Collaboration in scientific digital ecosystems: A socio-technical network analysis

This dissertation seeks to understand the formation, operation, organizational (collaboration) and the effect of scientific digital ecosystems that connect several online community networks in a single platform. The formation, mechanism and processes of online networks that influence members output is limited and contradictory. The dissertation is comprised of three papers that are guided by the following research questions: How does online community member’s productivity (or success) depend upon their ‘position’ in the digital networks? What are the network formation mechanism, structures and characteristics of an online community? How do scientific innovations traverse (diffuse) amongst users in online communities? A combination of exploratory, inductive and deductive research designs is applied sequentially but in a non-linear manner to address research question. The dissertation contributes to the literature on scientific collaboration, digital communities of creation, social network modelling and diffusion of innovation. The first paper applies network theory and spatial probit autocorrelative modelling technique to evaluate how member developer’s positioning in digital community correlate with his/her productivity. The second paper looks at the dynamics of developer’s participation in online developers’ network for a period spanning 7-years using exponential random graph models (ERGM). This paper applies theory of network (network science) to model network formation patterns in developer community. The third paper, like the first, applies network theory and to understand user network characteristics and communication channels which influence diffusion of scientific innovations. Bass and spatial probit autocorrelative models are applied for this analysis. Data from this study was mined from developers, authors and user communities of nanoHUB.org cyberinfrastructure platform. NanoHUB.org is a science and engineering online ecosystem comprising self-organized researchers, educators, and professional communities in eight member institutions that collaborate, share resources and solve nanotechnology related problems including development and usage of tools (scientific innovation). Data from collaboration and information sharing activities was used to create the developers, authors and user networks that were used for analysis. Results of the first paper show that the spatial autocorrelation parameter of the spatial probit model is negative and statistically different from zero. The negative spatial spillover effect in the developer network imply that developers that are embedded in the network have a lower probability of getting more output. The structural network characteristics of eigen vector centrality had statistically significant effects on probability of being more productive. Developers who are also authors were found to be more productive than those in one network. The implications of these findings is that developers will benefit from being in multiple network spaces and by associating with more accomplished developers. The autocorrelative and interaction models also reveal various new modelling approach of accounting for network autocorrelation effects to online member. Results of the second paper show that developers form in a manner that follow a pure uniform random distribution. Results also show that developer’s collaborative mechanisms are characterized by low tendencies to reciprocate and form homophiles (tendency of developers to associate with similar peers) but high tendency to form clusters. The implications of network formation mechanism and processes are that developers are forming in a purely random and self-organized manner and minimum efforts should be applied in trying to organize and influence the community organization. The results also reveal that a simple link to link ERGM and stochastic dominance criteria can be combined to characterize the network formation characteristics just like the ERG(p*) model but have an advantage of overcoming degeneracy challenges associated with ERG(p*) models. Results of the third paper show that bass model is a good predictor for diffusion of scientific innovations (tools) in online community setting. Results also show different innovations have varying levels and rates of adoption and these were influenced by both external and internal factors. Results of the micro-based model found degrees and betweeness centrality as some of the internal variables that have positive influence on the adoption of innovation while centrality measures of power or leadership were found to have negative influence of adoption process. The relative time taken to run a simulation (measured as job usage time) was also found to be negatively influencing diffusion. The implication of the study results is that bass model is a good fit for evaluating and forecasting adoption of innovation in online communities. Moreover, network structural characteristics are responsible for adoption of innovation adoption and policy making should consider tool adoption enhancing ones. Additionally, researchers could further explore the network structural characteristics that are driving diffusion of innovation

Deploying and Maintaining a Campus Grid at Clemson University

Many institutions have all the tools needed to create a local grid that aggregates commodity compute resources into an accessible grid service, while simultaneously maintaining user satisfaction and system security. In this thesis, the author presents a three-tiered strategy used at Clemson University to deploy and maintain a grid infrastructure by making resources available to both local and federated remote users for scientific research. Using this approach virtually no compute cycles are wasted. Usage trends and power consumption statistics collected from the Clemson campus grid are used as a reference for best-practices. The loosely-coupled components that comprise the campus grid work together to form a highly cohesive infrastructure that not only meets the computing needs of local users, but also helps to fill the needs of the scientific community at large. Experience gained from the deployment and management of this system may be adapted to other grid sites, allowing for the development of campus-wide, grid-connected cyberinfrastructures

National Science Foundation Advisory Committee for Cyberinfrastructure Task Force on Campus Bridging Final Report

The mission of the National Science Foundation (NSF) Advisory Committee on Cyberinfrastructure (ACCI) is to advise the NSF as a whole on matters related to vision and strategy regarding cyberinfrastructure (CI). In early 2009 the ACCI charged six task forces with making recommendations to the NSF in strategic areas of cyberinfrastructure: Campus Bridging; Cyberlearning and Workforce Development; Data and Visualization; Grand Challenges; High Performance Computing (HPC); and Software for Science and Engineering. Each task force was asked to offer advice on the basis of which the NSF would modify existing programs and create new programs. This document is the final, overall report of the Task Force on Campus Bridging.National Science Foundatio

Distributed Simulation: State-of-the-Art and Potential for Operational Research

In Operational Research conventional simulation practices typically focus on the conceptualization, development and use of a single model simulated on a single computer by a single analyst. Since the late 1970s the field of Distributed Simulation has led research into how to speed up simulation and how to compose large-scale simulations consisting of many reusable models running using distributed computers. There have been significant advances in the theories and technologies underpinning Distributed Simulation and there have been major successes in defence, computer systems design and smart urban environments. However, from an Operational Research perspective, Distributed Simulation has had little impact on mainstream research and practice. To argue the potential benefits of Distributed Simulation for Operational Research, this article gives an overview of Distributed Simulation approaches and technologies as well as discussing the state-of-the-art of Distributed Simulation applications. It will investigate the potential advantages of Distributed Simulation for Operational Research and present a possible sustainable future, based on experiences from e-Science, that will help Operational Research meet future challenges such as those emerging from Big Data Analytics, Cyber-physical systems, Industry 4.0, Digital Twins and Smart environments

National Center for Genome Analysis Program Year 3 Report – September 15, 2013 – September 14, 2014

On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the third 12 months of NCGASThe facilities supported by the Research Technologies division at Indiana University are supported by a number of grants. The authors would like to acknowledge that although the National Center for Genome Analysis Support is funded by NSF 1062432, our work would not be possible without the generous support of the following awards received by our parent organization, the Pervasive Technology Institute at Indiana University. • The Indiana University Pervasive Technology Institute was supported in part by two grants from the Lilly Endowment, Inc. • NCGAS has also been supported directly by the Indiana METACyt Initiative. The Indiana METACyt Initiative of Indiana University is supported in part by the Lilly Endowment, Inc. • This material is based in part upon work supported by the National Science Foundation under Grant No. CNS-0521433. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation (NSF)

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Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Ontic Occlusion and Exposure in Sociotechnical Systems

Living inside built environments - infrastructure - it is easy to take for granted the things that we do not need to engage, but are at work behind the scenes nonetheless. Well-designed systems become invisible, but to engage them, how do we know which perspectives, objects, and relationships are useful? I examine the University of Michigan Digital Library (UMDL), a mid-1990s interdisciplinary project attempting to build an agent-based digital library architecture. Through analyzing project data, I develop the concept of ontic occlusion and exposure - mechanisms of choice regarding objects and relationships that enter discourses and representations. By analyzing project artifacts, interview transcripts, and meeting records, this study iden- tifies key sets of discursive elements bridging concepts between disciplinary communities on the surface, but were the fundamental sites of contestation between groups’ understanding of project goals. I examine narratives of project personnel to understand the positioning of terms and ideas relating to project design, execution, and assessment, and discuss the role of the ontic in interdisciplinary work. Using data from the UMDL project, I discuss the tension between occlusion (the hidden) and exposure (the revealed) in understanding the digital library as an object through meet- ings of the project operating committee - the primary engagement site between researchers from different departments, primarily computer engineering and library science. Examining interpretive differences, use of fundamental terms, and observations about the contested responses toward resolution, we can better understand the outcomes of the project, the disciplinary positioning of institutional change, and perspectives of evaluating the project in the subsequent years. This dissertation contributes to an understanding of discourse development in interdisciplinary projects where shared language is important to design, execution, and evaluation. It combines perspectives in philosophy, digital libraries, and interdisciplinarity studies. The complementary mechanisms of ontic occlusion and exposure are useful devices to decode and describe change in sociotechnical systems, and highlight the need to examine more closely both what is rendered in accounts of infrastructure, and residual categories often left unaddressed.Ph.D.InformationUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/78763/1/cknobel_1.pd

Contexts and Contributions: Building the Distributed Library

This report updates and expands on A Survey of Digital Library Aggregation Services, originally commissioned by the DLF as an internal report in summer 2003, and released to the public later that year. It highlights major developments affecting the ecosystem of scholarly communications and digital libraries since the last survey and provides an analysis of OAI implementation demographics, based on a comparative review of repository registries and cross-archive search services. Secondly, it reviews the state-of-practice for a cohort of digital library aggregation services, grouping them in the context of the problem space to which they most closely adhere. Based in part on responses collected in fall 2005 from an online survey distributed to the original core services, the report investigates the purpose, function and challenges of next-generation aggregation services. On a case-by-case basis, the advances in each service are of interest in isolation from each other, but the report also attempts to situate these services in a larger context and to understand how they fit into a multi-dimensional and interdependent ecosystem supporting the worldwide community of scholars. Finally, the report summarizes the contributions of these services thus far and identifies obstacles requiring further attention to realize the goal of an open, distributed digital library system

Big Data and Large-scale Data Analytics: Efficiency of Sustainable Scalability and Security of Centralized Clouds and Edge Deployment Architectures

One of the significant shifts of the next-generation computing technologies will certainly be in the development of Big Data (BD) deployment architectures. Apache Hadoop, the BD landmark, evolved as a widely deployed BD operating system. Its new features include federation structure and many associated frameworks, which provide Hadoop 3.x with the maturity to serve different markets. This dissertation addresses two leading issues involved in exploiting BD and large-scale data analytics realm using the Hadoop platform. Namely, (i)Scalability that directly affects the system performance and overall throughput using portable Docker containers. (ii) Security that spread the adoption of data protection practices among practitioners using access controls. An Enhanced Mapreduce Environment (EME), OPportunistic and Elastic Resource Allocation (OPERA) scheduler, BD Federation Access Broker (BDFAB), and a Secure Intelligent Transportation System (SITS) of multi-tiers architecture for data streaming to the cloud computing are the main contribution of this thesis study