Stigmergic hyperlink's contributes to web search

Stigmergic hyperlinks are hyperlinks with a "heart beat": if used they stay healthy and online; if neglected, they fade, eventually getting replaced. Their life attribute is a relative usage measure that regular hyperlinks do not provide, hence PageRank-like measures have historically been well informed about the structure of webs of documents, but unaware of what users effectively do with the links. This paper elaborates on how to input the users’ perspective into Google’s original, structure centric, PageRank metric. The discussion then bridges to the Deep Web, some search challenges, and how stigmergic hyperlinks could help decentralize the search experience, facilitating user generated search solutions and supporting new related business models.info:eu-repo/semantics/publishedVersio

Evaluating advanced search interfaces using established information-seeking model

When users have poorly defined or complex goals search interfaces offering only keyword searching facilities provide inadequate support to help them reach their information-seeking objectives. The emergence of interfaces with more advanced capabilities such as faceted browsing and result clustering can go some way to some way toward addressing such problems. The evaluation of these interfaces, however, is challenging since they generally offer diverse and versatile search environments that introduce overwhelming amounts of independent variables to user studies; choosing the interface object as the only independent variable in a study would reveal very little about why one design out-performs another. Nonetheless if we could effectively compare these interfaces we would have a way to determine which was best for a given scenario and begin to learn why. In this article we present a formative framework for the evaluation of advanced search interfaces through the quantification of the strengths and weaknesses of the interfaces in supporting user tactics and varying user conditions. This framework combines established models of users, user needs, and user behaviours to achieve this. The framework is applied to evaluate three search interfaces and demonstrates the potential value of this approach to interactive IR evaluation

The Phyre2 web portal for protein modeling, prediction and analysis

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission

A Newly Discovered Bordetella Species Carries a Transcriptionally Active CRISPR-Cas with a Small Cas9 Endonuclease

Background Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) are widely distributed among bacteria. These systems provide adaptive immunity against mobile genetic elements specified by the spacer sequences stored within the CRISPR. Methods The CRISPR-Cas system has been identified using Basic Local Alignment Search Tool (BLAST) against other sequenced and annotated genomes and confirmed via CRISPRfinder program. Using Polymerase Chain Reactions (PCR) and Sanger DNA sequencing, we discovered CRISPRs in additional bacterial isolates of the same species of Bordetella. Transcriptional activity and processing of the CRISPR have been assessed via RT-PCR. Results Here we describe a novel Type II-C CRISPR and its associated genes—cas1, cas2, and cas9—in several isolates of a newly discovered Bordetella species. The CRISPR-cas locus, which is absent in all other Bordetella species, has a significantly lower GC-content than the genome-wide average, suggesting acquisition of this locus via horizontal gene transfer from a currently unknown source. The CRISPR array is transcribed and processed into mature CRISPR RNAs (crRNA), some of which have homology to prophages found in closely related species B. hinzii. Conclusions Expression of the CRISPR-Cas system and processing of crRNAs with perfect homology to prophages present in closely related species, but absent in that containing this CRISPR-Cas system, suggest it provides protection against phage predation. The 3,117-bp cas9 endonuclease gene from this novel CRISPR-Cas system is 990 bp smaller than that of Streptococcus pyogenes, the 4,017-bp allele currently used for genome editing, and which may make it a useful tool in various CRISPR-Cas technologies

Analysis tools for the interplay between genome layout and regulation

Genome layout and gene regulation appear to be interdependent. Understanding this interdependence is key to exploring the dynamic nature of chromosome conformation and to engineering functional genomes. Evidence for non-random genome layout, defined as the relative positioning of either co-functional or co-regulated genes, stems from two main approaches. Firstly, the analysis of contiguous genome segments across species, has highlighted the conservation of gene arrangement (synteny) along chromosomal regions. Secondly, the study of long-range interactions along a chromosome has emphasised regularities in the positioning of microbial genes that are co-regulated, co-expressed or evolutionarily correlated. While one-dimensional pattern analysis is a mature field, it is often powerless on biological datasets which tend to be incomplete, and partly incorrect. Moreover, there is a lack of comprehensive, user-friendly tools to systematically analyse, visualise, integrate and exploit regularities along genomes.Here we present the Genome REgulatory and Architecture Tools SCAN (GREAT:SCAN) software for the systematic study of the interplay between genome layout and gene expression regulation.SCAN is a collection of related and interconnected applications currently able to perform systematic analyses of genome regularities as well as to improve transcription factor binding sites (TFBS) and gene regulatory network predictions based on gene positional information.We demonstrate the capabilities of these tools by studying on one hand the regular patterns of genome layout in the major regulons of the bacterium Escherichia coli. On the other hand, we demonstrate the capabilities to improve TFBS prediction in microbes. Finally, we highlight, by visualisation of multivariate techniques, the interplay between position and sequence information for effective transcription regulation

Reach and rich : the new economics of information and the provision of on-line legal services in the UK

The paper considers a number of issues including the use of the Web as an opportunity for smaller firms to break free from the traditional indicators of reputation and expertise such as the size and opulence of offices. It also reflects on the use of client-specific Extranets in addition to publicly available Internet sites. The paper concludes that although the Web provides reach, offering richness and the sense of community required for creating and sustaining relationships with potential clients can be difficult. Some suggestions are made for enhancing 'Richness' in Web sites

INDEX STRATEGIES FOR EFFICIENT AND EFFECTIVE ENTITY SEARCH

The volume of structured data has rapidly grown in recent years, when data-entity emerged as an abstraction that captures almost every data pieces. As a result, searching for a desired piece of information on the web could be a challenge in term of time and relevancy because the number of matching entities could be very large for a given query. This project concerns with the efficiency and effectiveness of such entity queries. The work contains two major parts: implement inverted indexing strategies so that queries can be searched in minimal time, and rank results based on features that are independent of the query itself