QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/

No-reference bitstream-based visual quality impairment detection for high definition H.264/AVC encoded video sequences

Ensuring and maintaining adequate Quality of Experience towards end-users are key objectives for video service providers, not only for increasing customer satisfaction but also as service differentiator. However, in the case of High Definition video streaming over IP-based networks, network impairments such as packet loss can severely degrade the perceived visual quality. Several standard organizations have established a minimum set of performance objectives which should be achieved for obtaining satisfactory quality. Therefore, video service providers should continuously monitor the network and the quality of the received video streams in order to detect visual degradations. Objective video quality metrics enable automatic measurement of perceived quality. Unfortunately, the most reliable metrics require access to both the original and the received video streams which makes them inappropriate for real-time monitoring. In this article, we present a novel no-reference bitstream-based visual quality impairment detector which enables real-time detection of visual degradations caused by network impairments. By only incorporating information extracted from the encoded bitstream, network impairments are classified as visible or invisible to the end-user. Our results show that impairment visibility can be classified with a high accuracy which enables real-time validation of the existing performance objectives

Constructing a no-reference H.264/AVC bitstream-based video quality metric using genetic programming-based symbolic regression

In order to ensure optimal quality of experience toward end users during video streaming, automatic video quality assessment becomes an important field-of-interest to video service providers. Objective video quality metrics try to estimate perceived quality with high accuracy and in an automated manner. In traditional approaches, these metrics model the complex properties of the human visual system. More recently, however, it has been shown that machine learning approaches can also yield competitive results. In this paper, we present a novel no-reference bitstream-based objective video quality metric that is constructed by genetic programming-based symbolic regression. A key benefit of this approach is that it calculates reliable white-box models that allow us to determine the importance of the parameters. Additionally, these models can provide human insight into the underlying principles of subjective video quality assessment. Numerical results show that perceived quality can be modeled with high accuracy using only parameters extracted from the received video bitstream

XML schemas for common bioinformatic data types and their application in workflow systems

<p>Abstract</p> <p>Background</p> <p>Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats.</p> <p>Results</p> <p>Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at <url>http://bioschemas.sourceforge.net</url>, the BioDOM library can be obtained at <url>http://biodom.sourceforge.net</url>.</p> <p>Conclusion</p> <p>The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.</p

A comparison of parsing technologies for the biomedical domain

This paper reports on a number of experiments which are designed to investigate the extent to which current nlp resources are able to syntactically and semantically analyse biomedical text. We address two tasks: parsing a real corpus with a hand-built widecoverage grammar, producing both syntactic analyses and logical forms; and automatically computing the interpretation of compound nouns where the head is a nominalisation (e.g., hospital arrival means an arrival at hospital, while patient arrival means an arrival of a patient). For the former task we demonstrate that exible and yet constrained `preprocessing &apos; techniques are crucial to success: these enable us to use part-of-speech tags to overcome inadequate lexical coverage, and to `package up&apos; complex technical expressions prior to parsing so that they are blocked from creating misleading amounts of syntactic complexity. We argue that the xml-processing paradigm is ideally suited for automatically preparing the corpus for parsing. For the latter task, we compute interpretations of the compounds by exploiting surface cues and meaning paraphrases, which in turn are extracted from the parsed corpus. This provides an empirical setting in which we can compare the utility of a comparatively deep parser vs. a shallow one, exploring the trade-o between resolving attachment ambiguities on the one hand and generating errors in the parses on the other. We demonstrate that a model of the meaning of compound nominalisations is achievable with the aid of current broad-coverage parsers

Hybrid video quality prediction: reviewing video quality measurement for widening application scope

A tremendous number of objective video quality measurement algorithms have been developed during the last two decades. Most of them either measure a very limited aspect of the perceived video quality or they measure broad ranges of quality with limited prediction accuracy. This paper lists several perceptual artifacts that may be computationally measured in an isolated algorithm and some of the modeling approaches that have been proposed to predict the resulting quality from those algorithms. These algorithms usually have a very limited application scope but have been verified carefully. The paper continues with a review of some standardized and well-known video quality measurement algorithms that are meant for a wide range of applications, thus have a larger scope. Their individual artifacts prediction accuracy is usually lower but some of them were validated to perform sufficiently well for standardization. Several difficulties and shortcomings in developing a general purpose model with high prediction performance are identified such as a common objective quality scale or the behavior of individual indicators when confronted with stimuli that are out of their prediction scope. The paper concludes with a systematic framework approach to tackle the development of a hybrid video quality measurement in a joint research collaboration.Polish National Centre for Research and Development (NCRD) SP/I/1/77065/10, Swedish Governmental Agency for Innovation Systems (Vinnova