WormBase 2014: new views of curated biology

WormBase (http://www.wormbase.org/) is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans. With an electronic history predating the World Wide Web, WormBase contains information ranging from the sequence and phenotype of individual alleles to genome-wide studies generated using next-generation sequencing technologies. In recent years, we have expanded the contents to include data on additional nematodes of agricultural and medical significance, bringing the knowledge of C. elegans to bear on these systems and providing support for underserved research communities. Manual curation of the primary literature remains a central focus of the WormBase project, providing users with reliable, up-to-date and highly cross-linked information. In this update, we describe efforts to organize the original atomized and highly contextualized curated data into integrated syntheses of discrete biological topics. Next, we discuss our experiences coping with the vast increase in available genome sequences made possible through next-generation sequencing platforms. Finally, we describe some of the features and tools of the new WormBase Web site that help users better find and explore data of interest

Using Technology Enabled Qualitative Research to Develop Products for the Social Good, An Overview

This paper discusses the potential benefits of the convergence of three recent trends for the design of socially beneficial products and services: the increasing application of qualitative research techniques in a wide range of disciplines, the rapid mainstreaming of social media and mobile technologies, and the emergence of software as a service. Presented is a scenario facilitating the complex data collection, analysis, storage, and reporting required for the qualitative research recommended for the task of designing relevant solutions to address needs of the underserved. A pilot study is used as a basis for describing the infrastructure and services required to realize this scenario. Implications for innovation of enhanced forms of qualitative research are presented

EGI: anOpen e-Infrastructure Ecosystem for the Digital European Research Area

Bringing the digital European Research Area (ERA) online means modernising Europe’s research infrastructure by promoting open science through the availability, accessibility and reuse of scientific data and results, the use of web- based tools that facilitate scientific collaboration and ensuring public access to research. As the European Grid Infrastructure (EGI) is the largest European distributed computing infrastructure providing 24/7 access to large scale computing, storage and data resources through a federation of national resource providers, it allows scientists from all disciplines to make the most out of the latest computing technologies for the benefit of their research. This paper describes the methodology and approach for defining EGI’s role in bringing this digital ERA online. The work presented defines the roles and functions of EGI as an open ICT ecosystem, required service redesign, the added value of EGI for the European research communities and demonstrates the role that EGI plays in contributing to the Europe 2020 strategy for social-economic impact

Bringing the OpenMI to LIFE Progress Report No. 4 - 31st March 2008 – 30th September 2008

The Water Framework Directive demands an integrated approach to water management. This requires the ability to predict how catchment processes will behave and interact in response to the activities of water managers and others. In most contexts, it is not feasible to build a single predictive model that adequately represents all the processes; therefore a means of linking models of individual processes is required. This is met by the FP5 HarmonIT project’s Open Modelling Interface and Environment (the OpenMI). The purpose of this project is to transform the OpenMI from a research output to a sustainable operational Standard. It will build the capacity to use the OpenMI and will demonstrate it under operational conditions. It will also develop, test and demonstrate the future support organisation for the OpenMI. Finally, information about the OpenMI will be disseminated to users

The seamless integration of Web3D technologies with university curricula to engage the changing student cohort

The increasing tendency of many university students to study at least some courses at a distance limits their opportunities for the interactions fundamental to learning. Online learning can assist but relies heavily on text, which is limiting for some students. The popularity of computer games, especially among the younger students, and the emergence of networked games and game-like virtual worlds offers opportunities for enhanced interaction in educational applications. For virtual worlds to be widely adopted in higher education it is desirable to have approaches to design and development that are responsive to needs and limited in their resource requirements. Ideally it should be possible for academics without technical expertise to adapt virtual worlds to support their teaching needs. This project identified Web3D, a technology that is based on the X3D standards and which presents 3D virtual worlds within common web browsers, as an approach worth exploring for educational application. The broad goals of the project were to produce exemplars of Web3D for educational use, together with development tools and associated resources to support non-technical academic adopters, and to promote an Australian community of practice to support broader adoption of Web3D in education. During the first year of the project exemplar applications were developed and tested. The Web3D technology was found to be still in a relatively early stage of development in which the application of standards did not ensure reliable operation in different environments. Moreover, ab initio development of virtual worlds and associated tools proved to be more demanding of resources than anticipated and was judged unlikely in the near future to result in systems that non-technical academics could use with confidence. In the second year the emphasis moved to assisting academics to plan and implement teaching in existing virtual worlds that provided relatively easy to use tools for customizing an environment. A project officer worked with participating academics to support the teaching of significant elements of courses within Second LifeTM. This approach was more successful in producing examples of good practice that could be shared with and emulated by other academics. Trials were also conducted with ExitRealityTM, a new Australian technology that presents virtual worlds in a web browser. Critical factors in the success of the project included providing secure access to networked computers with the necessary capability; negotiating the complexity of working across education, design of virtual worlds, and technical requirements; and supporting participants with professional development in the technology and appropriate pedagogy for the new environments. Major challenges encountered included working with experimental technologies that are evolving rapidly and deploying new networked applications on secure university networks. The project has prepared the way for future expansion in the use of virtual worlds for teaching at USQ and has contributed to the emergence of a national network of tertiary educators interested in the educational applications of virtual worlds

CGIAR Excellence in Breeding Platform - Plan of Work and Budget 2020

At the end of 2019, all CGIAR centers had submitted improvement plans based on an EiB template and in close collaboration with EiB staff while – in a parallel process with breeding programs, funders and private sector representatives – a vision for breeding program modernization was developed and presented to CGIAR breeding leadership at the EiB Annual Meeting. This vision represents an evolution of EiB in the context of the Crops to End Hunger Initiative (CtEH) beyond the initial scope of providing tools, services and expert advice, and serves as a guide for Center leadership to drive changes with EiB support. In addition, EiB has taken the role of managing and disbursing funding, made available by Funders via CtEH to modernize breeding and enable CGIAR breeding programs to implement the vision provided by EiB

Evaluating the development of wearable devices, personal data assistants and the use of other mobile devices in further and higher education institutions

This report presents technical evaluation and case studies of the use of wearable and mobile computing mobile devices in further and higher education. The first section provides technical evaluation of the current state of the art in wearable and mobile technologies and reviews several innovative wearable products that have been developed in recent years. The second section examines three scenarios for further and higher education where wearable and mobile devices are currently being used. The three scenarios include: (i) the delivery of lectures over mobile devices, (ii) the augmentation of the physical campus with a virtual and mobile component, and (iii) the use of PDAs and mobile devices in field studies. The first scenario explores the use of web lectures including an evaluation of IBM's Web Lecture Services and 3Com's learning assistant. The second scenario explores models for a campus without walls evaluating the Handsprings to Learning projects at East Carolina University and ActiveCampus at the University of California San Diego . The third scenario explores the use of wearable and mobile devices for field trips examining San Francisco Exploratorium's tool for capturing museum visits and the Cybertracker field computer. The third section of the report explores the uses and purposes for wearable and mobile devices in tertiary education, identifying key trends and issues to be considered when piloting the use of these devices in educational contexts

National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease

Knowledge Cartography for Open Sensemaking Communities

Knowledge Cartography is the discipline of visually mapping the conceptual structure of ideas, such as the connections between issues, concepts, answers, arguments and evidence. The cognitive process of externalising one's understanding clarifies one's own grasp of the situation, as well as communicating it to others as a network that invites their contributions. This sensemaking activity lies at the heart of the Open Educational Resources movement's objectives. The aim of this paper is to describe the usage patterns of Compendium, a knowledge mapping tool from the OpenLearn OER project, using quantitative data from interaction logs and qualitative data from knowledge maps, forums and blog postings. This work explains nine roles played by maps in OpenLearn, and discusses some of the benefits and adoption obstacles, which motivate our ongoing work

Lessons Learned from a Decade of Providing Interactive, On-Demand High Performance Computing to Scientists and Engineers

For decades, the use of HPC systems was limited to those in the physical sciences who had mastered their domain in conjunction with a deep understanding of HPC architectures and algorithms. During these same decades, consumer computing device advances produced tablets and smartphones that allow millions of children to interactively develop and share code projects across the globe. As the HPC community faces the challenges associated with guiding researchers from disciplines using high productivity interactive tools to effective use of HPC systems, it seems appropriate to revisit the assumptions surrounding the necessary skills required for access to large computational systems. For over a decade, MIT Lincoln Laboratory has been supporting interactive, on-demand high performance computing by seamlessly integrating familiar high productivity tools to provide users with an increased number of design turns, rapid prototyping capability, and faster time to insight. In this paper, we discuss the lessons learned while supporting interactive, on-demand high performance computing from the perspectives of the users and the team supporting the users and the system. Building on these lessons, we present an overview of current needs and the technical solutions we are building to lower the barrier to entry for new users from the humanities, social, and biological sciences.Comment: 15 pages, 3 figures, First Workshop on Interactive High Performance Computing (WIHPC) 2018 held in conjunction with ISC High Performance 2018 in Frankfurt, German