CGHub: Kick-starting the Worldwide Genome Web

The University of California, Santa Cruz (UCSC) is under contract with the National Cancer Institute (NCI) to construct and operate the Cancer Genomics Hub (CGHub), a nation-scale library and user portal for cancer genomics data.  This contract covers growth of the library to 5 Petabytes. The NCI programs that feed into the library currently produce about 20 terabytes of data each month. We discuss the receiver-driven file transfer mechanism Annai GeneTorrent (GT) for use with the library. Annai GT uses multiple TCP streams from multiple computers at the library site to parallelize genome downloads.  We review our performance experience with the new transfer mechanism and also explain additions to the transfer protocol to support the security required in handling patient cancer genomics data

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

Understanding Budget Processes for Law Enforcement

Examines the budget process and explains the necessity of a successful approach in order to meet the mission of the agency

Brexit Report - Impact on Business Models of Scottish Companies

The Brexit Business Model Report is a preliminary assessment of research, interviews and survey results regarding the impact of Brexit on the business models of Scottish companies as they prepare for post-Brexit scenarios. The survey was used to compile data to support research questions gathered during the research and interview process for this graduate class project. Questions were designed to assess how Brexit is impacting the ability of Scottish companies in the areas of business model, contingency planning, supply chain, staffing, innovation, global reach, risk assessment, and opportunities. The questions reflected areas of the business model that may have present and future implications. The answers help measure the Brexit impact on Scottish firms’ business models and the potential for international growth. The upper management of Scottish companies from the “Insider Top 500” list, “FactSet list, and various trade organizations were selected to receive the survey. The focus of this study was on the potential impact of Brexit on Scottish companies’ business models. The survey findings show the importance of understanding the elements of a business model in the Brexit context (see Additional File, Executive Summary below for Business Model Brexit Implications on Scottish Companies based on Key Findings table)

Image annotation with Photocopain

Photo annotation is a resource-intensive task, yet is increasingly essential as image archives and personal photo collections grow in size. There is an inherent conflict in the process of describing and archiving personal experiences, because casual users are generally unwilling to expend large amounts of effort on creating the annotations which are required to organise their collections so that they can make best use of them. This paper describes the Photocopain system, a semi-automatic image annotation system which combines information about the context in which a photograph was captured with information from other readily available sources in order to generate outline annotations for that photograph that the user may further extend or amend

A northern powerhouse, or an unwelcome imposition? experts respond to George Osborne’s Greater Manchester Mayor proposals

The Chancellor recently announced that in order to help make his “Northern Powerhouse” idea reality that the Greater Manchester City Region would see itself gain an elected, “London-style” Mayor, despite residents of Manchester City Council narrowly rejecting proposals for an Directly Elected Mayor for their local authority in 2011. Democratic Audit asked experts to respond to the news, with mixed results

Forecasting infrastructure resilience to climate change

Resilience of the UK transport infrastructure network can be expressed as the imbalance between the physical condition of the network and the transport demands the network experiences. Forecasting changes of resilience in the long term (e.g. the 2050s) requires a structured, multi-disciplinary approach. The Engineering and Physical Sciences Research Council funded Futurenet project developed a model architecture to formalise such an approach and this paper addresses one component: the assessment of the influence of physical processes on asset condition. This requires the development of new, integrated physical-based models that respond to detailed inputs of forecast weather events (e.g. UK Climate Projections 2009). The results are plotted onto the infrastructure network for visualisation. Subsequent combination with user demand will then enable determination of network resilience at a range of spatial scales. The project has highlighted the need for better datasets, more sophisticated physical-based models and further analyses of complex feedbacks and interactions between physical processes and also with user behaviour

JTEC panel report on machine translation in Japan

The goal of this report is to provide an overview of the state of the art of machine translation (MT) in Japan and to provide a comparison between Japanese and Western technology in this area. The term 'machine translation' as used here, includes both the science and technology required for automating the translation of text from one human language to another. Machine translation is viewed in Japan as an important strategic technology that is expected to play a key role in Japan's increasing participation in the world economy. MT is seen in Japan as important both for assimilating information into Japanese as well as for disseminating Japanese information throughout the world. Most of the MT systems now available in Japan are transfer-based systems. The majority of them exploit a case-frame representation of the source text as the basis of the transfer process. There is a gradual movement toward the use of deeper semantic representations, and some groups are beginning to look at interlingua-based systems

Integrating information to bootstrap information extraction from web sites

In this paper we propose a methodology to learn to extract domain-specific information from large repositories (e.g. the Web) with minimum user intervention. Learning is seeded by integrating information from structured sources (e.g. databases and digital libraries). Retrieved information is then used to bootstrap learning for simple Information Extraction (IE) methodologies, which in turn will produce more annotation to train more complex IE engines. All the corpora for training the IE en- gines are produced automatically by integrating in- formation from different sources such as available corpora and services (e.g. databases or digital libraries, etc.). User intervention is limited to providing an initial URL and adding information missed by the different modules when the computation has finished. The information added or delete by the user can then be reused providing further training and therefore getting more information (recall) and/or more precision. We are currently applying this methodology to mining web sites of Computer Science departments.peer-reviewe

Mining web sites using adaptive information extraction

Adaptive Information Extraction systems (IES) are currently used by some Semantic Web (SW) annotation tools as support to annotation (Handschuh et al., 2002; Vargas-Vera et al., 2002). They are generally based on fully supervised methodologies requiring fairly intense domain-specific annotation. Unfortunately, selecting representative examples may be difficult and annotations can be incorrect and require time. In this paper we present a methodology that drastically reduce (or even remove) the amount of manual annotation required when annotating consistent sets of pages. A very limited number of user-defined examples are used to bootstrap learning. Simple, high precision (and possibly high recall) IE patterns are induced using such examples, these patterns will then discover more examples which will in turn discover more patterns, etc.peer-reviewe