BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Browser security : a requirements-based approach

A browser is a convenient way to access resources located remotely on computer networks. Security in browsers has become a crucial issue for users who use them for sensitive applications without knowledge ofthe hazards. This research utilises a structure approach to analyse and propose enhancements to browser security. Standard evaluation for computer products is important as it helps users to ensure that the product they use is appropriate for their needs. Security in browsers, therefore, has been evaluated using the Common Criteria. The outcome of this was a security requirements profile which attempts to formalise the security needs of browsers. The information collected during the research was used to produce a prototype model for a secure browser program. Modifications to the Lynx browser were made to demonstrate the proposed enhancements.

Chiesa dei Ss. Ippolito e Cassiano (The Church SS Ippolito e Cassiano in Cassano Valcuvia)

The development of the town of Cassano door, unknown time, first to build a chapel, a church filiare then, the town center, the building, intended for the cult of Mary, is described during the visit of Bishop Diocesan Pastoral Feliciano Ninguarda : "Item in the Middle huius pages, pro COMMODIT incolarum, east extructum sacellum, seu oratorium B. Dicatum Mariae Virginia, eastern parvum penes quo cum bell tower, ubi ab rates annis not fuit celebratum, quia non est to formam decretorum extructum [...]» [... down in Annex more information]

'The war of Canudos: a Euclidean interpretation.' [Guerra de Canudos: uma leitura euclidiana]

The publication of the book The interior, in 1902, would change the course of thinking about the War of Canudos, who for many years, had been known simply as' the history of Euclid. President Getulio Vargas became interested in the backwoods bloodbath after reading the book avenger-Euclidean. Liked the work he visited the place of occurrence of war promising enjoy the river poured-Barris with the construction of the weir Cocorobo. Euclides da Cunha lived and produced his work in a time of great change in thought, politics and technology. Despite having worked in the press throughout his life, was best known as an engineer, for having exercised the office during the reconstruction of the bridge, in Sao Jose do Rio Pardo. This article aims to illuminate the event of war in light of the Euclidean work. We will examine the trajectory of Euclides da Cunha in journalism. Your learning process to execute the office newsreader and war correspondent, the newspaper O Estado de S. Paul, as well as their reports and work-monument the hinterlands. Resumo: A publicação da obra Os sertões, em 1902, mudaria os rumos do pensamento sobre a Guerra de Canudos, que, por muitos anos, ficara conhecida, simplesmente, como ‘história de Euclides’. O presidente Getúlio Vargas interessou-se pela hecatombe sertaneja após ter lido o livro-vingador euclidiano. Gostou tanto da obra que visitou o lugar de acontecimento da guerra prometendo aproveitar as águas do rio Vaza-Barris com a construção do açude de Cocorobó. Euclides da Cunha viveu e produziu a sua obra em um momento de grandes transformações no pensamento, na política e na tecnologia. Apesar de ter atuado na imprensa ao longo de toda a sua vida, ficou mais conhecido como engenheiro, por ter exercido o ofício, durante a reconstrução da ponte, em São José do Rio Pardo. O presente artigo visa iluminar o acontecimento da guerra à luz da obra euclidiana. Examinaremos a trajetória de Euclides da Cunha no jornalismo. O seu processo de aprendizagem para exercer o ofício de noticiarista e correspondente de guerra, pelo jornal O Estado de S. Paulo, bem como, as suas reportagens e obra-monumento Os sertões.

Remote sensing utility expansion through Earth Portal internet browser

A modular, graphic-oriented Internet browser has been developed to enable non-technical client access to a literal spinning world of information and remotely sensed. The Earth Portal (www.earthportal.net) uses the ManyOne browser (www.manyone.net) to provide engaging point and click views of the Earth fully tessellated with remotely sensed imagery and geospatial data. The ManyOne browser technology use Mozilla with embedded plugins to apply multiple 3-D graphics engines, e.g. ArcGlobe or GeoFusion, that directly link with the open-systems architecture of the geo-spatial infrastructure. This innovation allows for rendering of satellite imagery directly over the Earth's surface and requires no technical training by the web user. Effective use of this global distribution system for the remote sensing community requires a minimal compliance with protocols and standards that have been promoted by NSDI and other open-systems standards organizations.

Clash of the titans: Apple, Adobe, and Microsoft under fire at IT pricing inquiry

Today, an Australian parliamentary committee grilled the IT titans - Apple, Adobe, and Microsoft - on price discrimination against Australian consumers. The IT companies were evasive under questioning.

RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

Background Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets. Results This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genome browsers into one platform. Conclusions The features of RNASeqBrowser: (1) RNASeqBrowser integrates UCSC genome browser and NGS visualization tools such as IGV. It extends the functionality of the UCSC genome browser by adding several new types of tracks to show NGS data such as individual raw reads, SNPs and InDels. (2) RNASeqBrowser can dynamically generate RNA secondary structure. It is useful for identifying non-coding RNA such as miRNA. (3) Overlaying NGS wiggle data is helpful in displaying differential expression and is simple to implement in RNASeqBrowser. (4) NGS data accumulates a lot of raw reads. Thus, RNASeqBrowser collapses exact duplicate reads to reduce visualization space. Normal PC’s can show many windows of NGS individual raw reads without much delay. (5) Multiple popup windows of individual raw reads provide users with more viewing space. This avoids existing approaches (such as IGV) which squeeze all raw reads into one window. This will be helpful for visualizing multiple datasets simultaneously. RNASeqBrowser and its manual are freely available at http://www.australianprostatecentre.org/research/software/rnaseqbrowser webcite or http://sourceforge.net/projects/rnaseqbrowser/ webcite