Workflow reuse in practice: a study of neuroimaging pipeline users

Workflow reuse is a major benefit of workflow systems and shared workflow repositories, but there are barely any studies that quantify the degree of reuse of workflows or the practical barriers that may stand in the way of successful reuse. In our own work, we hypothesize that defining workflow fragments improves reuse, since end-to-end workflows may be very specific and only partially reusable by others. This paper reports on a study of the current use of workflows and workflow fragments in labs that use the LONI Pipeline, a popular workflow system used mainly for neuroimaging research that enables users to define and reuse workflow fragments. We present an overview of the benefits of workflows and workflow fragments reported by users in informal discussions. We also report on a survey of researchers in a lab that has the LONI Pipeline installed, asking them about their experiences with reuse of workflow fragments and the actual benefits they perceive. This leads to quantifiable indicators of the reuse of workflows and workflow fragments in practice. Finally, we discuss barriers to further adoption of workflow fragments and workflow reuse that motivate further work

SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand

The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, evenwhennosuchgeneispresent.Thiscapabilitymeansthatsynteny-basedmethodsarefarmoreeffectivethansequencesimilaritybased methods in identifying true-negatives, a necessity forstudying gene loss and gene transposition. However, the identification of syntenicregionsrequirescomplexanalyseswhichmustberepeatedforpairwisecomparisonsbetweenanytwospecies.Therefore,as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of targetgenomes.SynFindiscapableofreportingper-geneinformation,usefulforresearchersstudyingspecificgenefamilies,aswellas genome-wide data sets of syntenic gene and predicted gene locations, critical for researchers focused on large-scale genomic analyses. Inference of syntenic homologs provides the basis for correlation of functional changes around genes of interests between related organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic data from over 15,000 organisms from all domains of life as well as supporting multiple releases of the same organism. SynFind makes use of a powerful job execution framework that promises scalability and reproducibility. SynFind can be accessed at http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc

Analyzing The Effects Of Single-sourcing Methodologies On The Role Of The Technical Communicator

This thesis discusses the specific effects of single sourcing methodologies on the role of the technical communicator, his or her job responsibilities, qualifications, collaboration with coworkers, employee and employer expectations, and the effects on career progression. The methodologies discussed included all types of single sourcing methods for technical documentation (such as XML-based), advanced and non-advanced Content Management Systems (CMS), and Digital Asset Management (DAM) systems. Other topics explored are an overview of single sourcing for technical documentation, a comparison of the craftsman model to the current trend of single sourcing and structured content, specific effects on technical communicators such as role changes, the effects of incorporating XML into a technical communicator\u27s daily work environment, and the effects of other emerging technologies such as advanced CMS and DAM systems on technical communicators. General findings include that the practice of single sourcing, whether a positive or negative development, has continued and likely will continue to increase in technical communication groups within organizations. Single sourcing, especially for dynamic, customized content is also increasing because of the current marketplace, but works best via the use of a CMS and other systems used by large organizations. Single sourcing is also best implemented after extensive strategic planning and training of employees. Many technical communicators will have to accept new roles and positions, the direction of which is greatly impacted by the extent of their skills. Recommendations are made for additional research on the effects of single sourcing implementation on the technical communicator, and how to adapt to changes. Additional research is also needed on XML, DITA (Darwinian Information Typing Architecture), and DAM systems, all related specifically to technical communication

Open Scientific Data

This book shows how the vision for open access to scientific data can be more readily achieved through a staged model that research funders, policy makers, scientists, and research organizations can adopt in their practice. Drawing on her own experiences with data processing, on early findings with open scientific data at CERN (the European Organization for Nuclear Research), and from case studies of shared clinical trial data, the author updates our understanding of research data - what it is; how it dynamically evolves across different scientific disciplines and across various stages of research practice; and how it can, and indeed should, be shared at any of those stages. The result is a flexible and pragmatic path for implementing open scientific data

Reuse and Repurposing of Online Digital Learning Resources within UK Higher Education: 2003-2010

This research set out to examine developments in reuse and repurposing of online digital resources within higher education (HE) in the United Kingdom (UK) over a period (2003-2010), when the emphasis of educational resource reuse and repurposing activity shifted from reusable learning objects (RLO) to open educational resources (OER). It aims to contribute to understanding of this transition, and locates this shift within a broader picture of UK HE activity within the UK, and a wider understanding of reuse of learning resources in digital, online form. The research presents a review and critical examination of the environment in which reuse practice occurred. It does this through macroenvironmental, mesoenvironmental and microenvironmental level reviews. The microenvionmental review is presented through research analysis of five case examples from UK HE and a sixth example from HE in Ireland. The mesoenvironmental review examines the significant changes in resource facilitation and practice during the research period. This thesis is particularly concerned with identifying and understanding how reuse of digital online learning resources was facilitated in practice, and whether reuse occurred, or occurred in the form(s) anticipated. The thesis identifies and examines themes and factors which appeared to have influenced, or had potential to influence, reuse in each case. Cross-case comparison offers a synthesis of the research observations. Finally, a structured approach to classifying factors is suggested based on this research. This leads to generalisable recommendations of how to facilitate digital online resource reuse in the future

Final FLaReNet deliverable: Language Resources for the Future - The Future of Language Resources

Language Technologies (LT), together with their backbone, Language Resources (LR), provide an essential support to the challenge of Multilingualism and ICT of the future. The main task of language technologies is to bridge language barriers and to help creating a new environment where information flows smoothly across frontiers and languages, no matter the country, and the language, of origin. To achieve this goal, all players involved need to act as a community able to join forces on a set of shared priorities. However, until now the field of Language Resources and Technology has long suffered from an excess of individuality and fragmentation, with a lack of coherence concerning the priorities for the field, the direction to move, not to mention a common timeframe. The context encountered by the FLaReNet project was thus represented by an active field needing a coherence that can only be given by sharing common priorities and endeavours. FLaReNet has contributed to the creation of this coherence by gathering a wide community of experts and making them participate in the definition of an exhaustive set of recommendations

Metadata enhanced content management in media companies

Media companies are facing new opportunities and challenges. Communications, computing, and content industries are converging into a single, horizontally connected content value chain, where changes are frequent and activities are highly interdependent. However, before convergence and digital content are taken seriously, media companies must understand what is expected from them, how their operations will be affected, and why they should be involved. The production, distribution, and use of content rely heavily on computers and automation. This requires the content essence to be enhanced with explicit descriptions of semantics, or more specifically, semantic metadata. However, semantic metadata is useful only if its nature is understood clearly, and when its structure and usage are well defined. For this purpose, ontologies are needed to capture the essential characteristics of the content domain into a limited set of meaningful concepts. The creation and management of ontologies and semantic metadata require skills and activities that do not necessarily exist in traditional print-based publishing or broadcasting. Companies developing ontologies must understand the essential characteristics of available content, user needs, and planned or existing use of content. Furthermore, they must be able to express this information explicitly in an ontology and then reflect changes in the environment back to that ontology. Content production and distribution should be flexible and able to support the reuse of content. This thesis introduces two abstract models, a component model and a process model. Both models assist in the understanding and analysis of electronic publishing of content for multiple media products and on multiple media platforms. When semantic metadata, ontologies, and improved publishing processes are available, new advanced content-based products, such as personalized information feeds, are possible. The SmartPush project, for which the author was the project manager and worked as a researcher, has shown that semantic metadata is useful in creating advanced content-based products, and that media companies are willing to alter their existing publishing processes. Media companies participating in the SmartPush project have acknowledged the impact of our work on their plans and operations. Their acknowledgement emphasizes the practical importance of semantic metadata, ontologies, improved electronic publishing process, and personalization research.reviewe