An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

How to improve robustness in Kohonen maps and display additional information in Factorial Analysis: application to text mining

This article is an extended version of a paper presented in the WSOM'2012 conference [1]. We display a combination of factorial projections, SOM algorithm and graph techniques applied to a text mining problem. The corpus contains 8 medieval manuscripts which were used to teach arithmetic techniques to merchants. Among the techniques for Data Analysis, those used for Lexicometry (such as Factorial Analysis) highlight the discrepancies between manuscripts. The reason for this is that they focus on the deviation from the independence between words and manuscripts. Still, we also want to discover and characterize the common vocabulary among the whole corpus. Using the properties of stochastic Kohonen maps, which define neighborhood between inputs in a non-deterministic way, we highlight the words which seem to play a special role in the vocabulary. We call them fickle and use them to improve both Kohonen map robustness and significance of FCA visualization. Finally we use graph algorithmic to exploit this fickleness for classification of words

Towards data grids for microarray expression profiles

The UK DTI funded Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) project developed a Grid infrastructure through which research into the genetic causes of hypertension could be supported by scientists within the large Wellcome Trust funded Cardiovascular Functional Genomics project. The BRIDGES project had a focus on developing a compute Grid and a data Grid infrastructure with security at its heart. Building on the work within BRIDGES, the BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project plans to provide an enhanced data Grid infrastructure to support richer queries needed for the discovery and analysis of microarray data sets, also based upon a fine-grained security infrastructure. This paper outlines the experiences gained within BRIDGES and outlines the status of the GEMEPS project, the open challenges that remain and plans for the future

El derecho a la muerte digital en la Federación de Rusia, UE y EE. UU

The purpose of this study is to identify common and specific features of the theoretical and legal foundations of the right to digital death. Today, the regulation of this right is at the initial stage, and only a few countries (USA, France, Spain) have established in their legislation the norms regulating the order of inheritance of virtual objects. The legislation of the Russian Federation does not contain any special norms, however, the latest amendments to the Civil Code of the Russian Federation, which come into force on October 1, 2019, have indicated a completely different vector of development of this sphere than that followed by other countries. The analysis of the existing legislation revealed the problems of fixing and implementing the right to digital death and suggested ways to solve them.    El propósito de este estudio es identificar características comunes y específicas de los fundamentos teóricos y legales del derecho a la muerte digital. Hoy, la regulación de este derecho se encuentra en la etapa inicial, y solo unos pocos países (EE. UU., Francia, España) han establecido en su legislación las normas que regulan el orden de herencia de los objetos virtuales. La legislación de la Federación de Rusia no contiene ninguna norma especial, sin embargo, las últimas enmiendas al Código Civil de la Federación de Rusia, que entraron en vigor el 1 de octubre de 2019, han indicado un vector de desarrollo de esta esfera completamente diferente al de seguido por otros países. El análisis de la legislación existente reveló los problemas de arreglar e implementar el derecho a la muerte digital y sugirió formas de resolverlos

Change decision support:extraction and analysis of late architecture changes using change characterization and software metrics

Software maintenance is one of the most crucial aspects of software development. Software engineering researchers must develop practical solutions to handle the challenges presented in maintaining mature software systems. Research that addresses practical means of mitigating the risks involved when changing software, reducing the complexity of mature software systems, and eliminating the introduction of preventable bugs is paramount to today’s software engineering discipline. Giving software developers the information that they need to make quality decisions about changes that will negatively affect their software systems is a key aspect to mitigating those risks. This dissertation presents work performed to assist developers to collect and process data that plays a role in change decision-making during the maintenance phase. To address these problems, developers need a way to better understand the effects of a change prior to making the change. This research addresses the problems associated with increasing architectural complexity caused by software change using a twoold approach. The first approach is to characterize software changes to assess their architectural impact prior to their implementation. The second approach is to identify a set of architecture metrics that correlate to system quality and maintainability and to use these metrics to determine the level of difficulty involved in making a change. The two approaches have been combined and the results presented provide developers with a beneficial analysis framework that offers insight into the change process