GeneLink: a database to facilitate genetic studies of complex traits

BACKGROUND: In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often critical to the success of these projects. To minimize the difficulties inherent in complex trait studies, we have developed GeneLink, a Web-accessible, password-protected Sybase database. RESULTS: GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data. Specifically designed to facilitate large-scale (multi-center) genetic linkage or association studies, GeneLink securely and efficiently handles large amounts of data and provides additional features to facilitate data analysis by existing software packages and quality control. These include the ability to download chromosome-specific data files containing marker data in map order in various formats appropriate for downstream analyses (e.g., GAS and LINKAGE). Furthermore, an unlimited number of phenotypes (either qualitative or quantitative) can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. CONCLUSIONS: GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC). GeneLink is freely available at

A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

MODELS AND SOLUTIONS FOR THE IMPLEMENTATION OF DISTRIBUTED SYSTEMS

Software applications may have different degrees of complexity depending on the problems they try to solve and can integrate very complex elements that bring together functionality that sometimes are competing or conflicting. We can take for example a mobile communications system. Functionalities of such a system are difficult to understand, and they add to the non-functional requirements such as the use in practice, performance, cost, durability and security. The transition from local computer networks to cover large networks that allow millions of machines around the world at speeds exceeding one gigabit per second allowed universal access to data and design of applications that require simultaneous use of computing power of several interconnected systems. The result of these technologies has enabled the evolution from centralized to distributed systems that connect a large number of computers. To enable the exploitation of the advantages of distributed systems one had developed software and communications tools that have enabled the implementation of distributed processing of complex solutions. The objective of this document is to present all the hardware, software and communication tools, closely related to the possibility of their application in integrated social and economic level as a result of globalization and the evolution of e-society. These objectives and national priorities are based on current needs and realities of Romanian society, while being consistent with the requirements of Romania's European orientation towards the knowledge society, strengthening the information society, the target goal representing the accomplishment of e-Romania, with its strategic e-government component. Achieving this objective repositions Romania and gives an advantage for sustainable growth, positive international image, rapid convergence in Europe, inclusion and strengthening areas of high competence, in line with Europe 2020, launched by the European Council in June 2010.information society, databases, distributed systems, e-society, implementation of distributed systems

The Digital Anatomist Foundational Model Server

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Middleware-based Database Replication: The Gaps between Theory and Practice

The need for high availability and performance in data management systems has been fueling a long running interest in database replication from both academia and industry. However, academic groups often attack replication problems in isolation, overlooking the need for completeness in their solutions, while commercial teams take a holistic approach that often misses opportunities for fundamental innovation. This has created over time a gap between academic research and industrial practice. This paper aims to characterize the gap along three axes: performance, availability, and administration. We build on our own experience developing and deploying replication systems in commercial and academic settings, as well as on a large body of prior related work. We sift through representative examples from the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies from real systems deployed at Fortune 500 customers. We propose two agendas, one for academic research and one for industrial R&D, which we believe can bridge the gap within 5-10 years. This way, we hope to both motivate and help researchers in making the theory and practice of middleware-based database replication more relevant to each other.Comment: 14 pages. Appears in Proc. ACM SIGMOD International Conference on Management of Data, Vancouver, Canada, June 200

KAPTUR: technical analysis report

Led by the Visual Arts Data Service (VADS) and funded by the JISC Managing Research Data programme (2011-13) KAPTUR will discover, create and pilot a sectoral model of best practice in the management of research data in the visual arts in collaboration with four institutional partners: Glasgow School of Art; Goldsmiths, University of London; University for the Creative Arts; and University of the Arts London. This report is framed around the research question: which technical system is most suitable for managing visual arts research data? The first stage involved a literature review including information gathered through attendance at meetings and events, and Internet research, as well as information on projects from the previous round of JISCMRD funding (2009-11). During February and March 2012, the Technical Manager carried out interviews with the four KAPTUR Project Officers and also met with IT staff at each institution. This led to the creation of a user requirement document (Appendix A), which was then circulated to the project team for additional comments and feedback. The Technical Manager selected 17 systems to compare with the user requirement document (Appendix B). Five of the systems had similar scores so these were short-listed. The Technical Manager created an online form into which the Project Officers entered priority scores for each of the user requirements in order to calculate a more accurate score for each of the five short-listed systems (Appendix C) and this resulted in the choice of EPrints as the software for the KAPTUR project

The Digital Anatomist Information System and Its Use in the Generation and Delivery of Web-Based Anatomy Atlases

Advances in network and imaging technology, coupled with the availability of 3-D datasets such as the Visible Human, provide a unique opportunity for developing information systems in anatomy that can deliver relevant knowledge directly to the clinician, researcher or educator. A software framework is described for developing such a system within a distributed architecture that includes spatial and symbolic anatomy information resources, Web and custom servers, and authoring and end-user client programs. The authoring tools have been used to create 3-D atlases of the brain, knee and thorax that are used both locally and throughout the world. For the one and a half year period from June 1995–January 1997, the on-line atlases were accessed by over 33,000 sites from 94 countries, with an average of over 4000 ‘‘hits’’ per day, and 25,000 hits per day during peak exam periods. The atlases have been linked to by over 500 sites, and have received at least six unsolicited awards by outside rating institutions. The flexibility of the software framework has allowed the information system to evolve with advances in technology and representation methods. Possible new features include knowledge-based image retrieval and tutoring, dynamic generation of 3-D scenes, and eventually, real-time virtual reality navigation through the body. Such features, when coupled with other on-line biomedical information resources, should lead to interesting new ways for managing and accessing structural information in medicine

Competing Technologies in the Database Management Systems Market

In this paper, we study the dynamics of the market for Database Management Systems (DBMS), which is commonly assumed to possess network effects and where there is still some viable competition in our study period, 2000 – 2004. Specifically, we make use of a unique and detailed dataset on several thousand UK firms to study individual organizations’ incentives to adopt a particular technology. We find that there are significant internal complement effects – in other words, using an operating system and a DBMS from the same vendor seems to confer some complementarities. We also find evidence for complementarities between enterprise resource planning systems (ERP) and DBMS and find that as ERP are frequently specific and customized, DBMS are unlikely to be changed once they have been customized to an ERP. We also find that organizations have an increasing tendency to use multiple DBMS on one site, which contradicts the notion that different DBMS are near-perfect substitutes