrodynamic interactions on the self-diffusion of super-paramagnetic colloidal particles suspended in water. The colloids interact via repulsive dipolar forces due to an applied magnetic field, and their motion is effectively confined to two dimensions. By comparing experimental data with the results from extensive computer simulations, where the water flow fields are treated at the Rotne-Prager level, we show that the diffusivity is enhanced at all times due to hydrodynamic interactions. The enhancement effect becomes stronger with increasing particle density, but is almost unaffected by the temperature

Cooperative Evaporation in Ordered Arrays of Volatile Droplets

We study the evaporation behaviour of regular arrays of volatile droplets on a solid substrate. We observe that under certain conditions the droplets do not evaporate independently of each other but in a cooperative manner. This results in the development of a superlattice which is explained in terms of matter exchange between adjacent droplets