goCluster integrates statistical analysis and functional interpretation of microarray expression data

Motivation: Several tools that facilitate the interpretation of transcriptional profiles using gene annotation data are available but most of them combine a particular statistical analysis strategy with functional information. goCluster extends this concept by providing a modular framework that facilitates integration of statistical and functional microarray data analysis with data interpretation. Results: goCluster enables scientists to employ annotation information, clustering algorithms and visualization tools in their array data analysis and interpretation strategy. The package provides four clustering algorithms and GeneOntology terms as prototype annotation data. The functional analysis is based on the hypergeometric distribution whereby the Bonferroni correction or the false discovery rate can be used to correct for multiple testing. The approach implemented in goCluster was successfully applied to interpret the results of complex mammalian and yeast expression data obtained with high density oligonucleotide microarrays (GeneChips). Availability: goCluster is available via the BioConductor portal at www.bioconductor.org. The software package, detailed documentation, user- and developer guides as well as other background information are also accessible via a web portal at http://www.bioz.unibas.ch/gocluster. Contact: [email protected]

He and Ne ages of large presolar silicon carbide grains: Solving the recoil problem

Knowledge about the age of presolar grains provides important insights into Galactic chemical evolution and the dynamics of grain formation and destruction processes in the Galaxy. Determination from the abundance of cosmic ray interaction products is straightforward, but in the past has suffered from uncertainties in correcting for recoil losses of spallation products. The problem is less serious in a class of large (tens of micrometer) grains. We describe the correction procedure and summarise results for He and Ne ages of presolar SiC "Jumbo" grains that range from close to zero to ~850 Myr, with the majority being less than 200 Myr. We also discuss the possibility of extending our approach to the majority of smaller SiC grains and explore possible contributions from trapping of cosmic rays.Comment: Publications of the Astronomical Society of Australia, Contribution to PASA special volume "The Origin of Elements Heavier than Iron in honor of the 70th birthday of Roberto Gallino

Impact of Complex-Logic Cell Layout on the Single-Event Transient Sensitivity

International audienceThe design methodology based on standard cells is widely used in a broad range of VLSI applications. Further, several optimization algorithms can be employed to address different constraints such as power consumption or reliability. This work evaluates the implications of the usage of complex-logic cells from a 45 nm Standard-Cell library to the Single-Event Transient sensitivity under heavy ions. Results show that even though a reduction in the layout area is obtained when adopting complex-logic gates, a slight reduction in the total sensitive area of the circuit is observed. Moreover, the effectiveness of logical masking can be suppressed, leading to a higher SET cross-section

He and Ne Ages of Large Presolar Silicon Carbide Grains: Solving the Recoil Problem

Knowledge about the age of presolar grains provides important insights into Galactic chemical evolution and the dynamics of grain formation and destruction processes in the Galaxy. Determination from the abundance of cosmic ray interaction products is straightforward, but in the past has suffered from uncertainties in correcting for recoil losses of spallation products. The problem is less serious in a class of large (tens of μm) grains. We describe the correction procedure and summarise results for He and Ne ages of presolar SiC ‘Jumbo' grains that range from close to zero to ∼850 Myr, with the majority being less than 200 Myr. We also discuss the possibility of extending our approach to the majority of smaller SiC grains and explore possible contributions from trapping of cosmic ray

Use of CCD to Detect Terrestrial Cosmic Rays at Ground Level: Altitude vs. Underground Experiments, Modeling and Numerical Monte Carlo Simulation

International audienceIn this work, we used a commercial charge-coupled device (CCD) camera to detect and monitor terrestrial cosmic rays at ground level. Multi-site characterization has been performed at sea level (Marseille), underground (Modane Underground Laboratory) and at mountain altitude (Aiguille du Midi-Chamonix Mont-Blanc at +3,780 m of altitude) to separate the atmospheric and alpha particle emitter's contributions in the CCD response. An additional experiment at avionics altitude during a long-haul flight has been also conducted. Experiment results demonstrate the importance of the alpha contamination in the CCD response at ground level and its sensitivity to charged particles. Experimental data as a function of CCD orientation also suggests an anisotropy of the particle flux for which the device is sensitive. A complete computational modeling of the CCD imager has been conducted, based on a simplified 3D CCD architecture deduced from a reverse engineering study using electron microscopy and physico-chemical analysis. Monte Carlo simulations evidence the major contribution of low energy (below a few MeV) protons and muons in the CCD response. Comparison between experiments and simulation shows a good agreement at ground level, fully validated at avionics altitudes with a much higher particle flux and a different particle cocktail composition

Monte Carlo simulation of particle-induced bit upsets

We investigate the issue of radiation-induced failures in electronic devices by developing a Monte Carlo tool called MC-Oracle. It is able to transport the particles in device, to calculate the energy deposited in the sensitive region of the device and to calculate the transient current induced by the primary particle and the secondary particles produced during nuclear reactions. We compare our simulation results with SRAM experiments irradiated with neutrons, protons and ions. The agreement is very good and shows that it is possible to predict the soft error rate (SER) for a given device in a given environment

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology

<p>Abstract</p> <p>Background</p> <p>High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently.</p> <p>Results</p> <p>We developed the Annotation, Mapping, Expression and Network (AMEN) software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i) uploading and pre-processing data from microarray expression profiling experiments, (ii) detecting groups of significantly co-expressed genes, and (iii) searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human.</p> <p>Conclusion</p> <p>AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.</p

Simulation tools for soft error rate calculations in SRAM

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Simulation tools for soft error rate calculations in SRAM

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Impact of natural radioactivity on the Soft Error Rate

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