Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

BACKGROUND: Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. RESULTS: We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. CONCLUSION: Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context

Scenarios about the long-time damage of silicon as material and detectors operating beyond LHC collider conditions

For the new hadron collider LHC and some of its updates in luminosity and energy, as SLHC and VLHC, the silicon detectors could represent an important option, especially for the tracking system and calorimetry. The main goal of this paper is to analyse the expected long-time degradation in the bulk of the silicon as material and for silicon detectors, in continuous radiation field, in these hostile conditions. The behaviour of silicon in relation to various scenarios for upgrade in energy and luminosity is discussed in the frame a phenomenological model developed previously by the authors. Different silicon material parameters resulting from different technologies are considered to evaluate what materials are harder to radiation and consequently could minimise the degradation of device parameters in conditions of continuous long time operation.Comment: submitted to Physica Scripta Work in the frame of CERN RD-50 Collaboratio

A flexible service selection for executing virtual services

[EN] With the adoption of a service-oriented paradigm on the Web, many software services are likely to fulfil similar functional needs for end-users. We propose to aggregate functionally equivalent software services within one single virtual service, that is, to associate a functionality, a graphical user interface (GUI), and a set of selection rules. When an end user invokes such a virtual service through its GUI to answer his/her functional need, the software service that best responds to the end-user s selection policy is selected and executed and the result is then rendered to the end-user through the GUI of the virtual service. A key innovation in this paper is the flexibility of our proposed service selection policy. First, each selection policy can refer to heterogeneous parameters (e.g., service price, end-user location, and QoS). Second, additional parameters can be added to an existing or new policy with little investment. Third, the end users themselves define a selection policy to apply during the selection process, thanks to the GUI element added as part of the virtual service design. This approach was validated though the design, implementation, and testing of an end-to-end architecture, including the implementation of several virtual services and utilizing several software services available today on the Web.This work was partially supported in part by SERVERY (Service Platform for Innovative Communication Environment), a CELTIC project that aims to create a Service Marketplace that bridges the Internet and Telco worlds by merging the flexibility and openness of the former with the trustworthiness and reliability of the latter, enabling effective and profitable cooperation among actors.Laga, N.; Bertin, E.; Crespi, N.; Bedini, I.; Molina Moreno, B.; Zhao, Z. (2013). A flexible service selection for executing virtual services. 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The repeatability of cognitive performance: a meta-analysis

International audienceOne contribution of 15 to a theme issue 'Causes and consequences of individual differences in cognitive abilities'. Behavioural and cognitive processes play important roles in mediating an individual's interactions with its environment. Yet, while there is a vast literature on repeatable individual differences in behaviour, relatively little is known about the repeatability of cognitive performance. To further our understanding of the evolution of cogni-tion, we gathered 44 studies on individual performance of 25 species across six animal classes and used meta-analysis to assess whether cognitive performance is repea-table. We compared repeatability (R) in performance (1) on the same task presented at different times (temporal repeat-ability), and (2) on different tasks that measured the same putative cognitive ability (contextual repeatability). We also addressed whether R estimates were influenced by seven extrinsic factors (moderators): type of cognitive performance measurement, type of cognitive task, delay between tests, origin of the subjects, experimental context, taxonomic class and publication status. We found support for both temporal and contextual repeatability of cognitive performance, with mean R estimates ranging between 0.15 and 0.28. Repeatability estimates were mostly influenced by the type of cognitive performance measures and publication status. Our findings highlight the widespread occurrence of consistent inter-individual variation in cog-nition across a range of taxa which, like behaviour, may be associated with fitness outcomes. This article is part of the theme issue 'Causes and consequences of individual differences in cognitive abilities'

Report of the study group on a superconducting proton linac as a PS Injector

A proposal was made at the end of 1996 to use the large inventory of RF hardware available after the decommissioning of LEP-2 for the construction of a 2 GeV Superconducting Proton Linac (SPL) to inject directly into the PS [1.1]. The brightness of the beam in the PS at low energy would double, helping the injector complex to satisfy the requirements of the LHC and benefiting the planned proton physics programme. Additional users could also be accommodated thanks to the capability of the SPL to operate at a much larger duty factor than that required for high-energy physics. Consequently, a small study group has been set up to analyse the major technical aspects of the SPL design as well as the processes of injection and capture in the PS. This report summarises the work done so far, and provides some information about the other possible uses of the SPL beam. The feasibility of such a cascade of accelerators is confirmed, although an in-depth design study is still required before the realistic performance and detailed design of that facility can be announced

Implementing a public web based GIS service for feedback of surveillance data on communicable diseases in Sweden

BACKGROUND: Surveillance data allow for analysis, providing public health officials and policy-makers with a basis for long-term priorities and timely information on possible outbreaks for rapid response (data for action). In this article we describe the considerations and technology behind a newly introduced public web tool in Sweden for easy retrieval of county and national surveillance data on communicable diseases. METHODS: The web service was designed to automatically present updated surveillance statistics of some 50 statutory notifiable diseases notified to the Swedish Institute for Infectious Disease Control (SMI). The surveillance data is based on clinical notifications from the physician having treated the patient and laboratory notifications, merged into cases using a unique personal identification number issued to all Swedish residents. The web service use notification data from 1997 onwards, stored in a relational database at the SMI. RESULTS: The web service presents surveillance data to the user in various ways; tabulated data containing yearly and monthly disease data per county, age and sex distribution, interactive maps illustrating the total number of cases and the incidence per county and time period, graphs showing the total number of cases per week and graphs illustrating trends in the disease data. The system design encompasses the database (storing the data), the web server (holding the web service) and an in-the-middle computer (to ensure good security standards). CONCLUSIONS: The web service has provided the health community, the media, and the public with easy access to both timely and detailed surveillance data presented in various forms. Since it was introduced in May 2003, the system has been accessed more than 1,000,000 times, by more than 10,000 different viewers (over 12.600 unique IP-numbers)

The Stanford Microarray Database accommodates additional microarray platforms and data formats

The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD

The Stanford Microarray Database: implementation of new analysis tools and open source release of software

The Stanford Microarray Database (SMD; ) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release

Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes