mLearning and Creative Practices: A Public Challenge?

ERIC Educational Resources Information Center

Antonczak, Laurent; Keegan, Helen; Cochrane, Thomas

2016-01-01

The ethos of open sharing of experiences and user generated content enabled by Mobile social media can be problematic in some cases (politics, gender, minorities), and it is not fully understood within the creative and academic sector. Creative people, students, and lecturers can misconceive the value and issues around open and public access to…

The Realities of "Reaching Out": Enacting the Public-Facing Open Scholar Role with Existing Online Communities

ERIC Educational Resources Information Center

Perryman, Leigh-Anne; Coughlan, Tony

2013-01-01

A core tenet of the open educational resources (OER) movement has long been that 'the world's knowledge is a public good' (Smith & Casserly, 2006, p.2) and should be available for everyone to use, reuse and share. However, this vision of openness and of the connection between OER and social justice, which McAndrew and Farrow…

Teaching physics mysteries versus pseudoscience

NASA Astrophysics Data System (ADS)

Kuttner, Fred

2007-04-01

The interpretation of quantum mechanics (and the encounter with consciousness) is contentious and has been called ``physics' skeleton in the closet.'' The reluctance of physicists to share this enigma with students and with the larger public has left the discussion open to the wild claims of purveyors of pseudoscience. The movie ``What the Bleep'' is a recent example. Bringing the enigma into the open is the best way to combat pseudoscience and share the true, deep mysteries that physics has uncovered. I will discuss my own experience and that of colleagues with ways of presenting this material to physics majors, non-majors, and the public.

Identifying diffusion patterns of research articles on Twitter: A case study of online engagement with open access articles.

PubMed

Alperin, Juan Pablo; Gomez, Charles J; Haustein, Stefanie

2018-03-01

The growing presence of research shared on social media, coupled with the increase in freely available research, invites us to ask whether scientific articles shared on platforms like Twitter diffuse beyond the academic community. We explore a new method for answering this question by identifying 11 articles from two open access biology journals that were shared on Twitter at least 50 times and by analyzing the follower network of users who tweeted each article. We find that diffusion patterns of scientific articles can take very different forms, even when the number of times they are tweeted is similar. Our small case study suggests that most articles are shared within single-connected communities with limited diffusion to the public. The proposed approach and indicators can serve those interested in the public understanding of science, science communication, or research evaluation to identify when research diffuses beyond insular communities.

Do open access data policies inhibit innovation?

USGS Publications Warehouse

Katzner, Todd E.

2015-01-01

There has been a great deal of attention paid recently to the idea of data sharing (Van Noorden 2014, Beardsley 2015, Nature Publishing Group2015, www.copdess.com). However, the vast majority of these arguments are in agreement and present as fait accompli the idea that data are a public good and that therefore, once published, they should become open access. In fact, although there are many good reasons for data sharing, there also are a number of cogent and coherent cases to be made against open-access policies (e.g., Fenichel and Skelly 2015). The goal of this piece is not to debate the relevance or accuracy of the points made in favor of data sharing but to elevate the discussion by pointing out key problems with open-access policies and to identify central issues that, if solved, will enhance the utility of data sharing to science and society.

Fulfilling Schmidt Ocean Institute's commitment to open sharing of information, data, and research outcomes: Successes and Lessons Learned from Proposal Evaluation to Public Repositories to Lasting Achievements

NASA Astrophysics Data System (ADS)

Miller, A.; Zykov, V.

2016-02-01

Schmidt Ocean Institute's vision is that the world's ocean be understood through technological advancement, intelligent observation, and open sharing of information. As such, making data collected aboard R/V Falkor available to the general public is a key pillar of the organization and a major strategic focus. Schmidt Ocean Institute supports open sharing of information about the ocean to stimulate the growth of its applications and user community, and amplify further exploration, discovery, and deeper understanding of our environment. These efforts are supported through partnerships with data management experts in the oceanographic community to enable standards-compliant sharing of scientific information and data collected during research cruises. To properly fulfill the commitment, proponents' data management plans are evaluated as part of the proposal process when applying for ship time. We request a thorough data management plan be submitted and expert reviewers evaluate the proposal's plan as part of the review process. Once a project is successfully selected, the chief scientist signs an agreement stating delivery dates for post-cruise data deliverables in a timely manner, R/V Falkor underway and meterological data is shared via public repositories, and links and reports are posted on the cruise webpage. This allows many more creative minds and thinkers to analyze, process, and study the data collected in the world ocean rather than privileging one scientist with the proprietary information, driving international and national scientific progress. This presentation will include the Institute's mission, vision, and strategy for sharing data, based on our Founders' passions, the process for evaluating proposed data management plans, and our partnering efforts to make data publically available in fulfillment of our commitment. Recent achievements and successes in data sharing, as well as future plans to improve our efforts will also be discussed.

When Two Worlds Don't Collide: Can Social Curation Address the Marginalisation of Open Educational Practices and Resources from Outside Academia?

ERIC Educational Resources Information Center

Perryman, Leigh-Anne; Coughlan, Tony

2014-01-01

A canyonesque gulf has long existed between open academia and many external subject communities. Since 2011, we have been developing and piloting the public open scholar role (Coughlan and Perryman 2012)--involving open academics discovering, sharing and discussing open educational resources (OER) with online communities outside formal education…

Open NASA Earth Exchange (OpenNEX): A Public-Private Partnership for Climate Change Research

NASA Astrophysics Data System (ADS)

Nemani, R. R.; Lee, T. J.; Michaelis, A.; Ganguly, S.; Votava, P.

2014-12-01

NASA Earth Exchange (NEX) is a data, computing and knowledge collaborative that houses satellite, climate and ancillary data where a community of researchers can come together to share modeling and analysis codes, scientific results, knowledge and expertise on a centralized platform with access to large supercomputing resources. As a part of broadening the community beyond NASA-funded researchers, NASA through an agreement with Amazon Inc. made available to the public a large collection of Climate and Earth Sciences satellite data. The data, available through the Open NASA Earth Exchange (OpenNEX) platform hosted by Amazon Web Services (AWS) public cloud, consists of large amounts of global land surface imaging, vegetation conditions, climate observations and climate projections. In addition to the data, users of OpenNEX platform can also watch lectures from leading experts, learn basic access and use of the available data sets. In order to advance White House initiatives such as Open Data, Big Data and Climate Data and the Climate Action Plan, NASA over the past six months conducted the OpenNEX Challenge. The two-part challenge was designed to engage the public in creating innovative ways to use NASA data and address climate change impacts on economic growth, health and livelihood. Our intention was that the challenges allow citizen scientists to realize the value of NASA data assets and offers NASA new ideas on how to share and use that data. The first "ideation" challenge, closed on July 31st attracted over 450 participants consisting of climate scientists, hobbyists, citizen scientists, IT experts and App developers. Winning ideas from the first challenge will be incorporated into the second "builder" challenge currently targeted to launch mid-August and close by mid-November. The winner(s) will be formally announced at AGU in December of 2014. We will share our experiences and lessons learned over the past year from OpenNEX, a public-private partnership for engaging and enabling a large community of citizen scientists to better understand global climate changes and in creating climate resilience.

YouTube Professors Scholars as Online Video Stars

ERIC Educational Resources Information Center

Young, Jeffrey R.

2008-01-01

This article takes a look at how professors are becoming the latest YouTube stars. The popularity of their appearances on YouTube and other video-sharing sites end up opening the classroom and making teaching--which once took place behind closed doors--a more public art. Web videos open a new form of public intellectualism to scholars looking to…

UNED OER Experience: From OCW to Open UNED

ERIC Educational Resources Information Center

Ros, Salvador; Hernández, Roberto; Read, Timothy; Artacho, Miguel Rodriguez; Pastor, Rafael; Orueta, Gabriel Diaz

2014-01-01

Much has happened with open software, there has been a global attitude shift in the education community toward the open sharing of educational courses and resources. As the largest public distance education university in Spain, Universidad Nacional de Educacio´n a Distancia (UNED) has had a clear commitment to open learning and content since its…

Making open data work for plant scientists.

PubMed

Leonelli, Sabina; Smirnoff, Nicholas; Moore, Jonathan; Cook, Charis; Bastow, Ruth

2013-11-01

Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers' needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity.

Learning from Each Other

ERIC Educational Resources Information Center

Phillips, Vicki L.

2011-01-01

The idea behind public charter schools was to develop flexible models of public schools and to incubate innovative ideas that then could be shared with the district's public schools. Today, almost 20 years since the first public charter school opened its doors in Minnesota, one still does not see consistent, productive collaboration and shared…

Through the glass ceiling - and back again: the experiences of two of the first non-medical directors of public health in England.

PubMed

Evans, David; Adams, Lee

2007-06-01

In 2001, the English Department of Health announced a radical re-organisation of the NHS under the banner of 'shifting the balance of power'. As part of this re-organisation health authorities were abolished and the main NHS public health responsibilities devolved to the new primary care trusts (PCTs) from April 2002. Following several years of campaigning by the Multidisciplinary Public Health Forum (MPHF), in November 2001 the Acting Minister for Public Health, Lord Hunt, announced that PCT director of public health (DPH) posts would be open to 'suitably qualified' candidates from any discipline. From April 2002 a number of new DsPH from backgrounds other than medicine were appointed. This paper reports on the experiences of two such DsPH who shared a commitment to multidisciplinary public health, but who did not wholly share the objectives of the MPHF. We place the opening of PCT DPH posts in the context of tensions within NHS public health between a focus on health services versus the wider determinants of health, and the development of multidisciplinary public health. The paper reflects on both the degree of change this opening represented and the limitations and tensions such appointments exposed.

Cyberinfrastructure for Open Science at the Montreal Neurological Institute

PubMed Central

Das, Samir; Glatard, Tristan; Rogers, Christine; Saigle, John; Paiva, Santiago; MacIntyre, Leigh; Safi-Harab, Mouna; Rousseau, Marc-Etienne; Stirling, Jordan; Khalili-Mahani, Najmeh; MacFarlane, David; Kostopoulos, Penelope; Rioux, Pierre; Madjar, Cecile; Lecours-Boucher, Xavier; Vanamala, Sandeep; Adalat, Reza; Mohaddes, Zia; Fonov, Vladimir S.; Milot, Sylvain; Leppert, Ilana; Degroot, Clotilde; Durcan, Thomas M.; Campbell, Tara; Moreau, Jeremy; Dagher, Alain; Collins, D. Louis; Karamchandani, Jason; Bar-Or, Amit; Fon, Edward A.; Hoge, Rick; Baillet, Sylvain; Rouleau, Guy; Evans, Alan C.

2017-01-01

Data sharing is becoming more of a requirement as technologies mature and as global research and communications diversify. As a result, researchers are looking for practical solutions, not only to enhance scientific collaborations, but also to acquire larger amounts of data, and to access specialized datasets. In many cases, the realities of data acquisition present a significant burden, therefore gaining access to public datasets allows for more robust analyses and broadly enriched data exploration. To answer this demand, the Montreal Neurological Institute has announced its commitment to Open Science, harnessing the power of making both clinical and research data available to the world (Owens, 2016a,b). As such, the LORIS and CBRAIN (Das et al., 2016) platforms have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing, including: Comprehensive linking of multimodal data (phenotypic, clinical, neuroimaging, biobanking, and genomics, etc.)Secure database encryption, specifically designed for institutional and multi-project data sharing, ensuring subject confidentiality (using multi-tiered identifiers).Querying capabilities with multiple levels of single study and institutional permissions, allowing public data sharing for all consented and de-identified subject data.Configurable pipelines and flags to facilitate acquisition and analysis, as well as access to High Performance Computing clusters for rapid data processing and sharing of software tools.Robust Workflows and Quality Control mechanisms ensuring transparency and consistency in best practices.Long term storage (and web access) of data, reducing loss of institutional data assets.Enhanced web-based visualization of imaging, genomic, and phenotypic data, allowing for real-time viewing and manipulation of data from anywhere in the world.Numerous modules for data filtering, summary statistics, and personalized and configurable dashboards. Implementing the vision of Open Science at the Montreal Neurological Institute will be a concerted undertaking that seeks to facilitate data sharing for the global research community. Our goal is to utilize the years of experience in multi-site collaborative research infrastructure to implement the technical requirements to achieve this level of public data sharing in a practical yet robust manner, in support of accelerating scientific discovery. PMID:28111547

Cyberinfrastructure for Open Science at the Montreal Neurological Institute.

PubMed

Das, Samir; Glatard, Tristan; Rogers, Christine; Saigle, John; Paiva, Santiago; MacIntyre, Leigh; Safi-Harab, Mouna; Rousseau, Marc-Etienne; Stirling, Jordan; Khalili-Mahani, Najmeh; MacFarlane, David; Kostopoulos, Penelope; Rioux, Pierre; Madjar, Cecile; Lecours-Boucher, Xavier; Vanamala, Sandeep; Adalat, Reza; Mohaddes, Zia; Fonov, Vladimir S; Milot, Sylvain; Leppert, Ilana; Degroot, Clotilde; Durcan, Thomas M; Campbell, Tara; Moreau, Jeremy; Dagher, Alain; Collins, D Louis; Karamchandani, Jason; Bar-Or, Amit; Fon, Edward A; Hoge, Rick; Baillet, Sylvain; Rouleau, Guy; Evans, Alan C

2016-01-01

Data sharing is becoming more of a requirement as technologies mature and as global research and communications diversify. As a result, researchers are looking for practical solutions, not only to enhance scientific collaborations, but also to acquire larger amounts of data, and to access specialized datasets. In many cases, the realities of data acquisition present a significant burden, therefore gaining access to public datasets allows for more robust analyses and broadly enriched data exploration. To answer this demand, the Montreal Neurological Institute has announced its commitment to Open Science, harnessing the power of making both clinical and research data available to the world (Owens, 2016a,b). As such, the LORIS and CBRAIN (Das et al., 2016) platforms have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing, including: Comprehensive linking of multimodal data (phenotypic, clinical, neuroimaging, biobanking, and genomics, etc.)Secure database encryption, specifically designed for institutional and multi-project data sharing, ensuring subject confidentiality (using multi-tiered identifiers).Querying capabilities with multiple levels of single study and institutional permissions, allowing public data sharing for all consented and de-identified subject data.Configurable pipelines and flags to facilitate acquisition and analysis, as well as access to High Performance Computing clusters for rapid data processing and sharing of software tools.Robust Workflows and Quality Control mechanisms ensuring transparency and consistency in best practices.Long term storage (and web access) of data, reducing loss of institutional data assets.Enhanced web-based visualization of imaging, genomic, and phenotypic data, allowing for real-time viewing and manipulation of data from anywhere in the world.Numerous modules for data filtering, summary statistics, and personalized and configurable dashboards. Implementing the vision of Open Science at the Montreal Neurological Institute will be a concerted undertaking that seeks to facilitate data sharing for the global research community. Our goal is to utilize the years of experience in multi-site collaborative research infrastructure to implement the technical requirements to achieve this level of public data sharing in a practical yet robust manner, in support of accelerating scientific discovery.

Open sharing of genomic data: Who does it and why?

PubMed

Haeusermann, Tobias; Greshake, Bastian; Blasimme, Alessandro; Irdam, Darja; Richards, Martin; Vayena, Effy

2017-01-01

We explored the characteristics and motivations of people who, having obtained their genetic or genomic data from Direct-To-Consumer genetic testing (DTC-GT) companies, voluntarily decide to share them on the publicly accessible web platform openSNP. The study is the first attempt to describe open data sharing activities undertaken by individuals without institutional oversight. In the paper we provide a detailed overview of the distribution of the demographic characteristics and motivations of people engaged in genetic or genomic open data sharing. The geographical distribution of the respondents showed the USA as dominant. There was no significant gender divide, the age distribution was broad, educational background varied and respondents with and without children were equally represented. Health, even though prominent, was not the respondents' primary or only motivation to be tested. As to their motivations to openly share their data, 86.05% indicated wanting to learn about themselves as relevant, followed by contributing to the advancement of medical research (80.30%), improving the predictability of genetic testing (76.02%) and considering it fun to explore genotype and phenotype data (75.51%). Whereas most respondents were well aware of the privacy risks of their involvement in open genetic data sharing and considered the possibility of direct, personal repercussions troubling, they estimated the risk of this happening to be negligible. Our findings highlight the diversity of DTC-GT consumers who decide to openly share their data. Instead of focusing exclusively on health-related aspects of genetic testing and data sharing, our study emphasizes the importance of taking into account benefits and risks that stretch beyond the health spectrum. Our results thus lend further support to the call for a broader and multi-faceted conceptualization of genomic utility.

Open innovation: Towards sharing of data, models and workflows.

PubMed

Conrado, Daniela J; Karlsson, Mats O; Romero, Klaus; Sarr, Céline; Wilkins, Justin J

2017-11-15

Sharing of resources across organisations to support open innovation is an old idea, but which is being taken up by the scientific community at increasing speed, concerning public sharing in particular. The ability to address new questions or provide more precise answers to old questions through merged information is among the attractive features of sharing. Increased efficiency through reuse, and increased reliability of scientific findings through enhanced transparency, are expected outcomes from sharing. In the field of pharmacometrics, efforts to publicly share data, models and workflow have recently started. Sharing of individual-level longitudinal data for modelling requires solving legal, ethical and proprietary issues similar to many other fields, but there are also pharmacometric-specific aspects regarding data formats, exchange standards, and database properties. Several organisations (CDISC, C-Path, IMI, ISoP) are working to solve these issues and propose standards. There are also a number of initiatives aimed at collecting disease-specific databases - Alzheimer's Disease (ADNI, CAMD), malaria (WWARN), oncology (PDS), Parkinson's Disease (PPMI), tuberculosis (CPTR, TB-PACTS, ReSeqTB) - suitable for drug-disease modelling. Organized sharing of pharmacometric executable model code and associated information has in the past been sparse, but a model repository (DDMoRe Model Repository) intended for the purpose has recently been launched. In addition several other services can facilitate model sharing more generally. Pharmacometric workflows have matured over the last decades and initiatives to more fully capture those applied to analyses are ongoing. In order to maximize both the impact of pharmacometrics and the knowledge extracted from clinical data, the scientific community needs to take ownership of and create opportunities for open innovation. Copyright © 2017 Elsevier B.V. All rights reserved.

IMPACT Observatory: tracking the evolution of clinical trial data sharing and research integrity.

PubMed

Krleža-Jerić, Karmela; Gabelica, Mirko; Banzi, Rita; Martinić, Marina Krnić; Pulido, Bibiana; Mahmić-Kaknjo, Mersiha; Reveiz, Ludovic; Šimić, Josip; Utrobičić, Ana; Hrgović, Irena

2016-10-15

The opening of research data is emerging thanks to the increasing possibilities of digital technology. The opening of clinical trial (CT) data is a part of this process, expected to have positive scientific, ethical, health, and economic impacts thus contributing to research integrity. The January 2016 proposal by the International Council of Medical Journal Editors triggered ample discussion about CT data sharing and reconfirmed the need for an ongoing assessment of its dynamics. The IMProving Access to Clinical Trials data (IMPACT) Observatory aims to play such a role, and assess the data sharing culture, policies, and practices of key players, the impact of their interventions on CTs, and contribute to a transformation of research. The objective of this paper is to present the IMPACT Observatory as well as share some of its preliminary findings. Methods include a scoping study of research, surveys, interviews, and an environmental scan of research data repositories. Our preliminary findings indicate that although opening of CT data has not yet been achieved, its evolution is encouraging. Initiatives by key players contribute to increasing of CT data sharing, and many barriers are shrinking or disappearing. The major barrier is the lack of data sharing standards, from preparing data for public sharing to its curatorship, findability and access. However, experiences accumulated by sharing CT data according to "upon request" or "open" mechanisms could inform the development of such standards. The Vivli, CORBEL-ECRIN and Open Trials projects are currently working in this direction.

Open Science and eGEMs: Our Role in Supporting a Culture of Collaboration in Learning Health Systems.

PubMed

Holve, Erin

2016-01-01

"Open science" includes a variety of approaches to facilitate greater access to data and the information produced by processes of scientific inquiry. Recently, the health sciences community has been grappling with the issue of potential pathways and models to achieve the goals of open science-namely, to create and rapidly share reproducible health research. eGEMs' continued dedication to and milestones regarding the publication of innovative, useful, and timely research to help contribute to the push towards open science is discussed, as well as the EDM Forum's new data sharing platform, CIELO. Although strides have been made, there is still more work to be done to help health sciences community truly embrace open science.

Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance

NASA Astrophysics Data System (ADS)

Gil, Yolanda; David, Cédric H.; Demir, Ibrahim; Essawy, Bakinam T.; Fulweiler, Robinson W.; Goodall, Jonathan L.; Karlstrom, Leif; Lee, Huikyo; Mills, Heath J.; Oh, Ji-Hyun; Pierce, Suzanne A.; Pope, Allen; Tzeng, Mimi W.; Villamizar, Sandra R.; Yu, Xuan

2016-10-01

Geoscientists now live in a world rich with digital data and methods, and their computational research cannot be fully captured in traditional publications. The Geoscience Paper of the Future (GPF) presents an approach to fully document, share, and cite all their research products including data, software, and computational provenance. This article proposes best practices for GPF authors to make data, software, and methods openly accessible, citable, and well documented. The publication of digital objects empowers scientists to manage their research products as valuable scientific assets in an open and transparent way that enables broader access by other scientists, students, decision makers, and the public. Improving documentation and dissemination of research will accelerate the pace of scientific discovery by improving the ability of others to build upon published work.

Uptake of OER by Staff in Distance Education in South Africa

ERIC Educational Resources Information Center

de Hart, Kerry; Chetty, Yuraisha; Archer, Elizabeth

2015-01-01

Open Educational Resources (OER) emerged within the context of open education which is typically characterized by the sharing of knowledge and resources and the exchange of ideas. Unisa as a mega open distance learning (ODL) university has publicly communicated its intention to take part in the use and creation of OER. As global and local…

Publishing in open access era: focus on respiratory journals

PubMed Central

Xu, Dingyao; Zhong, Xiyao; Li, Li; Ling, Qibo; Bu, Zhaode

2014-01-01

We have entered an open access publishing era. The impact and significance of open access is still under debate after two decades of evolution. Open access journals benefit researchers and the general public by promoting visibility, sharing and communicating. Non-mainstream journals should turn the challenge of open access into opportunity of presenting best research articles to the global readership. Open access journals need to optimize their business models to promote the healthy and continuous development. PMID:24822120

Publishing in open access era: focus on respiratory journals.

PubMed

Dai, Ni; Xu, Dingyao; Zhong, Xiyao; Li, Li; Ling, Qibo; Bu, Zhaode

2014-05-01

We have entered an open access publishing era. The impact and significance of open access is still under debate after two decades of evolution. Open access journals benefit researchers and the general public by promoting visibility, sharing and communicating. Non-mainstream journals should turn the challenge of open access into opportunity of presenting best research articles to the global readership. Open access journals need to optimize their business models to promote the healthy and continuous development.

Solutions for research data from a publisher's perspective

NASA Astrophysics Data System (ADS)

Cotroneo, P.

2015-12-01

Sharing research data has the potential to make research more efficient and reproducible. Elsevier has developed several initiatives to address the different needs of research data users. These include PANGEA Linked data, which provides geo-referenced, citable datasets from earth and life sciences, archived as supplementary data from publications by the PANGEA data repository; Mendeley Data, which allows users to freely upload and share their data; a database linking program that creates links between articles on ScienceDirect and datasets held in external data repositories such as EarthRef and EarthChem; a pilot for searching for research data through a map interface; an open data pilot that allows authors publishing in Elsevier journals to store and share research data and make this publicly available as a supplementary file alongside their article; and data journals, including Data in Brief, which allow researchers to share their data open access. Through these initiatives, researchers are not only encouraged to share their research data, but also supported in optimizing their research data management. By making data more readily citable and visible, and hence generating citations for authors, these initiatives also aim to ensure that researchers get the recognition they deserve for publishing their data.

Open source system OpenVPN in a function of Virtual Private Network

NASA Astrophysics Data System (ADS)

Skendzic, A.; Kovacic, B.

2017-05-01

Using of Virtual Private Networks (VPN) can establish high security level in network communication. VPN technology enables high security networking using distributed or public network infrastructure. VPN uses different security and managing rules inside networks. It can be set up using different communication channels like Internet or separate ISP communication infrastructure. VPN private network makes security communication channel over public network between two endpoints (computers). OpenVPN is an open source software product under GNU General Public License (GPL) that can be used to establish VPN communication between two computers inside business local network over public communication infrastructure. It uses special security protocols and 256-bit Encryption and it is capable of traversing network address translators (NATs) and firewalls. It allows computers to authenticate each other using a pre-shared secret key, certificates or username and password. This work gives review of VPN technology with a special accent on OpenVPN. This paper will also give comparison and financial benefits of using open source VPN software in business environment.

UK publicly funded Clinical Trials Units supported a controlled access approach to share individual participant data but highlighted concerns

PubMed Central

Hopkins, Carolyn; Sydes, Matthew; Murray, Gordon; Woolfall, Kerry; Clarke, Mike; Williamson, Paula; Tudur Smith, Catrin

2016-01-01

Objectives Evaluate current data sharing activities of UK publicly funded Clinical Trial Units (CTUs) and identify good practices and barriers. Study Design and Setting Web-based survey of Directors of 45 UK Clinical Research Collaboration (UKCRC)–registered CTUs. Results Twenty-three (51%) CTUs responded: Five (22%) of these had an established data sharing policy and eight (35%) specifically requested consent to use patient data beyond the scope of the original trial. Fifteen (65%) CTUs had received requests for data, and seven (30%) had made external requests for data in the previous 12 months. CTUs supported the need for increased data sharing activities although concerns were raised about patient identification, misuse of data, and financial burden. Custodianship of clinical trial data and requirements for a CTU to align its policy to their parent institutes were also raised. No CTUs supported the use of an open access model for data sharing. Conclusion There is support within the publicly funded UKCRC-registered CTUs for data sharing, but many perceived barriers remain. CTUs are currently using a variety of approaches and procedures for sharing data. This survey has informed further work, including development of guidance for publicly funded CTUs, to promote good practice and facilitate data sharing. PMID:26169841

Public attitudes about radioactive waste

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bisconti, A.S.

Public attitudes about radioactive waste are changeable. That is my conclusion from eight years of social science research which I have directed on this topic. The fact that public attitudes about radioactive waste are changeable is well-known to the hands-on practitioners who have opportunities to talk with the public and respond to their concerns-practitioners like Ginger King, who is sharing the podium with me today. The public`s changeability and open-mindedness are frequently overlooked in studies that focus narrowly on fear and dread. Such studies give the impression that the outlook for waste disposal solutions is dismal. I believe that impressionmore » is misleading, and I`d like to share research findings with you today that give a broader perspective.« less

Massive Open Online Grants (MOOG's): Connecting hundreds of thousands with ocean science by allowing the public to vote on research grants

NASA Astrophysics Data System (ADS)

McNeil, B.

2016-02-01

We know that universities who host Massive Open Online Courses (MOOC's) are driving deep global engagement by allowing the public to enrol in open and free quality course online. At thinkable.org, we have pioneered the development of 'Massive Open Online Grants or MOOG's, which allow research organizations & societies to host open grants, prizes & contests that allows the public to vote, connect & engage with high quality research for the first time. In order to reach a wide audience, researchers create short video summaries of their work that allows anyone to learn, vote, share and connect with research important to them. We have found this to help both research organizations and researchers reach a wide audience to demonstrate public impact & innovation, drive collaborative partnerships and raise public funding for their research. In this talk, I will outline our experience in developing MOOG's and the immense future opportunities to revolutionize how high-quality research engages with society by using technology to empower deep connections between ocean researchers & the wider public.

USDA Branded Food Products Database, Release 2

USDA-ARS?s Scientific Manuscript database

The USDA Branded Food Products Database is the ongoing result of a Public-Private Partnership (PPP), whose goal is to enhance public health and the sharing of open data by complementing the USDA National Nutrient Database for Standard Reference (SR) with nutrient composition of branded foods and pri...

Retrieval of publications addressing shared decision making: an evaluation of full-text searches on medical journal websites.

PubMed

Blanc, Xavier; Collet, Tinh-Hai; Auer, Reto; Iriarte, Pablo; Krause, Jan; Légaré, France; Cornuz, Jacques; Clair, Carole

2015-04-07

Full-text searches of articles increase the recall, defined by the proportion of relevant publications that are retrieved. However, this method is rarely used in medical research due to resource constraints. For the purpose of a systematic review of publications addressing shared decision making, a full-text search method was required to retrieve publications where shared decision making does not appear in the title or abstract. The objective of our study was to assess the efficiency and reliability of full-text searches in major medical journals for identifying shared decision making publications. A full-text search was performed on the websites of 15 high-impact journals in general internal medicine to look up publications of any type from 1996-2011 containing the phrase "shared decision making". The search method was compared with a PubMed search of titles and abstracts only. The full-text search was further validated by requesting all publications from the same time period from the individual journal publishers and searching through the collected dataset. The full-text search for "shared decision making" on journal websites identified 1286 publications in 15 journals compared to 119 through the PubMed search. The search within the publisher-provided publications of 6 journals identified 613 publications compared to 646 with the full-text search on the respective journal websites. The concordance rate was 94.3% between both full-text searches. Full-text searching on medical journal websites is an efficient and reliable way to identify relevant articles in the field of shared decision making for review or other purposes. It may be more widely used in biomedical research in other fields in the future, with the collaboration of publishers and journals toward open-access data.

Supporting open access to clinical trial data for researchers: The Duke Clinical Research Institute-Bristol-Myers Squibb Supporting Open Access to Researchers Initiative.

PubMed

Pencina, Michael J; Louzao, Darcy M; McCourt, Brian J; Adams, Monique R; Tayyabkhan, Rehbar H; Ronco, Peter; Peterson, Eric D

2016-02-01

There are growing calls for sponsors to increase transparency by providing access to clinical trial data. In response, Bristol-Myers Squibb and the Duke Clinical Research Institute have collaborated on a new initiative, Supporting Open Access to Researchers. The aim is to facilitate open sharing of Bristol-Myers Squibb trial data with interested researchers. Key features of the Supporting Open Access to Researchers data sharing model include an independent review committee that ensures expert consideration of each proposal, stringent data deidentification/anonymization and protection of patient privacy, requirement of prespecified statistical analysis plans, and independent review of manuscripts before submission for publication. We believe that these approaches will promote open science by allowing investigators to verify trial results as well as to pursue interesting secondary uses of trial data without compromising scientific integrity. Copyright © 2015 Elsevier Inc. All rights reserved.

Archiving Primary Data: Solutions for Long-Term Studies.

PubMed

Mills, James A; Teplitsky, Céline; Arroyo, Beatriz; Charmantier, Anne; Becker, Peter H; Birkhead, Tim R; Bize, Pierre; Blumstein, Daniel T; Bonenfant, Christophe; Boutin, Stan; Bushuev, Andrey; Cam, Emmanuelle; Cockburn, Andrew; Côté, Steeve D; Coulson, John C; Daunt, Francis; Dingemanse, Niels J; Doligez, Blandine; Drummond, Hugh; Espie, Richard H M; Festa-Bianchet, Marco; Frentiu, Francesca; Fitzpatrick, John W; Furness, Robert W; Garant, Dany; Gauthier, Gilles; Grant, Peter R; Griesser, Michael; Gustafsson, Lars; Hansson, Bengt; Harris, Michael P; Jiguet, Frédéric; Kjellander, Petter; Korpimäki, Erkki; Krebs, Charles J; Lens, Luc; Linnell, John D C; Low, Matthew; McAdam, Andrew; Margalida, Antoni; Merilä, Juha; Møller, Anders P; Nakagawa, Shinichi; Nilsson, Jan-Åke; Nisbet, Ian C T; van Noordwijk, Arie J; Oro, Daniel; Pärt, Tomas; Pelletier, Fanie; Potti, Jaime; Pujol, Benoit; Réale, Denis; Rockwell, Robert F; Ropert-Coudert, Yan; Roulin, Alexandre; Sedinger, James S; Swenson, Jon E; Thébaud, Christophe; Visser, Marcel E; Wanless, Sarah; Westneat, David F; Wilson, Alastair J; Zedrosser, Andreas

2015-10-01

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fostering EMA's transparency policy.

PubMed

Banzi, Rita; Bertele', Vittorio; Demotes-Mainard, Jacques; Garattini, Silvio; Gluud, Christian; Kubiak, Christine; Ohmann, Christian

2014-10-01

The European Medicines Agency has opened a window to access clinical trial data. This is an important step forward which deserves attention, support, and advice from all the stakeholders. Regulatory agencies are the most comprehensive repositories of clinical trial data on drugs and can also promote and develop standard practices for data sharing. The release of the EMA draft policy on publication and access to clinical trial data in 2013 has fueled a lively debate among academia, industry, and the public in general that is still ongoing. As clinical researchers and producers and users of clinical trial data, we endorse the European Medicines Agency's opening and offer a few suggestions for complete, safe, and effective data sharing. Copyright © 2014 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

Supporting Creativity in School Libraries: Finding, Sharing, and Connecting

ERIC Educational Resources Information Center

Techman, Melissa

2014-01-01

Creativity is about openness and connection, it signals the chance to get ideas, share ideas, and try new things or put together old things in new ways. Libraries have always had the potential to source and support creative activities. Public library events and opportunities bring together people, ideas, and stuff (whether fabric, paint, wood,…

Publish (Your Data) or (Let the Data) Perish! Why Not Publish Your Data Too?

ERIC Educational Resources Information Center

Wicherts, Jelte M.; Bakker, Marjan

2012-01-01

The authors argue that upon publication of a paper, the data should be made available through online archives or repositories. Reasons for not sharing data are discussed and contrasted with advantages of sharing, which include abiding by the scientific principle of openness, keeping the data for posterity, increasing one's impact, facilitation of…

77 FR 48157 - Office of the National Coordinator for Health Information Technology; Announcement of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-13

... on YouTube.com or Vimeo.com (the Video should be no longer than 2 minutes); A text description of... open call for the public to create short, inspiring videos sharing how you use technology to manage... Challenge invites you to create short, inspiring videos sharing how you use technology to manage your...

Publishing and sharing of hydrologic models through WaterHUB

NASA Astrophysics Data System (ADS)

Merwade, V.; Ruddell, B. L.; Song, C.; Zhao, L.; Kim, J.; Assi, A.

2011-12-01

Most hydrologists use hydrologic models to simulate the hydrologic processes to understand hydrologic pathways and fluxes for research, decision making and engineering design. Once these tasks are complete including publication of results, the models generally are not published or made available to the public for further use and improvement. Although publication or sharing of models is not required for journal publications, sharing of models may open doors for new collaborations, and avoids duplication of efforts if other researchers are interested in simulating a particular watershed for which a model already exists. For researchers, who are interested in sharing models, there are limited avenues to publishing their models to the wider community. Towards filling this gap, a prototype cyberinfrastructure (CI), called WaterHUB, is developed for sharing hydrologic data and modeling tools in an interactive environment. To test the utility of WaterHUB for sharing hydrologic models, a system to publish and share SWAT (Soil Water Assessment Tool) is developed. Users can utilize WaterHUB to search and download existing SWAT models, and also upload new SWAT models. Metadata such as the name of the watershed, name of the person or agency who developed the model, simulation period, time step, and list of calibrated parameters also published with individual model.

IMPACT Observatory: tracking the evolution of clinical trial data sharing and research integrity

PubMed Central

Krleža-Jerić, Karmela; Gabelica, Mirko; Banzi, Rita; Martinić, Marina Krnić; Pulido, Bibiana; Mahmić-Kaknjo, Mersiha; Reveiz, Ludovic; Šimić, Josip; Utrobičić, Ana; Hrgović, Irena

2016-01-01

Introduction The opening of research data is emerging thanks to the increasing possibilities of digital technology. The opening of clinical trial (CT) data is a part of this process, expected to have positive scientific, ethical, health, and economic impacts thus contributing to research integrity. The January 2016 proposal by the International Council of Medical Journal Editors triggered ample discussion about CT data sharing and reconfirmed the need for an ongoing assessment of its dynamics. The IMProving Access to Clinical Trials data (IMPACT) Observatory aims to play such a role, and assess the data sharing culture, policies, and practices of key players, the impact of their interventions on CTs, and contribute to a transformation of research. The objective of this paper is to present the IMPACT Observatory as well as share some of its preliminary findings. Materials and methods Methods include a scoping study of research, surveys, interviews, and an environmental scan of research data repositories. Results Our preliminary findings indicate that although opening of CT data has not yet been achieved, its evolution is encouraging. Initiatives by key players contribute to increasing of CT data sharing, and many barriers are shrinking or disappearing. Conclusions The major barrier is the lack of data sharing standards, from preparing data for public sharing to its curatorship, findability and access. However, experiences accumulated by sharing CT data according to “upon request” or “open” mechanisms could inform the development of such standards. The Vivli, CORBEL-ECRIN and Open Trials projects are currently working in this direction. PMID:27812300

Crowdsourcing Content to Promote Community and Collection Development in Public Libraries

ERIC Educational Resources Information Center

Carr, Melissa Eleftherion

2013-01-01

With the Poetry Center at San Francisco State University, the author has begun to build an open-access digital repository for poetry chapbooks. The repository is essentially a chapbook exchange: a place for poets to share their current works. Users are invited to share their chapbooks via upload and as such gain access to the chapbook repository.…

Experimental Directory Structure (Exdir): An Alternative to HDF5 Without Introducing a New File Format

PubMed Central

Dragly, Svenn-Arne; Hobbi Mobarhan, Milad; Lepperød, Mikkel E.; Tennøe, Simen; Fyhn, Marianne; Hafting, Torkel; Malthe-Sørenssen, Anders

2018-01-01

Natural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available specifications which facilitate data sharing and reproducible research. Hierarchical Data Format 5 (HDF5) is a popular open format widely used in neuroscience, often as a foundation for other, more specialized formats. However, drawbacks related to HDF5's complex specification have initiated a discussion for an improved replacement. We propose a novel alternative, the Experimental Directory Structure (Exdir), an open specification for data storage in experimental pipelines which amends drawbacks associated with HDF5 while retaining its advantages. HDF5 stores data and metadata in a hierarchy within a complex binary file which, among other things, is not human-readable, not optimal for version control systems, and lacks support for easy access to raw data from external applications. Exdir, on the other hand, uses file system directories to represent the hierarchy, with metadata stored in human-readable YAML files, datasets stored in binary NumPy files, and raw data stored directly in subdirectories. Furthermore, storing data in multiple files makes it easier to track for version control systems. Exdir is not a file format in itself, but a specification for organizing files in a directory structure. Exdir uses the same abstractions as HDF5 and is compatible with the HDF5 Abstract Data Model. Several research groups are already using data stored in a directory hierarchy as an alternative to HDF5, but no common standard exists. This complicates and limits the opportunity for data sharing and development of common tools for reading, writing, and analyzing data. Exdir facilitates improved data storage, data sharing, reproducible research, and novel insight from interdisciplinary collaboration. With the publication of Exdir, we invite the scientific community to join the development to create an open specification that will serve as many needs as possible and as a foundation for open access to and exchange of data. PMID:29706879

Experimental Directory Structure (Exdir): An Alternative to HDF5 Without Introducing a New File Format.

PubMed

Dragly, Svenn-Arne; Hobbi Mobarhan, Milad; Lepperød, Mikkel E; Tennøe, Simen; Fyhn, Marianne; Hafting, Torkel; Malthe-Sørenssen, Anders

2018-01-01

Natural sciences generate an increasing amount of data in a wide range of formats developed by different research groups and commercial companies. At the same time there is a growing desire to share data along with publications in order to enable reproducible research. Open formats have publicly available specifications which facilitate data sharing and reproducible research. Hierarchical Data Format 5 (HDF5) is a popular open format widely used in neuroscience, often as a foundation for other, more specialized formats. However, drawbacks related to HDF5's complex specification have initiated a discussion for an improved replacement. We propose a novel alternative, the Experimental Directory Structure (Exdir), an open specification for data storage in experimental pipelines which amends drawbacks associated with HDF5 while retaining its advantages. HDF5 stores data and metadata in a hierarchy within a complex binary file which, among other things, is not human-readable, not optimal for version control systems, and lacks support for easy access to raw data from external applications. Exdir, on the other hand, uses file system directories to represent the hierarchy, with metadata stored in human-readable YAML files, datasets stored in binary NumPy files, and raw data stored directly in subdirectories. Furthermore, storing data in multiple files makes it easier to track for version control systems. Exdir is not a file format in itself, but a specification for organizing files in a directory structure. Exdir uses the same abstractions as HDF5 and is compatible with the HDF5 Abstract Data Model. Several research groups are already using data stored in a directory hierarchy as an alternative to HDF5, but no common standard exists. This complicates and limits the opportunity for data sharing and development of common tools for reading, writing, and analyzing data. Exdir facilitates improved data storage, data sharing, reproducible research, and novel insight from interdisciplinary collaboration. With the publication of Exdir, we invite the scientific community to join the development to create an open specification that will serve as many needs as possible and as a foundation for open access to and exchange of data.

"Where On Mars?": An Open Planetary Mapping Platform for Researchers, Educators, and the General Public

NASA Astrophysics Data System (ADS)

Manaud, Nicolas; Carter, John; Boix, Oriol

2016-10-01

The "Where On Mars?" project is essentially the evolution of an existing outreach product developed in collaboration between ESA and CartoDB; an interactive map visualisation of the ESA's ExoMars Rover candidate landing sites (whereonmars.co). Planetary imagery data and maps are increasingly produced by the scientific community, and shared typically as images, in scientific publications, presentations or public outreach websites. However, this media lacks of interactivity and contextual information available for further exploration, making it difficult for any audience to relate one location-based information to another. We believe that interactive web maps are a powerful way of telling stories, engaging with and educating people who, over the last decade, have become familiar with tools such as Google Maps. A few planetary web maps exist but they are either too complex for non-experts, or are closed-systems that do not allows anyone to publish and share content. The long-term vision for the project is to provide researchers, communicators, educators and a worldwide public with an open planetary mapping and social platform enabling them to create, share, communicate and consume research-based content. We aim for this platform to become the reference website everyone will go to learn about Mars and other planets in our Solar System; just like people head to Google Maps to find their bearings or any location-based information. The driver is clearly to create for people an emotional connection with Mars. The short-term objectives for the project are (1) to produce and curate an open repository of basemaps, geospatial data sets, map visualisations, and story maps; (2) to develop a beautifully crafted and engaging interactive map of Mars. Based on user-generated content, the underlying framework should (3) make it easy to create and share additional interactive maps telling specific stories.

The Importance of Biodiversity E-infrastructures for Megadiverse Countries

PubMed Central

Canhos, Dora A. L.; Sousa-Baena, Mariane S.; de Souza, Sidnei; Maia, Leonor C.; Stehmann, João R.; Canhos, Vanderlei P.; De Giovanni, Renato; Bonacelli, Maria B. M.; Los, Wouter; Peterson, A. Townsend

2015-01-01

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil’s speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2–4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish. PMID:26204382

The Importance of Biodiversity E-infrastructures for Megadiverse Countries.

PubMed

Canhos, Dora A L; Sousa-Baena, Mariane S; de Souza, Sidnei; Maia, Leonor C; Stehmann, João R; Canhos, Vanderlei P; De Giovanni, Renato; Bonacelli, Maria B M; Los, Wouter; Peterson, A Townsend

2015-07-01

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil's speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2-4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish.

Office design and health: a systematic review.

PubMed

Richardson, Ann; Potter, John; Paterson, Margaret; Harding, Thomas; Tyler-Merrick, Gaye; Kirk, Ray; Reid, Kate; McChesney, Jane

2017-12-15

To carry out a systematic review of recent research into the effects of workplace design, comparing individual with shared workspaces, on the health of employees. The research question was "Does workplace design (specifically individual offices compared with shared workspaces) affect the health of workers?" A literature search limited to articles published between 2000 and 2017 was undertaken. A systematic review was carried out, and the findings of the reviewed studies grouped into themes according to the primary outcomes measured in the studies. The literature search identified 15 relevant studies addressing health effects of shared or open-plan offices compared with individual offices. Our systematic review found that, compared with individual offices, shared or open-plan office space is not beneficial to employees' health, with consistent findings of deleterious effects on staff health, wellbeing and productivity. Our findings are also consistent with those of earlier reviews. These findings have public health implications for the New Zealand workforce. Decisions about workplace design should include weighing the short-term financial benefits of open-plan or shared workspaces against the significant harms, including increased sickness absence, lower job satisfaction and productivity, and possible threats to recruitment and retention of staff.

Sharing clinical trial data on patient level: Opportunities and challenges

PubMed Central

Koenig, Franz; Slattery, Jim; Groves, Trish; Lang, Thomas; Benjamini, Yoav; Day, Simon; Bauer, Peter; Posch, Martin

2015-01-01

In recent months one of the most controversially discussed topics among regulatory agencies, the pharmaceutical industry, journal editors, and academia has been the sharing of patient-level clinical trial data. Several projects have been started such as the European Medicines Agency´s (EMA) “proactive publication of clinical trial data”, the BMJ open data campaign, or the AllTrials initiative. The executive director of the EMA, Dr. Guido Rasi, has recently announced that clinical trial data on patient level will be published from 2014 onwards (although it has since been delayed). The EMA draft policy on proactive access to clinical trial data was published at the end of June 2013 and open for public consultation until the end of September 2013. These initiatives will change the landscape of drug development and publication of medical research. They provide unprecedented opportunities for research and research synthesis, but pose new challenges for regulatory authorities, sponsors, scientific journals, and the public. Besides these general aspects, data sharing also entails intricate biostatistical questions such as problems of multiplicity. An important issue in this respect is the interpretation of multiple statistical analyses, both prospective and retrospective. Expertise in biostatistics is needed to assess the interpretation of such multiple analyses, for example, in the context of regulatory decision-making by optimizing procedural guidance and sophisticated analysis methods. PMID:24942505

Open Data and Open Science for better Research in the Geo and Space Domain

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2015-12-01

Main open data principles had been worked out in the run-up and finally adopted in the Open Data Charta at the G8 summit in Lough Erne, Northern Ireland in June 2013. Important principles are also valid for science data, such as Open Data by Default, Quality and Quantity, Useable by All, Releasing Data for Improved Governance, Releasing Data for Innovation. There is also an explicit relationship to such areas of high values as earth observation, education and geospatial data. The European union implementation plan of the Open Data Charta identifies among other things objectives such as making data available in an open format, enabling semantic interoperability, ensuring quality, documentation and where appropriate reconciliation across different data sources, implementing software solutionsallowing easy management, publication or visualization of datasets and simplifying clearance of intellectual property rights.Open Science is not just a list of already for a longer time known principles but stands for a lot of initiatives and projects around a better handling of scientific data and openly shared scientific knowledge. It is also about transparency in methodology and collection of data, availability and reuse of scientific data, public accessibility to scientific communication and using of social media to facility scientific collaboration. Some projects are concentrating on open sharing of free and open source software and even further hardware in kind of processing capabilities. In addition question about the mashup of data and publication and an open peer review process are addressed.Following the principles of open data and open science the newest results of the collaboration efforts in mashing up the data servers related to the Japanese IUGONET, the European Union ESPAS and the GFZ ISDC semantic Web projects will be presented here. The semantic Web based approach for the mashup is focusing on the design and implementation of a common but still distributed data catalog based on semantical interoperability including the transparent access to data in relational data bases. References: https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/207772/Open_Data_Charter.pdfhttp://www.openscience.org/blog/wp-content/uploads/2013/06/OpenSciencePoster.pdf

OpenFDA: an innovative platform providing access to a wealth of FDA's publicly available data.

PubMed

Kass-Hout, Taha A; Xu, Zhiheng; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-05-01

The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Using cutting-edge technologies deployed on FDA's new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved.

OpenFDA: an innovative platform providing access to a wealth of FDA’s publicly available data

PubMed Central

Kass-Hout, Taha A; Mohebbi, Matthew; Nelsen, Hans; Baker, Adam; Levine, Jonathan; Johanson, Elaine; Bright, Roselie A

2016-01-01

Objective The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Materials and Methods Using cutting-edge technologies deployed on FDA’s new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets; open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas; and infrastructure that can be adopted for other public health big data challenges. Results Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. Conclusion With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products. PMID:26644398

Neuroimaging Data Sharing on the Neuroinformatics Database Platform

PubMed Central

Book, Gregory A; Stevens, Michael; Assaf, Michal; Glahn, David; Pearlson, Godfrey D

2015-01-01

We describe the Neuroinformatics Database (NiDB), an open-source database platform for archiving, analysis, and sharing of neuroimaging data. Data from the multi-site projects Autism Brain Imaging Data Exchange (ABIDE), Bipolar-Schizophrenia Network on Intermediate Phenotypes parts one and two (B-SNIP1, B-SNIP2), and Monetary Incentive Delay task (MID) are available for download from the public instance of NiDB, with more projects sharing data as it becomes available. As demonstrated by making several large datasets available, NiDB is an extensible platform appropriately suited to archive and distribute shared neuroimaging data. PMID:25888923

The C6H6 NMR repository: An integral solution to control the flow of your data from the magnet to the public.

PubMed

Patiny, Luc; Zasso, Michaël; Kostro, Daniel; Bernal, Andrés; Castillo, Andrés M; Bolaños, Alejandro; Asencio, Miguel A; Pellet, Norman; Todd, Matthew; Schloerer, Nils; Kuhn, Stefan; Holmes, Elaine; Javor, Sacha; Wist, Julien

2017-10-05

NMR is a mature technique that is well established and adopted in a wide range of research facilities from laboratories to hospitals. This accounts for large amounts of valuable experimental data that may be readily exported into a standard and open format. Yet the publication of these data faces an important issue: Raw data are not made available; instead, the information is slimed down into a string of characters (the list of peaks). Although historical limitations of technology explain this practice, it is not acceptable in the era of Internet. The idea of modernizing the strategy for sharing NMR data is not new, and some repositories exist, but sharing raw data is still not an established practice. Here, we present a powerful toolbox built on recent technologies that runs inside the browser and provides a means to store, share, analyse, and interact with original NMR data. Stored spectra can be streamlined into the publication pipeline, to improve the revision process for instance. The set of tools is still basic but is intended to be extended. The project is open source under the Massachusetts Institute of Technology (MIT) licence. Copyright © 2017 John Wiley & Sons, Ltd.

Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences.

PubMed

Bird, Colin L; Frey, Jeremy G

2013-08-21

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information.

"You Cannot Collect Data Using Your Own Resources And Put It On Open Access": Perspectives From Africa About Public Health Data-Sharing.

PubMed

Anane-Sarpong, Evelyn; Wangmo, Tenzin; Ward, Claire Leonie; Sankoh, Osman; Tanner, Marcel; Elger, Bernice Simone

2017-07-25

Data-sharing is a desired default in the field of public health and a source of much ethical deliberation. Sharing data potentially contributes the largest, most efficient source of scientific data, but is fraught with contextual challenges which make stakeholders, particularly those in under-resourced contexts hesitant or slow to share. Relatively little empirical research has engaged stakeholders in discussing the issue. This study sought to explore relevant experiences, contextual, and subjective explanations around the topic to provide a rich and detailed presentation of what it means to different stakeholders and contexts to share data and how that can guide practice and ethical guidance. A qualitative design involving interviews was undertaken with professionals working in public health institutions endowed with data (HDSS), ethics committees, and advisory agencies which help shape health research in Africa. A descriptive form of thematic analysis was used to summarize results into six key themes: (1) The role of HDSSs in research using public health data and data-sharing; (2) Ownership and funding are critical factors influencing data-sharing; (3) Other factors discourage data-sharing; (4) Promoting and sustaining data-sharing; (5) Ethical guidance structures; and (6) Establishing effective guidance. The themes reveal factors regarding the willingness or not to share and an intricate ethical system that current discourse could reflect. Many of the concerns resonate with the literature, but a whole other gamut of people and process issues; commitments, investments, careers, and the right ethical guidance are needed to realize a sustainable goal of reaching 'share' as a default. © 2017 John Wiley & Sons Ltd.

Imagining the “open” university: Sharing scholarship to improve research and education

PubMed Central

2017-01-01

Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education as well as increase the impact universities can have beyond their own walls. To support this perspective, I present evidence from case studies, published literature, and personal experiences as a practicing open scholar. I describe some of the challenges inherent to practicing open scholarship and some of the tensions created by incompatibilities between institutional policies and personal practice. To address this, I propose several concrete actions universities could take to support open scholarship and outline ways in which such initiatives could benefit the public as well as institutions. Importantly, I do not think most of these actions would require new funding but rather a redistribution of existing funds and a rewriting of internal policies to better align with university missions of knowledge dissemination and societal impact. PMID:29065148

Can psychology walk the walk of open science?

PubMed

Hesse, Bradford W

2018-01-01

An "open science movement" is gaining traction across many disciplines within the research enterprise but is also precipitating consternation among those who worry that too much disruption may be hampering professional productivity. Despite this disruption, proponents of open data collaboration have argued that some of the biggest problems of the 21st century need to be solved with the help of many people and that data sharing will be the necessary engine to make that happen. In the United States, a national strategic plan for data sharing encouraged the federally funded scientific agencies to (a) publish open data for community use in discoverable, machine-readable, and useful ways; (b) work with public and civil society organizations to set priorities for data to be shared; (c) support innovation and feedback on open data solutions; and (d) continue efforts to release and enhance high-priority data sets funded by taxpayer dollars. One of the more visible open data projects in the psychological sciences is the presidentially announced "Brain Research Through Advancing Innovative Neurotechnologies" (BRAIN) initiative. Lessons learned from initiatives such as these are instructive both from the perspective of open science within psychology and from the perspective of understanding the psychology of open science. Recommendations for creating better pathways to "walk the walk" in open science include (a) nurturing innovation and agile learning, (b) thinking outside the paradigm, (c) creating simplicity from complexity, and (d) participating in continuous learning evidence platforms. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Big data, open science and the brain: lessons learned from genomics.

PubMed

Choudhury, Suparna; Fishman, Jennifer R; McGowan, Michelle L; Juengst, Eric T

2014-01-01

The BRAIN Initiative aims to break new ground in the scale and speed of data collection in neuroscience, requiring tools to handle data in the magnitude of yottabytes (10(24)). The scale, investment and organization of it are being compared to the Human Genome Project (HGP), which has exemplified "big science" for biology. In line with the trend towards Big Data in genomic research, the promise of the BRAIN Initiative, as well as the European Human Brain Project, rests on the possibility to amass vast quantities of data to model the complex interactions between the brain and behavior and inform the diagnosis and prevention of neurological disorders and psychiatric disease. Advocates of this "data driven" paradigm in neuroscience argue that harnessing the large quantities of data generated across laboratories worldwide has numerous methodological, ethical and economic advantages, but it requires the neuroscience community to adopt a culture of data sharing and open access to benefit from them. In this article, we examine the rationale for data sharing among advocates and briefly exemplify these in terms of new "open neuroscience" projects. Then, drawing on the frequently invoked model of data sharing in genomics, we go on to demonstrate the complexities of data sharing, shedding light on the sociological and ethical challenges within the realms of institutions, researchers and participants, namely dilemmas around public/private interests in data, (lack of) motivation to share in the academic community, and potential loss of participant anonymity. Our paper serves to highlight some foreseeable tensions around data sharing relevant to the emergent "open neuroscience" movement.

The NGEE Arctic Data Archive -- Portal for Archiving and Distributing Data and Documentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boden, Thomas A; Palanisamy, Giri; Devarakonda, Ranjeet

2014-01-01

The Next-Generation Ecosystem Experiments (NGEE Arctic) project is committed to implementing a rigorous and high-quality data management program. The goal is to implement innovative and cost-effective guidelines and tools for collecting, archiving, and sharing data within the project, the larger scientific community, and the public. The NGEE Arctic web site is the framework for implementing these data management and data sharing tools. The open sharing of NGEE Arctic data among project researchers, the broader scientific community, and the public is critical to meeting the scientific goals and objectives of the NGEE Arctic project and critical to advancing the mission ofmore » the Department of Energy (DOE), Office of Science, Biological and Environmental (BER) Terrestrial Ecosystem Science (TES) program.« less

Governing & Foundation Boards: Fostering Successful Relationships.

ERIC Educational Resources Information Center

Legon, Richard D.

1996-01-01

Public colleges and universities increasingly raise private funds through institutional foundations. A healthy relationship between governing and foundation boards requires open communication, regular interaction, and shared information. The fulcrum of this relationship is the college's president, who has specific responsibilities toward each…

76 FR 54498 - Meeting of the Department of Justice Global Justice Information Sharing Initiative Federal...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-01

... (GAC) to discuss the Global Initiative, as described at http://www.it.ojp.gov/global . DATES: [email protected]gov . SUPPLEMENTARY INFORMATION: This meeting is open to the public. Due to security measures...

75 FR 56557 - Meeting of the Department of Justice's (DOJ's) Global Justice Information Sharing Initiative...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-16

... Committee (GAC) to discuss the Global Initiative, as described at http://www.it.ojp.gov/global . DATES: [email protected]gov . SUPPLEMENTARY INFORMATION: This meeting is open to the public. Due to security measures...

Reproducible and reusable research: are journal data sharing policies meeting the mark?

PubMed

Vasilevsky, Nicole A; Minnier, Jessica; Haendel, Melissa A; Champieux, Robin E

2017-01-01

There is wide agreement in the biomedical research community that research data sharing is a primary ingredient for ensuring that science is more transparent and reproducible. Publishers could play an important role in facilitating and enforcing data sharing; however, many journals have not yet implemented data sharing policies and the requirements vary widely across journals. This study set out to analyze the pervasiveness and quality of data sharing policies in the biomedical literature. The online author's instructions and editorial policies for 318 biomedical journals were manually reviewed to analyze the journal's data sharing requirements and characteristics. The data sharing policies were ranked using a rubric to determine if data sharing was required, recommended, required only for omics data, or not addressed at all. The data sharing method and licensing recommendations were examined, as well any mention of reproducibility or similar concepts. The data was analyzed for patterns relating to publishing volume, Journal Impact Factor, and the publishing model (open access or subscription) of each journal. A total of 11.9% of journals analyzed explicitly stated that data sharing was required as a condition of publication. A total of 9.1% of journals required data sharing, but did not state that it would affect publication decisions. 23.3% of journals had a statement encouraging authors to share their data but did not require it. A total of 9.1% of journals mentioned data sharing indirectly, and only 14.8% addressed protein, proteomic, and/or genomic data sharing. There was no mention of data sharing in 31.8% of journals. Impact factors were significantly higher for journals with the strongest data sharing policies compared to all other data sharing criteria. Open access journals were not more likely to require data sharing than subscription journals. Our study confirmed earlier investigations which observed that only a minority of biomedical journals require data sharing, and a significant association between higher Impact Factors and journals with a data sharing requirement. Moreover, while 65.7% of the journals in our study that required data sharing addressed the concept of reproducibility, as with earlier investigations, we found that most data sharing policies did not provide specific guidance on the practices that ensure data is maximally available and reusable.

Going the extra mile - creating a co-operative model for supporting patient and public involvement in research.

PubMed

Horobin, Adele

2016-01-01

In 2014, the Chief Medical Officer and Director General of Research and Development commissioned a review of patient and public involvement in the National Institute for Health Research. The report on this review, entitled 'Going the Extra Mile' was published in March, 2015. It described the bold goal of expecting all people using health and social care, and increasing numbers of the public, to be aware of and choosing to be involved in research. This requires more effort to build public awareness of research and better support for the public and researchers to do patient and public involvement in research. The author has created a new way of providing support for patient and public involvement based on co-operation between organisations. Termed 'share-banking', this model pools limited resources across organisations to deliver a regional programme of support activities for patient and public involvement over the long term. This includes helping organisations to share and learn from each other to avoid 're-inventing wheels' (where separate organisations each develop the same thing from the beginning). The 'Going the Extra Mile' report recommends that local organisations should work together to deliver public involvement activities across a region. 'Share-banking' should help fulfil this recommendation. The 'Going the Extra Mile' final report opened with the ambition to increase the public's awareness, participation and involvement in research. It stated the need for public and researchers to be better supported to do public involvement. A new co-operative model, termed 'share-banking', has been developed whereby organisations pool limited resources to create and sustain support for patient and public involvement in research. This should fulfil the 'Going the Extra Mile' report's recommendation to take a collaborative, cross-organisational and regional approach to public involvement.

Technical note: Open-paleo-data implementation pilot - the PAGES 2k special issue

NASA Astrophysics Data System (ADS)

Kaufman, Darrell S.; Pages 2k Special-Issue Editorial Team

2018-05-01

Data stewardship is an essential element of the publication process. Knowing how to enact data polices that are described only in general terms can be difficult, however. Examples are needed to model the implementation of open-data polices in actual studies. Here we explain the procedure used to attain a high and consistent level of data stewardship across a special issue of the journal Climate of the Past. We discuss the challenges related to (1) determining which data are essential for public archival, (2) using data generated by others, and (3) understanding data citations. We anticipate that open-data sharing in paleo sciences will accelerate as the advantages become more evident and as practices that reduce data loss become the accepted convention.

Menu-driven cloud computing and resource sharing for R and Bioconductor.

PubMed

Bolouri, Hamid; Dulepet, Rajiv; Angerman, Michael

2011-08-15

We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. hbolouri@fhcrc.org.

Shared use agreements and leisure time physical activity in North Carolina public schools.

PubMed

Carlton, Troy A; Kanters, Michael A; Bocarro, Jason N; Floyd, Myron F; Edwards, Michael B; Suau, Luis J

2017-02-01

Although increasing community access to public schools through shared use agreements (SUAs) has been a recommended strategy for promoting physical activity (PA) among national, state and local organizations, empirical evidence examining the efficacy of SUAs is limited. This study examined the degree of usage and production of PA among schools with shared use, and how variation in PA output is related to characteristics of the school, type of activity, facility type, and when activity occurs. Data were collected in 20 schools across North Carolina using System for Observing Play and Recreation in Communities (SOPARC) and Structured Physical Activity Surveys (SPAS) to assess PA in school athletic facilities during out of school time. Findings indicated that although schools had a policy of shared or open use, most facilities were empty during non-school hours. Hierarchal linear regression models also showed that formal programming was positively associated with both use and PA levels. Given the abundance of empty facilities, community groups in need of space to facilitate structured PA programs should pursue avenues of sharing facilities with public schools. Furthermore, to increase the efficacy of shared use, structured physical activity programs may be needed. Future studies are encouraged to further explore the effects of the specific types of shared use programs on PA production as well other aspects of the built environment surrounding schools. Copyright © 2016 Elsevier Inc. All rights reserved.

Open NASA Earth Exchange (OpenNEX): Strategies for enabling cross organization collaboration in the earth sciences

NASA Astrophysics Data System (ADS)

Michaelis, A.; Ganguly, S.; Nemani, R. R.; Votava, P.; Wang, W.; Lee, T. J.; Dungan, J. L.

2014-12-01

Sharing community-valued codes, intermediary datasets and results from individual efforts with others that are not in a direct funded collaboration can be a challenge. Cross organization collaboration is often impeded due to infrastructure security constraints, rigid financial controls, bureaucracy, and workforce nationalities, etc., which can force groups to work in a segmented fashion and/or through awkward and suboptimal web services. We show how a focused community may come together, share modeling and analysis codes, computing configurations, scientific results, knowledge and expertise on a public cloud platform; diverse groups of researchers working together at "arms length". Through the OpenNEX experimental workshop, users can view short technical "how-to" videos and explore encapsulated working environment. Workshop participants can easily instantiate Amazon Machine Images (AMI) or launch full cluster and data processing configurations within minutes. Enabling users to instantiate computing environments from configuration templates on large public cloud infrastructures, such as Amazon Web Services, may provide a mechanism for groups to easily use each others work and collaborate indirectly. Moreover, using the public cloud for this workshop allowed a single group to host a large read only data archive, making datasets of interest to the community widely available on the public cloud, enabling other groups to directly connect to the data and reduce the costs of the collaborative work by freeing other individual groups from redundantly retrieving, integrating or financing the storage of the datasets of interest.

Institutions and Self-Governing Social Systems: Linking Reflexivity and Institutional Theories for Cybersecurity and Other Commons Governance Policies

ERIC Educational Resources Information Center

Clark, Kenneth Norman

2012-01-01

A "commons" is the conventional term that describes a widely accessible and shared resource, such as an ocean, open rangeland, a public park, or public portions of the Internet, which is difficult to exclude or limit use once naturally provided or humanly produced. Ruin of a commons can result when individuals use the resource recklessly…

78 FR 48658 - Defense Acquisition University Board of Visitors; Notice of Federal Advisory Committee Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-09

.... Knowledge Sharing Study 11:15 a.m. Team Training Initiatives and Mission Assistance Prioritization 12:00 p.m...-3.165, and the availability of space, this meeting is open to the public. However, because of space...

Data Collection, Collaboration, Analysis, and Publication Using the Open Data Repository's (ODR) Data Publisher

NASA Astrophysics Data System (ADS)

Lafuente, B.; Stone, N.; Bristow, T.; Keller, R. M.; Blake, D. F.; Downs, R. T.; Pires, A.; Dateo, C. E.; Fonda, M.

2017-12-01

In development for nearly four years, the Open Data Repository's (ODR) Data Publisher software has become a useful tool for researchers' data needs. Data Publisher facilitates the creation of customized databases with flexible permission sets that allow researchers to share data collaboratively while improving data discovery and maintaining ownership rights. The open source software provides an end-to-end solution from collection to final repository publication. A web-based interface allows researchers to enter data, view data, and conduct analysis using any programming language supported by JupyterHub (http://www.jupyterhub.org). This toolset makes it possible for a researcher to store and manipulate their data in the cloud from any internet capable device. Data can be embargoed in the system until a date selected by the researcher. For instance, open publication can be set to a date that coincides with publication of data analysis in a third party journal. In conjunction with teams at NASA Ames and the University of Arizona, a number of pilot studies are being conducted to guide the software development so that it allows them to publish and share their data. These pilots include (1) the Astrobiology Habitable Environments Database (AHED), a central searchable repository designed to promote and facilitate the integration and sharing of all the data generated by the diverse disciplines in astrobiology; (2) a database containing the raw and derived data products from the CheMin instrument on the MSL rover Curiosity (http://odr.io/CheMin), featuring a versatile graphing system, instructions and analytical tools to process the data, and a capability to download data in different formats; and (3) the Mineral Evolution project, which by correlating the diversity of mineral species with their ages, localities, and other measurable properties aims to understand how the episodes of planetary accretion and differentiation, plate tectonics, and origin of life lead to a selective evolution of mineral species through changes in temperature, pressure, and composition. Ongoing development will complete integration of third party meta-data standards and publishing data to the semantic web. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, MSL.

Demonstrating the value of publishing open data by linking DOI-based citations of source datasets to uses in research and policy

NASA Astrophysics Data System (ADS)

Copas, K.; Legind, J. K.; Hahn, A.; Braak, K.; Høftt, M.; Noesgaard, D.; Robertson, T.; Méndez Hernández, F.; Schigel, D.; Ko, C.

2017-12-01

GBIF—the Global Biodiversity Information Facility—has recently demonstrated a system that tracks publications back to individual datasets, giving data providers demonstrable evidence of the benefit and utility of sharing data to support an array of scholarly topics and practical applications. GBIF is an open-data network and research infrastructure funded by the world's governments. Its community consists of more than 90 formal participants and almost 1,000 data-publishing institutions, which currently make tens of thousands of datasets containing nearly 800 million species occurrence records freely and publicly available for discovery, use and reuse across a wide range of biodiversity-related research and policy investigations. Starting in 2015 with the help of DataONE, GBIF introduced DOIs as persistent identifiers for the datasets shared through its network. This enhancement soon extended to the assignment of DOIs to user downloads from GBIF.org, which typically filter the available records with a variety of taxonomic, geographic, temporal and other search terms. Despite the lack of widely accepted standards for citing data among researchers and publications, this technical infrastructure is beginning to take hold and support open, transparent, persistent and repeatable use and reuse of species occurrence data. These `download DOIs' provide canonical references for the search results researchers process and use in peer-reviewed articles—a practice GBIF encourages by confirming new DOIs with each download and offering guidelines on citation. GBIF has recently started linking these citation results back to dataset and publisher pages, offering more consistent, traceable evidence of the value of sharing data to support others' research. GBIF's experience may be a useful model for other repositories to follow.

Clinical Trial Data as Public Goods: Fair Trade and the Virtual Knowledge Bank as a Solution to the Free Rider Problem - A Framework for the Promotion of Innovation by Facilitation of Clinical Trial Data Sharing among Biopharmaceutical Companies in the Era of Omics and Big Data.

PubMed

Evangelatos, Nikolaos; Reumann, Matthias; Lehrach, Hans; Brand, Angela

2016-01-01

Knowledge in the era of Omics and Big Data has been increasingly conceptualized as a public good. Sharing of de-identified patient data has been advocated as a means to increase confidence and public trust in the results of clinical trials. On the other hand, research has shown that the current research and development model of the biopharmaceutical industry has reached its innovation capacity. In response to that, the biopharmaceutical industry has adopted open innovation practices, with sharing of clinical trial data being among the most interesting ones. However, due to the free rider problem, clinical trial data sharing among biopharmaceutical companies could undermine their innovativeness. Based on the theory of public goods, we have developed a commons arrangement and devised a model, which enables secure and fair clinical trial data sharing over a Virtual Knowledge Bank based on a web platform. Our model uses data as a virtual currency and treats knowledge as a club good. Fair sharing of clinical trial data over the Virtual Knowledge Bank has positive effects on the innovation capacity of the biopharmaceutical industry without compromising the intellectual rights, proprietary interests and competitiveness of the latter. The Virtual Knowledge Bank is a sustainable and self-expanding model for secure and fair clinical trial data sharing that allows for sharing of clinical trial data, while at the same time it increases the innovation capacity of the biopharmaceutical industry. © 2016 S. Karger AG, Basel.

Incomplete Intelligence: Is the Information Sharing Environment an Effective Platform?

DTIC Science & Technology

2012-09-01

Initiative NYFD New York Fire Department NYPD New York Police Department OLAP On Line Analytics Processing OSINT Open Source Intelligence...Intelligence ( OSINT ), from public websites, media sources, and other unclassified events and reports. Although some of these sources do not have a direct

Defining Success in Open Science

PubMed Central

Ali-Khan, Sarah E.; Jean, Antoine; MacDonald, Emily; Gold, E. Richard

2018-01-01

Mounting evidence indicates that worldwide, innovation systems are increasing unsustainable. Equally, concerns about inequities in the science and innovation process, and in access to its benefits, continue. Against a backdrop of growing health, economic and scientific challenges global stakeholders are urgently seeking to spur innovation and maximize the just distribution of benefits for all. Open Science collaboration (OS) – comprising a variety of approaches to increase open, public, and rapid mobilization of scientific knowledge – is seen to be one of the most promising ways forward. Yet, many decision-makers hesitate to construct policy to support the adoption and implementation of OS without access to substantive, clear and reliable evidence. In October 2017, international thought-leaders gathered at an Open Science Leadership Forum in the Washington DC offices of the Bill and Melinda Gates Foundation to share their views on what successful Open Science looks like. Delegates from developed and developing nations, national governments, science agencies and funding bodies, philanthropy, researchers, patient organizations and the biotechnology, pharma and artificial intelligence (AI) industries discussed the outcomes that would rally them to invest in OS, as well as wider issues of policy and implementation. This first of two reports, summarizes delegates' views on what they believe OS will deliver in terms of research, innovation and social impact in the life sciences. Through open and collaborative process over the next months, we will translate these success outcomes into a toolkit of quantitative and qualitative indicators to assess when, where and how open science collaborations best advance research, innovation and social benefit. Ultimately, this work aims to develop and openly share tools to allow stakeholders to evaluate and re-invent their innovation ecosystems, to maximize value for the global public and patients, and address long-standing questions about the mechanics of innovation. PMID:29553146

Defining Success in Open Science.

PubMed

Ali-Khan, Sarah E; Jean, Antoine; MacDonald, Emily; Gold, E Richard

2018-01-01

Mounting evidence indicates that worldwide, innovation systems are increasing unsustainable. Equally, concerns about inequities in the science and innovation process, and in access to its benefits, continue. Against a backdrop of growing health, economic and scientific challenges global stakeholders are urgently seeking to spur innovation and maximize the just distribution of benefits for all. Open Science collaboration (OS) - comprising a variety of approaches to increase open, public, and rapid mobilization of scientific knowledge - is seen to be one of the most promising ways forward. Yet, many decision-makers hesitate to construct policy to support the adoption and implementation of OS without access to substantive, clear and reliable evidence. In October 2017, international thought-leaders gathered at an Open Science Leadership Forum in the Washington DC offices of the Bill and Melinda Gates Foundation to share their views on what successful Open Science looks like. Delegates from developed and developing nations, national governments, science agencies and funding bodies, philanthropy, researchers, patient organizations and the biotechnology, pharma and artificial intelligence (AI) industries discussed the outcomes that would rally them to invest in OS, as well as wider issues of policy and implementation. This first of two reports, summarizes delegates' views on what they believe OS will deliver in terms of research, innovation and social impact in the life sciences. Through open and collaborative process over the next months, we will translate these success outcomes into a toolkit of quantitative and qualitative indicators to assess when, where and how open science collaborations best advance research, innovation and social benefit. Ultimately, this work aims to develop and openly share tools to allow stakeholders to evaluate and re-invent their innovation ecosystems, to maximize value for the global public and patients, and address long-standing questions about the mechanics of innovation.

A Bigger Slice of the Money Pie: Charters in Colorado and Florida Win Share of Local Tax Dollars

ERIC Educational Resources Information Center

Baxter, Parker; Ely, Todd L.; Teske, Paul

2018-01-01

Charter schools now educate nearly 3 million students in 43 states and the District of Columbia--more than 6 percent of the total K-12 public-school enrollment. Yet some 25 years after the first charter school opened in Minnesota, the merits of charters still incite debate among educators and the public. What is not often debated is that charter…

Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking.

PubMed

Joly, Yann; Dalpé, Gratien; So, Derek; Birko, Stanislav

2015-01-01

Biobanks are important resources which enable large-scale genomic research with human samples and data, raising significant ethical concerns about how participants' information is managed and shared. Three previous studies of the Canadian public's opinion about these topics have been conducted. Building on those results, an online survey representing the first study of public perceptions about biobanking spanning all Canadian provinces was conducted. Specifically, this study examined qualitative views about biobank objectives, governance structure, control and ownership of samples and data, benefit sharing, consent practices and data sharing norms, as well as additional questions and ethical concerns expressed by the public. Over half the respondents preferred to give a one-time general consent for the future sharing of their samples among researchers. Most expressed willingness for their data to be shared with the international scientific community rather than used by one or more Canadian institutions. Whereas more respondents indicated a preference for one-time general consent than any other model of consent, they constituted less than half of the total responses, revealing a lack of consensus among survey respondents regarding this question. Respondents identified biobank objectives, governance structure and accountability as the most important information to provide participants. Respondents' concerns about biobanking generally centred around the control and ownership of biological samples and data, especially with respect to potential misuse by insurers, the government and other third parties. Although almost half the respondents suggested that these should be managed by the researchers' institutions, results indicate that the public is interested in being well-informed about these projects and suggest the importance of increased involvement from participants. In conclusion, the study discusses the viability of several proposed models for informed consent, including e-governance, independent trustees and the use of exclusion clauses, in the context of these new findings about the views of the Canadian public.

Data Publications Correlate with Citation Impact.

PubMed

Leitner, Florian; Bielza, Concha; Hill, Sean L; Larrañaga, Pedro

2016-01-01

Neuroscience and molecular biology have been generating large datasets over the past years that are reshaping how research is being conducted. In their wake, open data sharing has been singled out as a major challenge for the future of research. We conducted a comparative study of citations of data publications in both fields, showing that the average publication tagged with a data-related term by the NCBI MeSH (Medical Subject Headings) curators achieves a significantly larger citation impact than the average in either field. We introduce a new metric, the data article citation index (DAC-index), to identify the most prolific authors among those data-related publications. The study is fully reproducible from an executable Rmd (R Markdown) script together with all the citation datasets. We hope these results can encourage authors to more openly publish their data.

Assessing the Extent and Impact of Online Data Sharing in Eddy Covariance Flux Research

NASA Astrophysics Data System (ADS)

Dai, Sheng-Qi; Li, Hong; Xiong, Jun; Ma, Jun; Guo, Hai-Qiang; Xiao, Xiangming; Zhao, Bin

2018-01-01

Research data sharing is appealing for its potential benefits on sharers' scientific impact and is also advocated by various policies. How do scientific benefits and policies correlate with practical ecological data sharing? In this study, we investigated data-sharing practices in eddy covariance flux research as a typical case. First, we collected researchers' data-sharing information from major observation networks. Then, we downloaded bibliometric data from the Web of Science and evaluated scientific impact using LeaderRank, a synthetic algorithm that takes both citation and cooperation impacts into consideration. Our results demonstrated the following: (1) specific to eddy covariance flux research, 8% of researchers published information in public data portals, whereas 64% of researchers provided their available data online in a downloadable form; (2) regional differences in data sharing, publications, and observation networks existed; and (3) the data sharers in impact-ranked ecologists followed a long-tail distribution, which suggested that, although sharing data is not necessary for researchers to be influential, data sharers are more likely to be high-impact researchers. Differentiated policies should be proposed to encourage ecologists in the long tail of data sharers, and from regions with little tradition of data sharing, to embrace a more open model of science.

Visionmaker NYC: A bottom-up approach to finding shared socioeconomic pathways in New York City

NASA Astrophysics Data System (ADS)

Sanderson, E. W.; Fisher, K.; Giampieri, M.; Barr, J.; Meixler, M.; Allred, S. B.; Bunting-Howarth, K. E.; DuBois, B.; Parris, A. S.

2015-12-01

Visionmaker NYC is a free, public participatory, bottom-up web application to develop and share climate mitigation and adaptation strategies for New York City neighborhoods. The goal is to develop shared socioeconomic pathways by allowing a broad swath of community members - from schoolchildren to architects and developers to the general public - to input their concepts for a desired future. Visions are comprised of climate scenarios, lifestyle choices, and ecosystem arrangements, where ecosystems are broadly defined to include built ecosystems (e.g. apartment buildings, single family homes, etc.), transportation infrastructure (e.g. highways, connector roads, sidewalks), and natural land cover types (e.g. wetlands, forests, estuary.) Metrics of water flows, carbon cycling, biodiversity patterns, and population are estimated for the user's vision, for the same neighborhood today, and for that neighborhood as it existed in the pre-development state, based on the Welikia Project (welikia.org.) Users can keep visions private, share them with self-defined groups of other users, or distribute them publicly. Users can also propose "challenges" - specific desired states of metrics for specific parts of the city - and others can post visions in response. Visionmaker contributes by combining scenario planning, scientific modelling, and social media to create new, wide-open possibilities for discussion, collaboration, and imagination regarding future, shared socioeconomic pathways.

Magnifying Democracy and Sovereignty In Indonesian Maritime Governance Through Open Marine Spatial Data Practice

NASA Astrophysics Data System (ADS)

Yudono, Adipandang

2018-05-01

This research has attempted to discover a new approach in magnifying democracy and sovereignty in the Indonesian maritime governance through open marine spatial data practices between governments and citizens. The research has been done in order to fill in the gap of bridging marine spatial data or information at all government levels and between citizen and government. The research predominantly used qualitative methods with specifically approach was discourse analysis using legal document analysis and in-depth interview to elites, and local digital mapping communities. The coherence and synergy of maritime development can be achieved through dialogue between the elites and the public. A solution to bridge political communication between the elite and the public is sharing or open marine spatial data and information.

Freeing data through The Polar Information Commons

NASA Astrophysics Data System (ADS)

de Bruin, Taco; Chen, Robert; Parsons, Mark; Carlson, David

2010-05-01

The polar regions are changing rapidly with dramatic global effect. Wise management of resources, improved decision support, and effective international cooperation on resource and geopolitical issues require deeper understanding and better prediction of these changes. Unfortunately, polar data and information remain scattered, scarce, and sporadic. Inspired by the Antarctic Treaty of 1959 that established the Antarctic as a global commons to be used only for peaceful purposes and scientific research, we assert that data and information about the polar regions are themselves "public goods" that should be shared ethically and with minimal constraint. We therefore envision the Polar Information Commons (PIC) as an open, virtual repository for vital scientific data and information that would provide a shared, community-based cyber-infrastructure fostering innovation, improving scientific efficiency, and encouraging participation in polar research, education, planning, and management. The PIC will build on the legacy of the International Polar Year (IPY), providing a long-term framework for access to and preservation of both existing and future data and information about the polar regions. Rapid change demands rapid data access. The PIC system will enable scientists to quickly expose their data to the world and share them through open protocols on the Internet. A PIC digital label will alert users and data centers to new polar data and ensure that usage rights are clear. The PIC will utilize the Science Commons Protocol for Implementing Open Access Data, which promotes open data access through the public domain coupled with community norms of practice to ensure use of data in a fair and equitable manner. A set of PIC norms is currently being developed in consultation with key polar data organizations and other stakeholders. We welcome inputs from the broad science community as we further develop and refine the PIC approach and move ahead with implementation.

Freeing data through The Polar Information Commons

NASA Astrophysics Data System (ADS)

de Bruin, T.; Chen, R. S.; Parsons, M. A.; Carlson, D. J.

2009-12-01

The polar regions are changing rapidly with dramatic global effect. Wise management of resources, improved decision support, and effective international cooperation on resource and geopolitical issues require deeper understanding and better prediction of these changes. Unfortunately, polar data and information remain scattered, scarce, and sporadic. Inspired by the Antarctic Treaty of 1959 that established the Antarctic as a global commons to be used only for peaceful purposes and scientific research, we assert that data and information about the polar regions are themselves “public goods” that should be shared ethically and with minimal constraint. We therefore envision the Polar Information Commons (PIC) as an open, virtual repository for vital scientific data and information that would provide a shared, community-based cyber-infrastructure fostering innovation, improving scientific efficiency, and encouraging participation in polar research, education, planning, and management. The PIC will build on the legacy of the International Polar Year (IPY), providing a long-term framework for access to and preservation of both existing and future data and information about the polar regions. Rapid change demands rapid data access. The PIC system will enable scientists to quickly expose their data to the world and share them through open protocols on the Internet. A PIC digital label will alert users and data centers to new polar data and ensure that usage rights are clear. The PIC will utilize the Science Commons Protocol for Implementing Open Access Data, which promotes open data access through the public domain coupled with community norms of practice to ensure use of data in a fair and equitable manner. A set of PIC norms is currently being developed in consultation with key polar data organizations and other stakeholders. We welcome inputs from the broad science community as we further develop and refine the PIC approach and move ahead with implementation.

Freeing data through The Polar Information Commons

NASA Astrophysics Data System (ADS)

de Bruin, T.; Chen, R. S.; Parsons, M. A.; Carlson, D. J.; Cass, K.; Finney, K.; Wilbanks, J.; Jochum, K.

2010-12-01

The polar regions are changing rapidly with dramatic global effect. Wise management of resources, improved decision support, and effective international cooperation on resource and geopolitical issues require deeper understanding and better prediction of these changes. Unfortunately, polar data and information remain scattered, scarce, and sporadic. Inspired by the Antarctic Treaty of 1959 that established the Antarctic as a global commons to be used only for peaceful purposes and scientific research, we assert that data and information about the polar regions are themselves “public goods” that should be shared ethically and with minimal constraint. ICSU’s Committee on Data (CODATA) therefore started the Polar Information Commons (PIC) as an open, virtual repository for vital scientific data and information. The PIC provides a shared, community-based cyber-infrastructure fostering innovation, improving scientific efficiency, and encouraging participation in polar research, education, planning, and management. The PIC builds on the legacy of the International Polar Year (IPY), providing a long-term framework for access to and preservation of both existing and future data and information about the polar regions. Rapid change demands rapid data access. The PIC system enables scientists to quickly expose their data to the world and share them through open protocols on the Internet. A PIC digital label will alert users and data centers to new polar data and ensure that usage rights are clear. The PIC utilizes the Science Commons Protocol for Implementing Open Access Data, which promotes open data access through the public domain coupled with community norms of practice to ensure use of data in a fair and equitable manner. A set of PIC norms has been developed in consultation with key polar data organizations and other stakeholders. We welcome inputs from the broad science community as we further develop and refine the PIC approach and move ahead with implementation.

Menu-driven cloud computing and resource sharing for R and Bioconductor

PubMed Central

Bolouri, Hamid; Angerman, Michael

2011-01-01

Summary: We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. Availability and Implementation: CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. Contact: hbolouri@fhcrc.org PMID:21685055

Precision global health in the digital age.

PubMed

Flahault, Antoine; Geissbuhler, Antoine; Guessous, Idris; Guérin, Philippe; Bolon, Isabelle; Salathé, Marcel; Escher, Gérard

2017-04-19

Precision global health is an approach similar to precision medicine, which facilitates, through innovation and technology, better targeting of public health interventions on a global scale, for the purpose of maximising their effectiveness and relevance. Illustrative examples include: the use of remote sensing data to fight vector-borne diseases; large databases of genomic sequences of foodborne pathogens helping to identify origins of outbreaks; social networks and internet search engines for tracking communicable diseases; cell phone data in humanitarian actions; drones to deliver healthcare services in remote and secluded areas. Open science and data sharing platforms are proposed for fostering international research programmes under fair, ethical and respectful conditions. Innovative education, such as massive open online courses or serious games, can promote wider access to training in public health and improving health literacy. The world is moving towards learning healthcare systems. Professionals are equipped with data collection and decision support devices. They share information, which are complemented by external sources, and analysed in real time using machine learning techniques. They allow for the early detection of anomalies, and eventually guide appropriate public health interventions. This article shows how information-driven approaches, enabled by digital technologies, can help improving global health with greater equity.

NSF Anticipates Pushing Boundaries on Open-Access Plan

ERIC Educational Resources Information Center

Basken, Paul

2013-01-01

The National Science Foundation (NSF), in carrying out the Obama administration's new push for greater public access to research published in scientific journals, will consider exclusivity periods shorter than the 12-month standard in the White House directive, as well as trade-offs involving data-sharing and considerations of publishers'…

Networked Scholarship and Motivations for Social Media Use in Scholarly Communication

ERIC Educational Resources Information Center

Manca, Stefania; Ranier, Maria

2017-01-01

Research on scholars' use of social media suggests that these sites are increasingly being used to enhance scholarly communication by strengthening relationships, facilitating collaboration among peers, publishing and sharing research products, and discussing research topics in open and public formats. However, very few studies have investigated…

22nd Spring Research Festival Just One Week Away | Poster

Cancer.gov

This year’s annual Spring Research Festival, scheduled for May 9 and 10, is nearly here. As usual, it is free and open to the public and promises to offer a forum for sharing scientific research and celebrating collaboration at Fort Detrick and NCI at Frederick.

The Black Belt Librarian: Real-World Safety & Security

ERIC Educational Resources Information Center

Graham, Warren

2012-01-01

Sharing expertise gleaned from more than two decades as a library security manager, Graham demonstrates that libraries can maintain their best traditions of openness and public access by creating an unobtrusive yet effective security plan. In straightforward language, the author: (1) Shows how to easily set clear expectations for visitors'…

Public-Private Consortium Aims to Cut Preclinical Cancer Drug Discovery from Six Years to Just One | Frederick National Laboratory for Cancer Research

Cancer.gov

Scientists from two U.S. national laboratories, industry, and academia today launched an unprecedented effort to transform the way cancer drugs are discovered by creating an open and sharable platform that integrates high-performance computing, share

PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing.

PubMed

Wang, Yanli; Cheng, Tiejun; Bryant, Stephen H

2017-07-01

High-throughput screening (HTS) is now routinely conducted for drug discovery by both pharmaceutical companies and screening centers at academic institutions and universities. Rapid advance in assay development, robot automation, and computer technology has led to the generation of terabytes of data in screening laboratories. Despite the technology development toward HTS productivity, fewer efforts were devoted to HTS data integration and sharing. As a result, the huge amount of HTS data was rarely made available to the public. To fill this gap, the PubChem BioAssay database ( https://www.ncbi.nlm.nih.gov/pcassay/ ) was set up in 2004 to provide open access to the screening results tested on chemicals and RNAi reagents. With more than 10 years' development and contributions from the community, PubChem has now become the largest public repository for chemical structures and biological data, which provides an information platform to worldwide researchers supporting drug development, medicinal chemistry study, and chemical biology research. This work presents a review of the HTS data content in the PubChem BioAssay database and the progress of data deposition to stimulate knowledge discovery and data sharing. It also provides a description of the database's data standard and basic utilities facilitating information access and use for new users.

Advancing Collaboration through Hydrologic Data and Model Sharing

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Idaszak, R.; Horsburgh, J. S.; Ames, D. P.; Goodall, J. L.; Band, L. E.; Merwade, V.; Couch, A.; Hooper, R. P.; Maidment, D. R.; Dash, P. K.; Stealey, M.; Yi, H.; Gan, T.; Castronova, A. M.; Miles, B.; Li, Z.; Morsy, M. M.

2015-12-01

HydroShare is an online, collaborative system for open sharing of hydrologic data, analytical tools, and models. It supports the sharing of and collaboration around "resources" which are defined primarily by standardized metadata, content data models for each resource type, and an overarching resource data model based on the Open Archives Initiative's Object Reuse and Exchange (OAI-ORE) standard and a hierarchical file packaging system called "BagIt". HydroShare expands the data sharing capability of the CUAHSI Hydrologic Information System by broadening the classes of data accommodated to include geospatial and multidimensional space-time datasets commonly used in hydrology. HydroShare also includes new capability for sharing models, model components, and analytical tools and will take advantage of emerging social media functionality to enhance information about and collaboration around hydrologic data and models. It also supports web services and server/cloud based computation operating on resources for the execution of hydrologic models and analysis and visualization of hydrologic data. HydroShare uses iRODS as a network file system for underlying storage of datasets and models. Collaboration is enabled by casting datasets and models as "social objects". Social functions include both private and public sharing, formation of collaborative groups of users, and value-added annotation of shared datasets and models. The HydroShare web interface and social media functions were developed using the Django web application framework coupled to iRODS. Data visualization and analysis is supported through the Tethys Platform web GIS software stack. Links to external systems are supported by RESTful web service interfaces to HydroShare's content. This presentation will introduce the HydroShare functionality developed to date and describe ongoing development of functionality to support collaboration and integration of data and models.

Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking

PubMed Central

Joly, Yann; Dalpé, Gratien; So, Derek; Birko, Stanislav

2015-01-01

Context Biobanks are important resources which enable large-scale genomic research with human samples and data, raising significant ethical concerns about how participants’ information is managed and shared. Three previous studies of the Canadian public’s opinion about these topics have been conducted. Building on those results, an online survey representing the first study of public perceptions about biobanking spanning all Canadian provinces was conducted. Specifically, this study examined qualitative views about biobank objectives, governance structure, control and ownership of samples and data, benefit sharing, consent practices and data sharing norms, as well as additional questions and ethical concerns expressed by the public. Results Over half the respondents preferred to give a one-time general consent for the future sharing of their samples among researchers. Most expressed willingness for their data to be shared with the international scientific community rather than used by one or more Canadian institutions. Whereas more respondents indicated a preference for one-time general consent than any other model of consent, they constituted less than half of the total responses, revealing a lack of consensus among survey respondents regarding this question. Respondents identified biobank objectives, governance structure and accountability as the most important information to provide participants. Respondents’ concerns about biobanking generally centred around the control and ownership of biological samples and data, especially with respect to potential misuse by insurers, the government and other third parties. Although almost half the respondents suggested that these should be managed by the researchers’ institutions, results indicate that the public is interested in being well-informed about these projects and suggest the importance of increased involvement from participants. In conclusion, the study discusses the viability of several proposed models for informed consent, including e-governance, independent trustees and the use of exclusion clauses, in the context of these new findings about the views of the Canadian public. PMID:26154134

Leveraging Crowdsourcing and Linked Open Data for Geoscience Data Sharing and Discovery

NASA Astrophysics Data System (ADS)

Narock, T. W.; Rozell, E. A.; Hitzler, P.; Arko, R. A.; Chandler, C. L.; Wilson, B. D.

2013-12-01

Data citation standards can form the basis for increased incentives, recognition, and rewards for scientists. Additionally, knowing which data were utilized in a particular publication can enhance discovery and reuse. Yet, a lack of data citation information in existing publications as well as ambiguities across datasets can limit the accuracy of automated linking approaches. We describe a crowdsourcing approach, based on Linked Open Data, in which AGU abstracts are linked to the data used in those presentations. We discuss our efforts to incentivize participants through promotion of their research, the role that the Semantic Web can play in this effort, and how this work differs from existing platforms such as Mendeley and ResearchGate. Further, we discuss the benefits and challenges of Linked Open Data as a technical solution including the role of provenance, trust, and computational reasoning.

Data Rescue in Collaboration with Federal Open Access Efforts

NASA Astrophysics Data System (ADS)

Avila, R.

2017-12-01

The recent calls to rescue scientific data is a real opportunity to collaborate with federal agencies which have been spending years managing research data and making it secure. The 2013 memos from the White House Office of Science and Technology Policy and Office of Management and Budget have spurred innovation across federal agencies to make publicly funded data accessible. Now is the time for stakeholders to take advantage of the groundwork laid by federal government, support the work to expand data sharing, thereby encouraging open science.

tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research.

PubMed

Athey, Brian D; Braxenthaler, Michael; Haas, Magali; Guo, Yike

2013-01-01

tranSMART is an emerging global open source public private partnership community developing a comprehensive informatics-based analysis and data-sharing cloud platform for clinical and translational research. The tranSMART consortium includes pharmaceutical and other companies, not-for-profits, academic entities, patient advocacy groups, and government stakeholders. The tranSMART value proposition relies on the concept that the global community of users, developers, and stakeholders are the best source of innovation for applications and for useful data. Continued development and use of the tranSMART platform will create a means to enable "pre-competitive" data sharing broadly, saving money and, potentially accelerating research translation to cures. Significant transformative effects of tranSMART includes 1) allowing for all its user community to benefit from experts globally, 2) capturing the best of innovation in analytic tools, 3) a growing 'big data' resource, 4) convergent standards, and 5) new informatics-enabled translational science in the pharma, academic, and not-for-profit sectors.

Has open data arrived at the British Medical Journal (BMJ)? An observational study.

PubMed

Rowhani-Farid, Anisa; Barnett, Adrian G

2016-10-13

To quantify data sharing trends and data sharing policy compliance at the British Medical Journal (BMJ) by analysing the rate of data sharing practices, and investigate attitudes and examine barriers towards data sharing. Observational study. The BMJ research archive. 160 randomly sampled BMJ research articles from 2009 to 2015, excluding meta-analysis and systematic reviews. Percentages of research articles that indicated the availability of their raw data sets in their data sharing statements, and those that easily made their data sets available on request. 3 articles contained the data in the article. 50 out of 157 (32%) remaining articles indicated the availability of their data sets. 12 used publicly available data and the remaining 38 were sent email requests to access their data sets. Only 1 publicly available data set could be accessed and only 6 out of 38 shared their data via email. So only 7/157 research articles shared their data sets, 4.5% (95% CI 1.8% to 9%). For 21 clinical trials bound by the BMJ data sharing policy, the per cent shared was 24% (8% to 47%). Despite the BMJ's strong data sharing policy, sharing rates are low. Possible explanations for low data sharing rates could be: the wording of the BMJ data sharing policy, which leaves room for individual interpretation and possible loopholes; that our email requests ended up in researchers spam folders; and that researchers are not rewarded for sharing their data. It might be time for a more effective data sharing policy and better incentives for health and medical researchers to share their data. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Cross-Jurisdictional Resource Sharing in Local Health Departments: Implications for Services, Quality, and Cost.

PubMed

Humphries, Debbie L; Hyde, Justeen; Hahn, Ethan; Atherly, Adam; O'Keefe, Elaine; Wilkinson, Geoffrey; Eckhouse, Seth; Huleatt, Steve; Wong, Samuel; Kertanis, Jennifer

2018-01-01

Forty one percent of local health departments in the U.S. serve jurisdictions with populations of 25,000 or less. Researchers, policymakers, and advocates have long questioned how to strengthen public health systems in smaller municipalities. Cross-jurisdictional sharing may increase quality of service, access to resources, and efficiency of resource use. To characterize perceived strengths and challenges of independent and comprehensive sharing approaches, and to assess cost, quality, and breadth of services provided by independent and sharing health departments in Connecticut (CT) and Massachusetts (MA). We interviewed local health directors or their designees from 15 comprehensive resource-sharing jurisdictions and 54 single-municipality jurisdictions in CT and MA using a semi-structured interview. Quantitative data were drawn from closed-ended questions in the semi-structured interviews; municipal demographic data were drawn from the American Community Survey and other public sources. Qualitative data were drawn from open-ended questions in the semi-structured interviews. The findings from this multistate study highlight advantages and disadvantages of two common public health service delivery models - independent and shared. Shared service jurisdictions provided more community health programs and services, and invested significantly more ($120 per thousand (1K) population vs. $69.5/1K population) on healthy food access activities. Sharing departments had more indicators of higher quality food safety inspections (FSIs), and there was a non-linear relationship between cost per FSI and number of FSI. Minimum cost per FSI was reached above the total number of FSI conducted by all but four of the jurisdictions sampled. Independent jurisdictions perceived their governing bodies to have greater understanding of the roles and responsibilities of local public health, while shared service jurisdictions had fewer staff per 1,000 population. There are trade-offs with sharing and remaining independent. Independent health departments serving small jurisdictions have limited resources but strong local knowledge. Multi-municipality departments have more resources but require more time and investment in governance and decision-making. When making decisions about the right service delivery model for a given municipality, careful consideration should be given to local culture and values. Some economies of scale may be achieved through resource sharing for municipalities <25,000 population.

Information Sharing in the Age of Hyper-Competition: Opening an International Branch Campus

ERIC Educational Resources Information Center

Streitwieser, Bernhard; Beecher, Bradley

2017-01-01

Higher education institutions today are locked in fierce global competition. This is driven by many factors, but perhaps mostly by the highly public international rankings that exert tremendous pressures on institutional leaders. The importance that rankings have taken on recently (Yudkevich, Altbach, & Rumbley, 2016) critically affects the…

77 FR 7124 - Information Sharing With Agency Stakeholders; Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-10

... efforts to transform itself into a customer-focused, high-performing organization. In this context, USDA's... relationships. As part of a larger effort to enhance stakeholder communication, APHIS is hosting an open meeting... headquarters for support? Why? As we continue to look at ways to improve our processes and enhance customer...

Opening the Door

ERIC Educational Resources Information Center

Fontes, Kris

2012-01-01

Teenagers' bedrooms are reflections of their personalities. Their bedrooms showcase their individuality and define the world as they see it. Their bedrooms are private and public--shared with some and off limits to others. Each day students wake up and begin the rituals of the day, and in the evening they return to their sanctuaries and close the…

They Pledge Allegiance: PR People and Their Presidents Tell How They Forge a Bond through Open, Honest Communication.

ERIC Educational Resources Information Center

Shoemaker, Donna

1993-01-01

Interviews with five college presidents and their chief public relations officers concerning their professional relationships and approaches to program administration are summarized. Comments focus on the importance of trust, adaptability, communication, shared roles in policymaking, staying informed, and use of strategic thinking in effective…

PLUME and research sotware

NASA Astrophysics Data System (ADS)

Baudin, Veronique; Gomez-Diaz, Teresa

2013-04-01

The PLUME open platform (https://www.projet-plume.org) has as first goal to share competences and to value the knowledge of software experts within the French higher education and research communities. The project proposes in its platform the access to more than 380 index cards describing useful and economic software for this community, with open access to everybody. The second goal of PLUME focuses on to improve the visibility of software produced by research laboratories within the higher education and research communities. The "development-ESR" index cards briefly describe the main features of the software, including references to research publications associated to it. The platform counts more than 300 cards describing research software, where 89 cards have an English version. In this talk we describe the theme classification and the taxonomy of the index cards and the evolution with new themes added to the project. We will also focus on the organisation of PLUME as an open project and its interests in the promotion of free/open source software from and for research, contributing to the creation of a community of shared knowledge.

Technical and policy approaches to balancing patient privacy and data sharing in clinical and translational research.

PubMed

Malin, Bradley; Karp, David; Scheuermann, Richard H

2010-01-01

Clinical researchers need to share data to support scientific validation and information reuse and to comply with a host of regulations and directives from funders. Various organizations are constructing informatics resources in the form of centralized databases to ensure reuse of data derived from sponsored research. The widespread use of such open databases is contingent on the protection of patient privacy. We review privacy-related problems associated with data sharing for clinical research from technical and policy perspectives. We investigate existing policies for secondary data sharing and privacy requirements in the context of data derived from research and clinical settings. In particular, we focus on policies specified by the US National Institutes of Health and the Health Insurance Portability and Accountability Act and touch on how these policies are related to current and future use of data stored in public database archives. We address aspects of data privacy and identifiability from a technical, although approachable, perspective and summarize how biomedical databanks can be exploited and seemingly anonymous records can be reidentified using various resources without hacking into secure computer systems. We highlight which clinical and translational data features, specified in emerging research models, are potentially vulnerable or exploitable. In the process, we recount a recent privacy-related concern associated with the publication of aggregate statistics from pooled genome-wide association studies that have had a significant impact on the data sharing policies of National Institutes of Health-sponsored databanks. Based on our analysis and observations we provide a list of recommendations that cover various technical, legal, and policy mechanisms that open clinical databases can adopt to strengthen data privacy protection as they move toward wider deployment and adoption.

Technical and Policy Approaches to Balancing Patient Privacy and Data Sharing in Clinical and Translational Research

PubMed Central

Malin, Bradley; Karp, David; Scheuermann, Richard H.

2010-01-01

Clinical researchers need to share data to support scientific validation and information reuse, and to comply with a host of regulations and directives from funders. Various organizations are constructing informatics resources in the form of centralized databases to ensure widespread availability of data derived from sponsored research. The widespread use of such open databases is contingent on the protection of patient privacy. In this paper, we review several aspects of the privacy-related problems associated with data sharing for clinical research from technical and policy perspectives. We begin with a review of existing policies for secondary data sharing and privacy requirements in the context of data derived from research and clinical settings. In particular, we focus on policies specified by the U.S. National Institutes of Health and the Health Insurance Portability and Accountability Act and touch upon how these policies are related to current, as well as future, use of data stored in public database archives. Next, we address aspects of data privacy and “identifiability” from a more technical perspective, and review how biomedical databanks can be exploited and seemingly anonymous records can be “re-identified” using various resources without compromising or hacking into secure computer systems. We highlight which data features specified in clinical research data models are potentially vulnerable or exploitable. In the process, we recount a recent privacy-related concern associated with the publication of aggregate statistics from pooled genome-wide association studies that has had a significant impact on the data sharing policies of NIH-sponsored databanks. Finally, we conclude with a list of recommendations that cover various technical, legal, and policy mechanisms that open clinical databases can adopt to strengthen data privacy protections as they move toward wider deployment and adoption. PMID:20051768

Collaborative Data Publication Utilizing the Open Data Repository's Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R. M.; Downs, R. T.; Blake, D.; Fonda, M.; Dateo, C.; Pires, A.

2017-01-01

For small communities in multidisciplinary fields such as astrobiology, publishing and sharing data can be challenging. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, a number of pilot studies are being conducted to assess the needs of these research groups and to guide the software development so that it allows them to publish and share their data collaboratively.

Sensing Slow Mobility and Interesting Locations for Lombardy Region (italy): a Case Study Using Pointwise Geolocated Open Data

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Oxoli, D.; Zurbarán, M. A.

2016-06-01

During the past years Web 2.0 technologies have caused the emergence of platforms where users can share data related to their activities which in some cases are then publicly released with open licenses. Popular categories for this include community platforms where users can upload GPS tracks collected during slow travel activities (e.g. hiking, biking and horse riding) and platforms where users share their geolocated photos. However, due to the high heterogeneity of the information available on the Web, the sole use of these user-generated contents makes it an ambitious challenge to understand slow mobility flows as well as to detect the most visited locations in a region. Exploiting the available data on community sharing websites allows to collect near real-time open data streams and enables rigorous spatial-temporal analysis. This work presents an approach for collecting, unifying and analysing pointwise geolocated open data available from different sources with the aim of identifying the main locations and destinations of slow mobility activities. For this purpose, we collected pointwise open data from the Wikiloc platform, Twitter, Flickr and Foursquare. The analysis was confined to the data uploaded in Lombardy Region (Northern Italy) - corresponding to millions of pointwise data. Collected data was processed through the use of Free and Open Source Software (FOSS) in order to organize them into a suitable database. This allowed to run statistical analyses on data distribution in both time and space by enabling the detection of users' slow mobility preferences as well as places of interest at a regional scale.

Out of the archaeologist's desk drawer: communicating archaeological data online

NASA Astrophysics Data System (ADS)

Abate, D.; David, M.

2015-08-01

During archaeological field work a huge amount of data is collected, processed and elaborated for further studies and scientific publications. However, access and communication of linked data; associated tools for interrogation, analysis and sharing are often limited at the first stage of the archaeological research, mainly due to issues related to IPR. Information is often released months if not years after the fieldwork. Nowadays great deal of archaeological data is `born digital' in the field or lab. This means databases, pictures and 3D models of finds and excavation contexts could be available for public communication and sharing. Researchers usually restrict access to their data to a small group of people. It follows that data sharing is not so widespread among archaeologists, and dissemination of research is still mostly based on traditional pre-digital means like scientific papers, journal articles and books. This project has implemented a web approach for sharing and communication purposes, exploiting mainly open source technologies which allow a high level of interactivity. The case study presented is the newly Mithraeum excavated in Ostia Antica archaeological site in the framework of the Ostia Marina Project.

Stem cell research funding policies and dynamic innovation: a survey of open access and commercialization requirements.

PubMed

Lévesque, Maroussia; Kim, Jihyun Rosel; Isasi, Rosario; Knoppers, Bartha Maria; Plomer, Aurora; Joly, Yann

2014-08-01

This article compares and contrasts the pressures of both open access data sharing and commercialization policies in the context of publicly funded embryonic stem cell research (SCR). First, normative guidelines of international SCR organizations were examined. We then examined SCR funding guidelines and the project evaluation criteria of major funding organizations in the EU, the United Kingdom (UK), Spain, Canada and the United States. Our survey of policies revealed subtle pressures to commercialize research that include: increased funding availability for commercialization opportunities, assistance for obtaining intellectual property rights (IPRs) and legislation mandating commercialization. In lieu of open access models, funders are increasingly opting for limited sharing models or "protected commons" models that make the research available to researchers within the same region or those receiving the same funding. Meanwhile, there still is need for funding agencies to clarify and standardize terms such as "non-profit organizations" and "for-profit research," as more universities are pursuing for-profit or commercial opportunities.

Anatomy of open access publishing: a study of longitudinal development and internal structure

PubMed Central

2012-01-01

Background Open access (OA) is a revolutionary way of providing access to the scholarly journal literature made possible by the Internet. The primary aim of this study was to measure the volume of scientific articles published in full immediate OA journals from 2000 to 2011, while observing longitudinal internal shifts in the structure of OA publishing concerning revenue models, publisher types and relative distribution among scientific disciplines. The secondary aim was to measure the share of OA articles of all journal articles, including articles made OA by publishers with a delay and individual author-paid OA articles in subscription journals (hybrid OA), as these subsets of OA publishing have mostly been ignored in previous studies. Methods Stratified random sampling of journals in the Directory of Open Access Journals (n = 787) was performed. The annual publication volumes spanning 2000 to 2011 were retrieved from major publication indexes and through manual data collection. Results An estimated 340,000 articles were published by 6,713 full immediate OA journals during 2011. OA journals requiring article-processing charges have become increasingly common, publishing 166,700 articles in 2011 (49% of all OA articles). This growth is related to the growth of commercial publishers, who, despite only a marginal presence a decade ago, have grown to become key actors on the OA scene, responsible for 120,000 of the articles published in 2011. Publication volume has grown within all major scientific disciplines, however, biomedicine has seen a particularly rapid 16-fold growth between 2000 (7,400 articles) and 2011 (120,900 articles). Over the past decade, OA journal publishing has steadily increased its relative share of all scholarly journal articles by about 1% annually. Approximately 17% of the 1.66 million articles published during 2011 and indexed in the most comprehensive article-level index of scholarly articles (Scopus) are available OA through journal publishers, most articles immediately (12%) but some within 12 months of publication (5%). Conclusions OA journal publishing is disrupting the dominant subscription-based model of scientific publishing, having rapidly grown in relative annual share of published journal articles during the last decade. PMID:23088823

Sharing regulatory data as tools for strengthening health systems in the Region of the Americas.

PubMed

Sousa, Varley Dias; Ramalho, Pedro I; Silveira, Dâmaris

2016-05-01

Regulatory transparency is an imperative characteristic of a reliable National Regulatory Authority. In the region of the Americas, the process of building an open government is still fragile and fragmented across various Health Regulatory Agencies (HRAs) and Regional Reference Authorities (RRAs). This study assessed the transparency status of RRAs, focusing on various medicine life-cycle documents (the Medicine Dossier, Clinical Trial Report, and Inspection Report) as tools for strengthening health systems. Based on a narrative (nonsystematic) review of RRA regulatory transparency, transparency status was classified as one of two types: public disclosure of information (intra-agency data) and data- and work-sharing (inter-agency data). The risks/benefits of public disclosure of medicine-related information were assessed, taking into account 1) the involvement and roles of multiple stakeholders (health care professionals, regulators, industry, community, and academics) and 2) the protection of commercial and personal confidential data. Inter-agency data- and work-sharing was evaluated in the context of harmonization and cooperation projects that focus on regulatory convergence. Technical and practical steps for establishing an openness directive for the pharmaceutical regulatory environment are proposed to improve and strengthen health systems in the Americas. Addressing these challenges requires leadership from entities such as the Pan American Health Organization to steer and support collaborative regional alliances that advance the development and establishment of a trustworthy regulatory environment and a sustainable public health system in the Americas, using international successful initiatives as reference and taking into account the domestic characteristics and experiences of each individual country.

Safecast: How disaster led to empowerment of crowdsourced citizen science for radiation measurement and communication after Fukushima

NASA Astrophysics Data System (ADS)

Brown, Azby; Franken, Peter; Bonner, Sean; Moross, Joe; Dolezal, Nick

2016-04-01

Safecast, an international, volunteer-based organization devoted to monitoring and openly sharing information on environmental radiation and other pollutants, was initiated on March 12, 2011, one day following the start of the Fukushima Daichi Nuclear Power Plant accident, in response to the lack of publicly available, accurate and trustworthy information about the spread of radioactive fallout. Since its inception, Safecast has grown in size, scope, and geographical reach, as well as in the technical sophistication of its citizen-science-based hardware and software systems. The focus of the group's work is to provide citizens worldwide with the tools they need to inform themselves by gathering and sharing accurate environmental data, in an open and participatory fashion. This effort combines hardware and software design for original radiation and air quality measurement devices; visualizations which are made available online and as applications for mobile and desktop; strong public outreach and education programs; and open forums for discussion of radiation, air pollution, and other hazards. The Safecast system is agile and flexible in terms of development and deployment, and all designs, software programs, and data is provided on an open-source basis. In addition, because the group takes no public stance either for or against nuclear power, it has become an important unbiased source of information regarding radiation risks. The Fukushima Daichi NPP disaster provided a crucial opportunity to evaluate the state of preparation on the part the powerplant operator, government agencies, and international oversight bodies, to gather necessary information on radiation risks quickly and to share it both with emergency responders and the general public. The inadequacy of this preparation and the chaotic nature of inter-agency and inter-governmental communication has been well noted in several official reports on the disaster, including those issued by The National Diet of Japan Fukushima Nuclear Accident Independent Investigation Commission (NAIIC) and by the International Atomic Energy Agency (IAEA). During the initial weeks of the disaster in particular, citizens were given little actionable information concerning actual radiation levels, and what was presented both by official spokespersons and in the media was often incomplete and /or contradictory. Many citizens stepped in to fill the gaps, share information and technical knowledge, and provide credible independent alternatives to official information, and Safecast has been held up as the most successful and noteworthy example. The experience of the Safecast project provides an extremely instructive opportunity to evaluate the potential for citizen scientists to make crucial public contributions in emergency situations as well as on a longterm basis, and to help formulate guidelines for the most mutually beneficial relationships between citizens' groups and government. This paper will describe the methodology and toolsets Safecast has developed and deployed, as well as a summary of the key results obtained to date, and lessons learned.

Sharing Lessons-Learned on Effective Open Data, Open-Source Practices from OpenAQ, a Global Open Air Quality Community.

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.

2017-12-01

Increasingly, open data, open-source projects are unearthing rich datasets and tools, previously impossible for more traditional avenues to generate. These projects are possible, in part, because of the emergence of online collaborative and code-sharing tools, decreasing costs of cloud-based services to fetch, store, and serve data, and increasing interest of individuals to contribute their time and skills to 'open projects.' While such projects have generated palpable enthusiasm from many sectors, many of these projects face uncharted paths for sustainability, visibility, and acceptance. Our project, OpenAQ, is an example of an open-source, open data community that is currently forging its own uncharted path. OpenAQ is an open air quality data platform that aggregates and universally formats government and research-grade air quality data from 50 countries across the world. To date, we make available more than 76 million air quality (PM2.5, PM10, SO2, NO2, O3, CO and black carbon) data points through an open Application Programming Interface (API) and a user-customizable download interface at https://openaq.org. The goal of the platform is to enable an ecosystem of users to advance air pollution efforts from science to policy to the private sector. The platform is also an open-source project (https://github.com/openaq) and has only been made possible through the coding and data contributions of individuals around the world. In our first two years of existence, we have seen requests for data to our API skyrocket to more than 6 million datapoints per month, and use-cases as varied as ingesting data aggregated from our system into real-time models of wildfires to building open-source statistical packages (e.g. ropenaq and py-openaq) on top of the platform to creating public-friendly apps and chatbots. We will share a whirl-wind trip through our evolution and the many lessons learned so far related to platform structure, community engagement, organizational model type and sustainability.

The Devil's in the Details - Lessons in Operationalising Data Sharing and Credit in the Geosciences

NASA Astrophysics Data System (ADS)

Callaghan, S.

2017-12-01

There are many drivers for sharing and opening data, and the consensus opinion is gradually becoming that sharing data is the right thing to do, as is providing appropriate credit and attribution for those who put the effort in to making their data open and usable. The idea of data citation is now well defined in principle. Unsurprisingly, when trying to implement principles, edge cases rapidly appear, resulting in extra thinking and complications. Citation for journal papers is well established and understood, and most researchers have a good understanding of what is, and is not, a publication. Datasets can be considered as a "special type of paper" - but only a small proportion of datasets can actually fit into "paper-like" publication processes. The vast majority of datasets are too big, too complicated, or are being continually modified and/or updated. Data publication (piggy-backing as it does on academic publication to obtain credit for data producers) is only one metaphor that can be used for data - different metaphors can provide other routes for providing credit for data producers. Explaining those metaphors, and how they apply to data and provide credit for producers, can be difficult to those who until now have solely judged research productivity on the numbers of papers produced in high impact factor journals. Different research domains seek to address these issues in different ways, and it is important to recognise that there is no "one size fits all" approach that will cover all disciplines from astronomy to zoology. Similarly, the amount of journal publications are increasing dramatically, resulting in a peer-review system that is creaking at the seams. Adding peer review of data (in order to quantify the "quality" of the data) to the task list of already over-burdened volunteer reviewers will result in less reviewers being willing to take on the task, or reviewers putting less effort into their reviews. This presentation will consist of a series of "lessons learned" from the point of view of the author, who started as a researcher creating long term datasets, was "encouraged" to share the data (and as a result got scooped); and then moved into data management, data citation and publication as part of a discipline-specific data repository, while acting as editor-in-chief of an academic journal, the Data Science Journal.

Strategies for Positive Engagement with the Public in the Geosciences

NASA Astrophysics Data System (ADS)

Johnson, R.

2017-12-01

Strategies for engaging with the public about the geosciences are abundant. Whether engaging in these endeavors through professional opportunties associated with their research activities, or in their personal lives, scientists have numerous ways in which they can share the science they care so much about with the public. While participating in tried and true well-designed "outreach" activities associated with research projects has become a classic approach over the past 20 years, this is not the only way to reach "the public". Indeed, as we have recently learned, such approaches depend on the availability of funding for research projects and outreach components. With potentially large research funding cuts looming at federal agencies, and the future of "education and outreach" associated with funded projects in question, we need to think hard about approaches that are not so closely tied to the federal government. Engaging with the public through involvement in the K-12 educational arena provides another avenue to reach people - not only students and teachers, but also the parents of the students. Furthermore, engagement in local communities - on school boards as a member or regular attendee, in civic groups, in museums on their boards or as volunteers, in congregations, and in more informal local associations are additional opportunities. Indeed, one of the most important resources we have, as geoscientists, is ourselves. While many of us may be involved with groups in our communities, our willingness to openly talk about our science in ways that are accessible to members of the public is less clear. Indeed, some of us may intentionally avoid discussing our research with neighbors and friends for any number of reasons. But by doing so, we have effectively allowed scientists to be framed as "the other" - rather than the neighbor with a kid on the soccer team who occasionally hosts a sleepover for the team, or who really knows how to grill a nice steak, or who shares a ride to yoga class. A fundamental aspect of effective communication is to identify and take advantage of common ground shared with the audience, and to build on this shared understanding. And in all communication, avoiding condescension and employing common courtesy helps to keep minds open.

Mapping the hinterland: Data issues in open science.

PubMed

Grand, Ann; Wilkinson, Clare; Bultitude, Karen; Winfield, Alan F T

2016-01-01

Open science is a practice in which the scientific process is shared completely and in real time. It offers the potential to support information flow, collaboration and dialogue among professional and non-professional participants. Using semi-structured interviews and case studies, this research investigated the relationship between open science and public engagement. This article concentrates on three particular areas of concern that emerged: first, how to effectively contextualise and narrate information to render it accessible, as opposed to simply available; second, concerns about data quantity and quality; and third, concerns about the skills required for effective contextualisation, mapping and interpretation of information. © The Author(s) 2014.

Mapping the hinterland: Data issues in open science

PubMed Central

Grand, Ann; Wilkinson, Clare; Bultitude, Karen; Winfield, Alan F. T.

2016-01-01

Open science is a practice in which the scientific process is shared completely and in real time. It offers the potential to support information flow, collaboration and dialogue among professional and non-professional participants. Using semi-structured interviews and case studies, this research investigated the relationship between open science and public engagement. This article concentrates on three particular areas of concern that emerged: first, how to effectively contextualise and narrate information to render it accessible, as opposed to simply available; second, concerns about data quantity and quality; and third, concerns about the skills required for effective contextualisation, mapping and interpretation of information. PMID:24769860

The OpenPlanetary initiative

NASA Astrophysics Data System (ADS)

Manaud, Nicolas; Rossi, Angelo Pio; Hare, Trent; Aye, Michael; Galluzzi, Valentina; van Gasselt, Stephan; Martinez, Santa; McAuliffe, Jonathan; Million, Chase; Nass, Andrea; Zinzi, Angelo

2016-10-01

"Open" has become attached to several concepts: science, data, and software are some of the most obvious. It is already common practice within the planetary science community to share spacecraft missions data freely and openly [1]. However, this is not historically the case for software tools, source code, and derived data sets, which are often reproduced independently by multiple individuals and groups. Sharing data, tools and overall knowledge would increase scientific return and benefits [e.g. 2], and recent projects and initiatives are helping toward this goal [e.g. 3,4,5,6].OpenPlanetary is a bottom-up initiative to address the need of the planetary science community for sharing ideas and collaborating on common planetary research and data analysis problems, new challenges, and opportunities. It started from an initial participants effort to stay connected and share information related to and beyond the ESA's first Planetary GIS Workshop [7]. It then continued during the 2nd (US) Planetary Data Workshop [8], and aggregated more people.Our objective is to build an online distributed framework enabling open collaborations within the planetary science community. We aim to co-create, curate and publish resource materials and data sets; to organise online events, to support community-based projects development; and to offer a real-time communication channel at and between conferences and workshops.We will present our current framework and resources, developing projects and ideas, and solicit for feedback and participation. OpenPlanetary is intended for research and education professionals: scientists, engineers, designers, teachers and students, as well as the general public that includes enthusiasts and citizen scientists. All are welcome to join and contribute at openplanetary.co[1] International Planetary Data Alliance, planetarydata.org. [2] Nosek et al (2015), dx.doi.org/10.1126/science.aab2374. [3] Erard S. et al. (2016), EGU2016-17527. [4] Proposal for a PDS Software Node, bit.ly/PDS_SN. [5] Zinzi et al. (2016), dx.doi.org/10.1016/j.ascom.2016.02.006. [6] Open Universe initiave, bit.ly/OpenUniverse, [7] Manaud N. et al. (2016), LPSC47-1387. [8] bit.ly/PlanetaryDataWorkshops

Troubleshooting Public Data Archiving: Suggestions to Increase Participation

PubMed Central

Roche, Dominique G.; Lanfear, Robert; Binning, Sandra A.; Haff, Tonya M.; Schwanz, Lisa E.; Cain, Kristal E.; Kokko, Hanna; Jennions, Michael D.; Kruuk, Loeske E. B.

2014-01-01

An increasing number of publishers and funding agencies require public data archiving (PDA) in open-access databases. PDA has obvious group benefits for the scientific community, but many researchers are reluctant to share their data publicly because of real or perceived individual costs. Improving participation in PDA will require lowering costs and/or increasing benefits for primary data collectors. Small, simple changes can enhance existing measures to ensure that more scientific data are properly archived and made publicly available: (1) facilitate more flexible embargoes on archived data, (2) encourage communication between data generators and re-users, (3) disclose data re-use ethics, and (4) encourage increased recognition of publicly archived data. PMID:24492920

Events Calendar: Smithsonian Marine Ecosystems Exhibit: Smithsonian Marine

Science.gov Websites

Tours FREE | Behind-the-Scenes Tour of the Research Station tour participant Third Thursday of each month at 2PM - Free. Registration is required. Once a month we open our doors to the public to share scenes tours. All activities are included with the price of admission. FREE DAY | First Tuesday of each

75 FR 69130 - Proposed Extension of Information Collection Request Submitted for Public Comment; Prohibited...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-10

.... Description: Without the relief provided by this exemption, an open-end mutual fund would be unable to sell... investment advisor for the mutual fund. As a result, plans would be compelled to liquidate their existing... disclosure requirements. The first requires at the time of the purchase or sale of such mutual fund shares...

Cohesion, Sharing and Integration? Migrant Languages and Cultural Spaces in Northern Ireland's Urban Environment

ERIC Educational Resources Information Center

McDermott, Philip

2012-01-01

This article investigates the position of migrant languages in Northern Ireland's two largest cities, Belfast and Derry/Londonderry. The paper comments on how deliberations around public policy objectives in a post-conflict era have led to a broader understanding of cultural identity and consequently to an "opening-up" of urban spaces…

Cloud-based Jupyter Notebooks for Water Data Analysis

NASA Astrophysics Data System (ADS)

Castronova, A. M.; Brazil, L.; Seul, M.

2017-12-01

The development and adoption of technologies by the water science community to improve our ability to openly collaborate and share workflows will have a transformative impact on how we address the challenges associated with collaborative and reproducible scientific research. Jupyter notebooks offer one solution by providing an open-source platform for creating metadata-rich toolchains for modeling and data analysis applications. Adoption of this technology within the water sciences, coupled with publicly available datasets from agencies such as USGS, NASA, and EPA enables researchers to easily prototype and execute data intensive toolchains. Moreover, implementing this software stack in a cloud-based environment extends its native functionality to provide researchers a mechanism to build and execute toolchains that are too large or computationally demanding for typical desktop computers. Additionally, this cloud-based solution enables scientists to disseminate data processing routines alongside journal publications in an effort to support reproducibility. For example, these data collection and analysis toolchains can be shared, archived, and published using the HydroShare platform or downloaded and executed locally to reproduce scientific analysis. This work presents the design and implementation of a cloud-based Jupyter environment and its application for collecting, aggregating, and munging various datasets in a transparent, sharable, and self-documented manner. The goals of this work are to establish a free and open source platform for domain scientists to (1) conduct data intensive and computationally intensive collaborative research, (2) utilize high performance libraries, models, and routines within a pre-configured cloud environment, and (3) enable dissemination of research products. This presentation will discuss recent efforts towards achieving these goals, and describe the architectural design of the notebook server in an effort to support collaborative and reproducible science.

Protecting the pipeline of science: openness, scientific methods and the lessons from ticagrelor and the PLATO trial.

PubMed

Coats, Andrew J Stewart; Nijjer, Sukhjinder S; Francis, Darrel P

2014-10-20

Ticagrelor, a potent antiplatelet, has been shown to be beneficial in patients with acute coronary syndromes in a randomised controlled trial published in a highly ranked peer reviewed journal. Accordingly it has entered guidelines and has been approved for clinical use by authorities. However, there remains a controversy regarding aspects of the PLATO trial, which are not immediately apparent from the peer-reviewed publications. A number of publications have sought to highlight potential discrepancies, using data available in publicly published documents from the US Food and Drug Administration (FDA) leading to disagreement regarding the value of open science and data sharing. We reflect upon potential sources of bias present in even rigorously performed randomised controlled trials, on whether peer review can establish the presence of bias and the need to constantly challenge and question even accepted data. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

First Universities Allied for Essential Medicines (UAEM) Neglected Diseases and Innovation Symposium.

PubMed

Musselwhite, Laura W; Maciag, Karolina; Lankowski, Alex; Gretes, Michael C; Wellems, Thomas E; Tavera, Gloria; Goulding, Rebecca E; Guillen, Ethan

2012-01-01

Universities Allied for Essential Medicines organized its first Neglected Diseases and Innovation Symposium to address expanding roles of public sector research institutions in innovation in research and development of biomedical technologies for treatment of diseases, particularly neglected tropical diseases. Universities and other public research institutions are increasingly integrated into the pharmaceutical innovation system. Academic entities now routinely undertake robust high-throughput screening and medicinal chemistry research programs to identify lead compounds for small molecule drugs and novel drug targets. Furthermore, product development partnerships are emerging between academic institutions, non-profit entities, and biotechnology and pharmaceutical companies to create diagnostics, therapies, and vaccines for diseases of the poor. With not for profit mission statements, open access publishing standards, open source platforms for data sharing and collaboration, and a shift in focus to more translational research, universities and other public research institutions are well-placed to accelerate development of medical technologies, particularly for neglected tropical diseases.

Public Lab: Community-Based Approaches to Urban and Environmental Health and Justice.

PubMed

Rey-Mazón, Pablo; Keysar, Hagit; Dosemagen, Shannon; D'Ignazio, Catherine; Blair, Don

2018-06-01

This paper explores three cases of Do-It-Yourself, open-source technologies developed within the diverse array of topics and themes in the communities around the Public Laboratory for Open Technology and Science (Public Lab). These cases focus on aerial mapping, water quality monitoring and civic science practices. The techniques discussed have in common the use of accessible, community-built technologies for acquiring data. They are also concerned with embedding collaborative and open source principles into the objects, tools, social formations and data sharing practices that emerge from these inquiries. The focus is on developing processes of collaborative design and experimentation through material engagement with technology and issues of concern. Problem-solving, here, is a tactic, while the strategy is an ongoing engagement with the problem of participation in its technological, social and political dimensions especially considering the increasing centralization and specialization of scientific and technological expertise. The authors also discuss and reflect on the Public Lab's approach to civic science in light of ideas and practices of citizen/civic veillance, or "sousveillance", by emphasizing people before data, and by investigating the new ways of seeing and doing that this shift in perspective might provide.

Who Owns the Data? Open Data for Healthcare

PubMed Central

Kostkova, Patty; Brewer, Helen; de Lusignan, Simon; Fottrell, Edward; Goldacre, Ben; Hart, Graham; Koczan, Phil; Knight, Peter; Marsolier, Corinne; McKendry, Rachel A.; Ross, Emma; Sasse, Angela; Sullivan, Ralph; Chaytor, Sarah; Stevenson, Olivia; Velho, Raquel; Tooke, John

2016-01-01

Research on large shared medical datasets and data-driven research are gaining fast momentum and provide major opportunities for improving health systems as well as individual care. Such open data can shed light on the causes of disease and effects of treatment, including adverse reactions side-effects of treatments, while also facilitating analyses tailored to an individual’s characteristics, known as personalized or “stratified medicine.” Developments, such as crowdsourcing, participatory surveillance, and individuals pledging to become “data donors” and the “quantified self” movement (where citizens share data through mobile device-connected technologies), have great potential to contribute to our knowledge of disease, improving diagnostics, and delivery of ­healthcare and treatment. There is not only a great potential but also major concerns over privacy, confidentiality, and control of data about individuals once it is shared. Issues, such as user trust, data privacy, transparency over the control of data ownership, and the implications of data analytics for personal privacy with potentially intrusive inferences, are becoming increasingly scrutinized at national and international levels. This can be seen in the recent backlash over the proposed implementation of care.data, which enables individuals’ NHS data to be linked, retained, and shared for other uses, such as research and, more controversially, with businesses for commercial exploitation. By way of contrast, through increasing popularity of social media, GPS-enabled mobile apps and tracking/wearable devices, the IT industry and MedTech giants are pursuing new projects without clear public and policy discussion about ownership and responsibility for user-generated data. In the absence of transparent regulation, this paper addresses the opportunities of Big Data in healthcare together with issues of responsibility and accountability. It also aims to pave the way for public policy to support a balanced agenda that safeguards personal information while enabling the use of data to improve public health. PMID:26925395

Who Owns the Data? Open Data for Healthcare.

PubMed

Kostkova, Patty; Brewer, Helen; de Lusignan, Simon; Fottrell, Edward; Goldacre, Ben; Hart, Graham; Koczan, Phil; Knight, Peter; Marsolier, Corinne; McKendry, Rachel A; Ross, Emma; Sasse, Angela; Sullivan, Ralph; Chaytor, Sarah; Stevenson, Olivia; Velho, Raquel; Tooke, John

2016-01-01

Research on large shared medical datasets and data-driven research are gaining fast momentum and provide major opportunities for improving health systems as well as individual care. Such open data can shed light on the causes of disease and effects of treatment, including adverse reactions side-effects of treatments, while also facilitating analyses tailored to an individual's characteristics, known as personalized or "stratified medicine." Developments, such as crowdsourcing, participatory surveillance, and individuals pledging to become "data donors" and the "quantified self" movement (where citizens share data through mobile device-connected technologies), have great potential to contribute to our knowledge of disease, improving diagnostics, and delivery of -healthcare and treatment. There is not only a great potential but also major concerns over privacy, confidentiality, and control of data about individuals once it is shared. Issues, such as user trust, data privacy, transparency over the control of data ownership, and the implications of data analytics for personal privacy with potentially intrusive inferences, are becoming increasingly scrutinized at national and international levels. This can be seen in the recent backlash over the proposed implementation of care.data, which enables individuals' NHS data to be linked, retained, and shared for other uses, such as research and, more controversially, with businesses for commercial exploitation. By way of contrast, through increasing popularity of social media, GPS-enabled mobile apps and tracking/wearable devices, the IT industry and MedTech giants are pursuing new projects without clear public and policy discussion about ownership and responsibility for user-generated data. In the absence of transparent regulation, this paper addresses the opportunities of Big Data in healthcare together with issues of responsibility and accountability. It also aims to pave the way for public policy to support a balanced agenda that safeguards personal information while enabling the use of data to improve public health.

A study of institutional spending on open access publication fees in Germany.

PubMed

Jahn, Najko; Tullney, Marco

2016-01-01

Publication fees as a revenue source for open access publishing hold a prominent place on the agendas of researchers, policy makers, and academic publishers. This study contributes to the evolving empirical basis for funding these charges and examines how much German universities and research organisations spent on open access publication fees. Using self-reported cost data from the Open APC initiative, the analysis focused on the amount that was being spent on publication fees, and compared these expenditure with data from related Austrian (FWF) and UK (Wellcome Trust, Jisc) initiatives, in terms of both size and the proportion of articles being published in fully and hybrid open access journals. We also investigated how thoroughly self-reported articles were indexed in Crossref, a DOI minting agency for scholarly literature, and analysed how the institutional spending was distributed across publishers and journal titles. According to self-reported data from 30 German universities and research organisations between 2005 and 2015, expenditures on open access publication fees increased over the years in Germany and amounted to € 9,627,537 for 7,417 open access journal articles. The average payment was € 1,298, and the median was € 1,231. A total of 94% of the total article volume included in the study was supported in accordance with the price cap of € 2,000, a limit imposed by the Deutsche Forschungsgemeinschaft (DFG) as part of its funding activities for open access funding at German universities. Expenditures varied considerably at the institutional level. There were also differences in how much the institutions spent per journal and publisher. These differences reflect, at least in part, the varying pricing schemes in place including discounted publication fees. With an indexing coverage of 99%, Crossref thoroughly indexed the open access journals articles included in the study. A comparison with the related openly available cost data from Austria and the UK revealed that German universities and research organisations primarily funded articles in fully open access journals. By contrast, articles in hybrid journal accounted for the largest share of spending according to the Austrian and UK data. Fees paid for hybrid journals were on average more expensive than those paid for fully open access journals.

A study of institutional spending on open access publication fees in Germany

PubMed Central

Tullney, Marco

2016-01-01

Publication fees as a revenue source for open access publishing hold a prominent place on the agendas of researchers, policy makers, and academic publishers. This study contributes to the evolving empirical basis for funding these charges and examines how much German universities and research organisations spent on open access publication fees. Using self-reported cost data from the Open APC initiative, the analysis focused on the amount that was being spent on publication fees, and compared these expenditure with data from related Austrian (FWF) and UK (Wellcome Trust, Jisc) initiatives, in terms of both size and the proportion of articles being published in fully and hybrid open access journals. We also investigated how thoroughly self-reported articles were indexed in Crossref, a DOI minting agency for scholarly literature, and analysed how the institutional spending was distributed across publishers and journal titles. According to self-reported data from 30 German universities and research organisations between 2005 and 2015, expenditures on open access publication fees increased over the years in Germany and amounted to € 9,627,537 for 7,417 open access journal articles. The average payment was € 1,298, and the median was € 1,231. A total of 94% of the total article volume included in the study was supported in accordance with the price cap of € 2,000, a limit imposed by the Deutsche Forschungsgemeinschaft (DFG) as part of its funding activities for open access funding at German universities. Expenditures varied considerably at the institutional level. There were also differences in how much the institutions spent per journal and publisher. These differences reflect, at least in part, the varying pricing schemes in place including discounted publication fees. With an indexing coverage of 99%, Crossref thoroughly indexed the open access journals articles included in the study. A comparison with the related openly available cost data from Austria and the UK revealed that German universities and research organisations primarily funded articles in fully open access journals. By contrast, articles in hybrid journal accounted for the largest share of spending according to the Austrian and UK data. Fees paid for hybrid journals were on average more expensive than those paid for fully open access journals. PMID:27602289

Claiming justice: knowing mental illness in the public art of Anna Schuleit's 'Habeas Corpus' and 'Bloom'.

PubMed

Bell, Susan E

2011-05-01

This study investigates two public art performances by artist Anna Schuleit in the early 2000s commemorating the life and history of two state hospitals ('asylums') in Massachusetts and the people who built, worked, and were patients in them. Public art is made for and sited in the public domain, outside, freely accessible, frequently collaborative, and often ephemeral. This study addresses a series of questions: What can public art 'do' for understanding mental illness? What use is a public art project for those living with (and caring for those who live with) mental illness? How can a public work of art sustain and portray meaning in an expressive way, open up a shared discursive space, and demand witness through embodiment?

Open semantic annotation of scientific publications using DOMEO.

PubMed

Ciccarese, Paolo; Ocana, Marco; Clark, Tim

2012-04-24

Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies.Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF's next full release.Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.

Open semantic annotation of scientific publications using DOMEO

PubMed Central

2012-01-01

Background Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Methods The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies. Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. Results We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF’s next full release. Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework. PMID:22541592

The impact of the cigarette market opening in Taiwan

PubMed Central

Wen, C; Cheng, T; Eriksen, M; Tsai, S; Hsu, C

2005-01-01

Objective: To assess the effect of the opening of the Taiwanese cigarette market on cigarette consumption, changes in market share, and the effects on tobacco control efforts. Methods: With the use of key word "Taiwan", the Legacy Tobacco Documents Library of the University of California, San Francisco, was searched for internal documents related to smuggling activities, promotion of light cigarettes, and market share analyses in Taiwan. Age adjusted smoking rates and cigarette and betel quid consumption before and after market opening were compared. Results: By 2000, the market share of imported cigarettes increased from less than 2% in 1986 to nearly 50%, and per capita cigarette consumption increased 15% following market opening. Because of the sharp increase in smuggling, with contraband cigarettes being as popular as legal imports, and the rapid proliferation of retail outlets, such as betel quid stalls, the market penetration by foreign tobacco companies was greater in Taiwan than among the other Super 301 Asian countries. Aggressive cigarette marketing strategies were associated with a 6% increase in adult male smoking prevalence, and with a 13% increase in the youth rate, within three years after market opening. The market opening also had an incidental effect on increasing the popularity of betel quid. Betel quid chewing has since become a major public health problem in Taiwan. Conclusion: The opening of the cigarette market in 1987 had a long lasting impact on Taiwan. It increased smoking prevalence and the market has become dominated by foreign companies. The seriousness of smuggling and its associated loss of revenue by the government, the extent of increased youth smoking and its associated future health care costs, and the increased use of betel quid and the associated doubling of oral cancer mortality rates each pose significant problems to Taiwan. However, the market opening galvanised anti-smoking sentiment and forced the government to initiate and intensify a series of tobacco control efforts. PMID:15923448

The impact of the cigarette market opening in Taiwan.

PubMed

Wen, C P; Cheng, T Y; Eriksen, M P; Tsai, S P; Hsu, C C

2005-06-01

To assess the effect of the opening of the Taiwanese cigarette market on cigarette consumption, changes in market share, and the effects on tobacco control efforts. With the use of key word "Taiwan", the Legacy Tobacco Documents Library of the University of California, San Francisco, was searched for internal documents related to smuggling activities, promotion of light cigarettes, and market share analyses in Taiwan. Age adjusted smoking rates and cigarette and betel quid consumption before and after market opening were compared. By 2000, the market share of imported cigarettes increased from less than 2% in 1986 to nearly 50%, and per capita cigarette consumption increased 15% following market opening. Because of the sharp increase in smuggling, with contraband cigarettes being as popular as legal imports, and the rapid proliferation of retail outlets, such as betel quid stalls, the market penetration by foreign tobacco companies was greater in Taiwan than among the other Super 301 Asian countries. Aggressive cigarette marketing strategies were associated with a 6% increase in adult male smoking prevalence, and with a 13% increase in the youth rate, within three years after market opening. The market opening also had an incidental effect on increasing the popularity of betel quid. Betel quid chewing has since become a major public health problem in Taiwan. The opening of the cigarette market in 1987 had a long lasting impact on Taiwan. It increased smoking prevalence and the market has become dominated by foreign companies. The seriousness of smuggling and its associated loss of revenue by the government, the extent of increased youth smoking and its associated future health care costs, and the increased use of betel quid and the associated doubling of oral cancer mortality rates each pose significant problems to Taiwan. However, the market opening galvanised anti-smoking sentiment and forced the government to initiate and intensify a series of tobacco control efforts.

YouTube Professors: Scholars as Online Video Stars

ERIC Educational Resources Information Center

Young, Jeffrey R.

2008-01-01

This article takes a look at the rising popularity of professors as the latest YouTube stars. The popularity of their appearances on YouTube and other video-sharing sites is making it possible for classrooms to be opened up and making teaching--which once took place behind closed doors--a more public art. Web video has generated a new form of…

The Academic Ethics of Open Access to Research and Scholarship

ERIC Educational Resources Information Center

Willinsky, John; Alperin, Juan Pablo

2011-01-01

In this article, we present the case for regarding the principles by which scholarly publications are disseminated and shared as a matter of academic ethics. The ethics of access have to do with recognizing people's right to know what is known, as well as the value to humanity of having one of its best forms of arriving at knowledge as widely…

New York City's Smaller Schools Movement: Bronx Lab School, New York City Public Schools

ERIC Educational Resources Information Center

Schachter, Ron

2009-01-01

This article profiles the 5-year-old Bronx Lab School, a shining achievement in Chancellor Joel Klein's aggressive program of creating new, small schools, almost 400 of which have opened over the past seven years. It's unprecedented anywhere in America. Bronx Lab--which shares the building with similarly sized schools focused on areas such as…

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.

PubMed

Taboada, Eduardo N; Graham, Morag R; Carriço, João A; Van Domselaar, Gary

2017-01-01

Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.

Publishing descriptions of non-public clinical datasets: proposed guidance for researchers, repositories, editors and funding organisations.

PubMed

Hrynaszkiewicz, Iain; Khodiyar, Varsha; Hufton, Andrew L; Sansone, Susanna-Assunta

2016-01-01

Sharing of experimental clinical research data usually happens between individuals or research groups rather than via public repositories, in part due to the need to protect research participant privacy. This approach to data sharing makes it difficult to connect journal articles with their underlying datasets and is often insufficient for ensuring access to data in the long term. Voluntary data sharing services such as the Yale Open Data Access (YODA) and Clinical Study Data Request (CSDR) projects have increased accessibility to clinical datasets for secondary uses while protecting patient privacy and the legitimacy of secondary analyses but these resources are generally disconnected from journal articles-where researchers typically search for reliable information to inform future research. New scholarly journal and article types dedicated to increasing accessibility of research data have emerged in recent years and, in general, journals are developing stronger links with data repositories. There is a need for increased collaboration between journals, data repositories, researchers, funders, and voluntary data sharing services to increase the visibility and reliability of clinical research. Using the journal Scientific Data as a case study, we propose and show examples of changes to the format and peer-review process for journal articles to more robustly link them to data that are only available on request. We also propose additional features for data repositories to better accommodate non-public clinical datasets, including Data Use Agreements (DUAs).

The Open Faculty: To Share or Not to Share--Is That the Question?

ERIC Educational Resources Information Center

Andersen, Maria H.

2010-01-01

In this article, the author shares her view of "open faculty." To truly understand "open faculty," one needs to step back to a time before the Internet, before it was so easy and inexpensive to share anything and everything. In the pre-Internet era, faculty fell on the same continuum between those who freely share ideas and resources and those who…

Enabling the sharing of neuroimaging data through well-defined intermediate levels of visibility.

PubMed

Smith, Kenneth; Jajodia, Sushil; Swarup, Vipin; Hoyt, Jeffrey; Hamilton, Gail; Faatz, Donald; Cornett, Todd

2004-08-01

The sharing of neuroimagery data offers great benefits to science, however, data owners sharing their data face substantial custodial responsibilities, such as ensuring data sets are correctly interpreted in their new shared context, protecting the identity and privacy of human research participants, and safeguarding the understood order of use. Given choices of sharing widely or not at all, the result will often be no sharing, due to the inability of data owners to control their exposure to the risks associated with data sharing. In this context, data sharing is enabled by providing data owners with well-defined intermediate levels of data visibility, progressing incrementally toward public visibility. In this paper, we define a novel and general data sharing model, Structured Sharing Communities (SSC), meeting this requirement. Arbitrary visibility levels representing collaborative agreements, consortium memberships, research organizations, and other affiliations are structured into a policy space through explicit paths of permissible information flow. Operations enable users and applications to manage the visibility of data and enforce access permissions and restrictions. We show how a policy space can be implemented in realistic neuroinformatic architectures with acceptable assurance of correctness, and briefly describe an open source implementation effort.

Intelligent transportation systems and intermodal freight transportation. Final report, May-December 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aylward, A.D.

1996-12-01

This paper describes the various advanced technologies already in use in the intermodal freight transportation industry and addresses the opportunity for improved communication between the public and private sector regarding technology applications to the freight transportation system that could enhance the capacity of the system as a whole. The current public interest in freight transportation policy creates an opportunity to develop a shared vision of the future needs of international intermodal freight transportation in the United States. The Federal government can impact this vision by taking action in the following areas: Provide Infrastructure Funding to Support Efficiency and Global Competitiveness;more » Support Regional and Corridor Efforts; Understand the Freight Sector and Develop a Shared Vision of Technology Benefits; Lead Transportation Technology Efforts of Federal Agencies; and Maintain Commitment to Open ITS Architecture.« less

COINSTAC: A Privacy Enabled Model and Prototype for Leveraging and Processing Decentralized Brain Imaging Data.

PubMed

Plis, Sergey M; Sarwate, Anand D; Wood, Dylan; Dieringer, Christopher; Landis, Drew; Reed, Cory; Panta, Sandeep R; Turner, Jessica A; Shoemaker, Jody M; Carter, Kim W; Thompson, Paul; Hutchison, Kent; Calhoun, Vince D

2016-01-01

The field of neuroimaging has embraced the need for sharing and collaboration. Data sharing mandates from public funding agencies and major journal publishers have spurred the development of data repositories and neuroinformatics consortia. However, efficient and effective data sharing still faces several hurdles. For example, open data sharing is on the rise but is not suitable for sensitive data that are not easily shared, such as genetics. Current approaches can be cumbersome (such as negotiating multiple data sharing agreements). There are also significant data transfer, organization and computational challenges. Centralized repositories only partially address the issues. We propose a dynamic, decentralized platform for large scale analyses called the Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC). The COINSTAC solution can include data missing from central repositories, allows pooling of both open and "closed" repositories by developing privacy-preserving versions of widely-used algorithms, and incorporates the tools within an easy-to-use platform enabling distributed computation. We present an initial prototype system which we demonstrate on two multi-site data sets, without aggregating the data. In addition, by iterating across sites, the COINSTAC model enables meta-analytic solutions to converge to "pooled-data" solutions (i.e., as if the entire data were in hand). More advanced approaches such as feature generation, matrix factorization models, and preprocessing can be incorporated into such a model. In sum, COINSTAC enables access to the many currently unavailable data sets, a user friendly privacy enabled interface for decentralized analysis, and a powerful solution that complements existing data sharing solutions.

COINSTAC: A Privacy Enabled Model and Prototype for Leveraging and Processing Decentralized Brain Imaging Data

PubMed Central

Plis, Sergey M.; Sarwate, Anand D.; Wood, Dylan; Dieringer, Christopher; Landis, Drew; Reed, Cory; Panta, Sandeep R.; Turner, Jessica A.; Shoemaker, Jody M.; Carter, Kim W.; Thompson, Paul; Hutchison, Kent; Calhoun, Vince D.

2016-01-01

The field of neuroimaging has embraced the need for sharing and collaboration. Data sharing mandates from public funding agencies and major journal publishers have spurred the development of data repositories and neuroinformatics consortia. However, efficient and effective data sharing still faces several hurdles. For example, open data sharing is on the rise but is not suitable for sensitive data that are not easily shared, such as genetics. Current approaches can be cumbersome (such as negotiating multiple data sharing agreements). There are also significant data transfer, organization and computational challenges. Centralized repositories only partially address the issues. We propose a dynamic, decentralized platform for large scale analyses called the Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC). The COINSTAC solution can include data missing from central repositories, allows pooling of both open and “closed” repositories by developing privacy-preserving versions of widely-used algorithms, and incorporates the tools within an easy-to-use platform enabling distributed computation. We present an initial prototype system which we demonstrate on two multi-site data sets, without aggregating the data. In addition, by iterating across sites, the COINSTAC model enables meta-analytic solutions to converge to “pooled-data” solutions (i.e., as if the entire data were in hand). More advanced approaches such as feature generation, matrix factorization models, and preprocessing can be incorporated into such a model. In sum, COINSTAC enables access to the many currently unavailable data sets, a user friendly privacy enabled interface for decentralized analysis, and a powerful solution that complements existing data sharing solutions. PMID:27594820

The Open Data Repositorys Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Downs, R. T.; Blake, D.; Bristow, T.; Fonda, M.; Pires, A.

2015-01-01

Data management and data publication are becoming increasingly important components of researcher's workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity.

Health Information-Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease.

PubMed

Pesälä, Samuli; Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-11-06

People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician's Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs' queries, and what causes possible differences in behavior. The aim of our study was to evaluate how the general public's and HCPs' information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public's information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician's Databases, were used. We compared the general public's article openings on Lyme disease from Health Library to HCPs' article openings on Lyme disease from Physician's Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Both databases, Health Library and Physician's Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Lyme disease-related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public's article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public's access to Health Library. ©Samuli Pesälä, Mikko J Virtanen, Jussi Sane, Pekka Mustonen, Minna Kaila, Otto Helve. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.11.2017.

ISSLive!

NASA Technical Reports Server (NTRS)

Price, Jennifer B.; Snook, Bryan

2011-01-01

The ISSLive! project is a JSC innovation award- winning, combined MOD/Education project to publish export control and PAO-approved ISS telemetry, and simplified and scrubbed crew timelines. The publication of this data will be real-time or near real time and will include links to the crew's social media feeds and existing streaming public video/audio feeds, via public-friendly website, mobile devices and tablet applications. Additionally, the project will offer interactive virtual 3D views of an ISS model based on real-time telemetry and a 3D virtual mission control center based on existing Front Room console positions in made for public displays. The ISSLive! project is MOD-managed and includes collaborations with subject-matter expertise from the ISS flight controllers regarding daily operations and planning, education program specialists from the JSC Office of Education, instructional designers, human computer interface experts, and software/hardware experts from MOD facility organization, and senior web designers. In support of the Agency s Strategic Goal #6 with respect to using the ISS National Laboratory for education activities, ISSLive! uses the Station itself as STEM education subject matter and provides data for STEM-based lessons plans using national standards. Specifically, ISSLive! supports and enables the National Laboratory Education (NLE) project to address the Agency s Strategic Goal #6. This goal mandates, sharing NASA with the public, educators, and students to provide opportunities to participate in our Mission, foster innovation .. ISSLive! satisfies the Agency s outcomes of Strategic Goal; that is, engages the public in NASA's missions by providing new pathways for participation (Outcome 6.3) and it informs, engages, and inspires the public by sharing NASA s missions, challenges, and results (Outcome 6.4). Additionally, ISSLive! enables MOD s support of JSC Outreach and NASA's Open Data and Open Government Initiatives. The audience for the ISSLive! website and its application(s) are: teachers, students, citizen scientists, and the general public who will be given new and interactive insights on how the ISS Operates.

Research Integrity and Peer Review-past highlights and future directions.

PubMed

Boughton, Stephanie L; Kowalczuk, Maria K; Meerpohl, Joerg J; Wager, Elizabeth; Moylan, Elizabeth C

2018-01-01

In May 2016, we launched Research Integrity and Peer Review , an international, open access journal with fully open peer review (reviewers are identified on their reports and named reports are published alongside the article) to provide a home for research on research and publication ethics, research reporting, and research on peer review. As the journal enters its third year, we reflect on recent events and highlights for the journal and explore how the journal is faring in terms of gender and diversity in peer review. We also share the particular interests of our Editors-in-Chief regarding models of peer review, reporting quality, common research integrity issues that arise during the publishing process, and how people interact with the published literature. We continue to encourage further research into peer review, research and publication ethics and research reporting, as we believe that all new initiatives should be evidence-based. We also remain open to constructive discussions of the developments in the field that offer new solutions.

#IHeartChemistryNCSU: Free Choice, Content, and Elements of Science Communication as the Framework for an Introductory Organic Chemistry Project

ERIC Educational Resources Information Center

Frohock, Bram H.; Winterrowd, Samantha T.; Gallardo-Williams, Maria T.

2018-01-01

Students in a large introductory organic chemistry class were given the freedom to choose an organic compound of interest and were challenged to develop an educational object (physical or digital) designed to be shared with the broader public via social media. Analysis of the project results shows that most students appreciated the open nature of…

Data Sharing in Astrobiology: the Astrobiology Habitable Environments Database (AHED)

NASA Astrophysics Data System (ADS)

Bristow, T.; Lafuente Valverde, B.; Keller, R.; Stone, N.; Downs, R. T.; Blake, D. F.; Fonda, M.; Pires, A.

2016-12-01

Astrobiology is a multidisciplinary area of scientific research focused on studying the origins of life on Earth and the conditions under which life might have emerged elsewhere in the universe. The understanding of complex questions in astrobiology requires integration and analysis of data spanning a range of disciplines including biology, chemistry, geology, astronomy and planetary science. However, the lack of a centralized repository makes it difficult for astrobiology teams to share data and benefit from resultant synergies. Moreover, in recent years, federal agencies are requiring that results of any federally funded scientific research must be available and useful for the public and the science community. Astrobiology, as any other scientific discipline, needs to respond to these mandates. The Astrobiology Habitable Environments Database (AHED) is a central, high quality, long-term searchable repository designed to help the community by promoting the integration and sharing of all the data generated by these diverse disciplines. AHED provides public and open-access to astrobiology-related research data through a user-managed web portal implemented using the open-source software The Open Data Repository's (ODR) Data Publisher [1]. ODR-DP provides a user-friendly interface that research teams or individual scientists can use to design, populate and manage their own databases or laboratory notebooks according to the characteristics of their data. AHED is then a collection of databases housed in the ODR framework that store information about samples, along with associated measurements, analyses, and contextual information about field sites where samples were collected, the instruments or equipment used for analysis, and people and institutions involved in their collection. Advanced graphics are implemented together with advanced online tools for data analysis (e.g. R, MATLAB, Project Jupyter-http://jupyter.org). A permissions system will be put in place so that as data are being actively collected and interpreted, they will remain proprietary. A citation system will allow research data to be used and appropriately referenced by other researchers after the data are made public. This project is supported by SERA and NASA NNX11AP82A, MSL. [1] Stone et al. (2016) AGU, submitted.

Resurrecting Legacy Code Using Ontosoft Knowledge-Sharing and Digital Object Management to Revitalize and Reproduce Software for Groundwater Management Research

NASA Astrophysics Data System (ADS)

Kwon, N.; Gentle, J.; Pierce, S. A.

2015-12-01

Software code developed for research is often used for a relatively short period of time before it is abandoned, lost, or becomes outdated. This unintentional abandonment of code is a valid problem in the 21st century scientific process, hindering widespread reusability and increasing the effort needed to develop research software. Potentially important assets, these legacy codes may be resurrected and documented digitally for long-term reuse, often with modest effort. Furthermore, the revived code may be openly accessible in a public repository for researchers to reuse or improve. For this study, the research team has begun to revive the codebase for Groundwater Decision Support System (GWDSS), originally developed for participatory decision making to aid urban planning and groundwater management, though it may serve multiple use cases beyond those originally envisioned. GWDSS was designed as a java-based wrapper with loosely federated commercial and open source components. If successfully revitalized, GWDSS will be useful for both practical applications as a teaching tool and case study for groundwater management, as well as informing theoretical research. Using the knowledge-sharing approaches documented by the NSF-funded Ontosoft project, digital documentation of GWDSS is underway, from conception to development, deployment, characterization, integration, composition, and dissemination through open source communities and geosciences modeling frameworks. Information assets, documentation, and examples are shared using open platforms for data sharing and assigned digital object identifiers. Two instances of GWDSS version 3.0 are being created: 1) a virtual machine instance for the original case study to serve as a live demonstration of the decision support tool, assuring the original version is usable, and 2) an open version of the codebase, executable installation files, and developer guide available via an open repository, assuring the source for the application is accessible with version control and potential for new branch developments. Finally, metadata about the software has been completed within the OntoSoft portal to provide descriptive curation, make GWDSS searchable, and complete documentation of the scientific software lifecycle.

Improving data workflow systems with cloud services and use of open data for bioinformatics research.

PubMed

Karim, Md Rezaul; Michel, Audrey; Zappa, Achille; Baranov, Pavel; Sahay, Ratnesh; Rebholz-Schuhmann, Dietrich

2017-04-16

Data workflow systems (DWFSs) enable bioinformatics researchers to combine components for data access and data analytics, and to share the final data analytics approach with their collaborators. Increasingly, such systems have to cope with large-scale data, such as full genomes (about 200 GB each), public fact repositories (about 100 TB of data) and 3D imaging data at even larger scales. As moving the data becomes cumbersome, the DWFS needs to embed its processes into a cloud infrastructure, where the data are already hosted. As the standardized public data play an increasingly important role, the DWFS needs to comply with Semantic Web technologies. This advancement to DWFS would reduce overhead costs and accelerate the progress in bioinformatics research based on large-scale data and public resources, as researchers would require less specialized IT knowledge for the implementation. Furthermore, the high data growth rates in bioinformatics research drive the demand for parallel and distributed computing, which then imposes a need for scalability and high-throughput capabilities onto the DWFS. As a result, requirements for data sharing and access to public knowledge bases suggest that compliance of the DWFS with Semantic Web standards is necessary. In this article, we will analyze the existing DWFS with regard to their capabilities toward public open data use as well as large-scale computational and human interface requirements. We untangle the parameters for selecting a preferable solution for bioinformatics research with particular consideration to using cloud services and Semantic Web technologies. Our analysis leads to research guidelines and recommendations toward the development of future DWFS for the bioinformatics research community. © The Author 2017. Published by Oxford University Press.

The Geoscience Paper of the Future: Best Practices for Documenting and Sharing Research from Data to Software to Provenance

NASA Astrophysics Data System (ADS)

Gil, Y.; Yu, X.; David, C. H.; Demir, I.; Essawy, B.; Fulweiler, R. W.; Goodall, J. L.; Karlstrom, L.; Lee, H.; Mills, H. J.; Pierce, S. A.; Pope, A.; Tzeng, M.; Villamizar, S. R.

2016-12-01

Geoscientists live in a world rich with digital data and methods, and their computational research cannot be fully captured in traditional publications. The Geoscience Paper of the Future (GPF) proposes best practices for GPF authors to make data, software, and methods openly accessible, citable, and well documented. Those best practices come from recommendations by both scholars and organizations concerning open science, reproducible publications, and digital scholarship. The publication of digital objects empowers scientists to manage their research products as valuable scientific assets in an open and transparent way that enables broader access by other scientists, students, decision makers, and the public. Improving documentation and dissemination of research will accelerate the pace of scientific discovery by improving the ability of others to build upon published work. This presentation summarizes these best practices, as well as the practical experiences of several GPF authors in different geosciences disciplines. It will also discuss existing challenges for authors and publishers to produce GPFs in practice, and the opportunities to develop new approaches and infrastructure to implement those best practices. The adoption of GPF recommendations requires awareness and social change in the scientific community, including clear communication of the benefits and best practices that may be new to geoscientists.

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

Faculty Perception of Openness and Attitude to Open Sharing at the Indian National Open University

ERIC Educational Resources Information Center

Panda, Santosh; Santosh, Sujata

2017-01-01

In the past decade, the educational scenario world over has significantly been impacted by open access and open education movements. The philosophy of openness and sharing forms the cornerstone of the open education movement. The distance education approaches, together with open educational resources (OER) and massive open online courses (MOOCs),…

Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure

PubMed Central

Boué, Stéphanie; Exner, Thomas; Ghosh, Samik; Belcastro, Vincenzo; Dokler, Joh; Page, David; Boda, Akash; Bonjour, Filipe; Hardy, Barry; Vanscheeuwijck, Patrick; Hoeng, Julia; Peitsch, Manuel

2017-01-01

The US FDA defines modified risk tobacco products (MRTPs) as products that aim to reduce harm or the risk of tobacco-related disease associated with commercially marketed tobacco products.  Establishing a product’s potential as an MRTP requires scientific substantiation including toxicity studies and measures of disease risk relative to those of cigarette smoking.  Best practices encourage verification of the data from such studies through sharing and open standards. Building on the experience gained from the OpenTox project, a proof-of-concept database and website ( INTERVALS) has been developed to share results from both in vivo inhalation studies and in vitro studies conducted by Philip Morris International R&D to assess candidate MRTPs. As datasets are often generated by diverse methods and standards, they need to be traceable, curated, and the methods used well described so that knowledge can be gained using data science principles and tools. The data-management framework described here accounts for the latest standards of data sharing and research reproducibility. Curated data and methods descriptions have been prepared in ISA-Tab format and stored in a database accessible via a search portal on the INTERVALS website. The portal allows users to browse the data by study or mechanism (e.g., inflammation, oxidative stress) and obtain information relevant to study design, methods, and the most important results. Given the successful development of the initial infrastructure, the goal is to grow this initiative and establish a public repository for 21 st-century preclinical systems toxicology MRTP assessment data and results that supports open data principles. PMID:29123642

Is Biblioleaks inevitable?

PubMed

Dunn, Adam G; Coiera, Enrico; Mandl, Kenneth D

2014-04-22

In 2014, the vast majority of published biomedical research is still hidden behind paywalls rather than open access. For more than a decade, similar restrictions over other digitally available content have engendered illegal activity. Music file sharing became rampant in the late 1990s as communities formed around new ways to share. The frequency and scale of cyber-attacks against commercial and government interests has increased dramatically. Massive troves of classified government documents have become public through the actions of a few. Yet we have not seen significant growth in the illegal sharing of peer-reviewed academic articles. Should we truly expect that biomedical publishing is somehow at less risk than other content-generating industries? What of the larger threat--a "Biblioleaks" event--a database breach and public leak of the substantial archives of biomedical literature? As the expectation that all research should be available to everyone becomes the norm for a younger generation of researchers and the broader community, the motivations for such a leak are likely to grow. We explore the feasibility and consequences of a Biblioleaks event for researchers, journals, publishers, and the broader communities of doctors and the patients they serve.

Numerical Analysis of the Cavity Flow subjected to Passive Controls Techniques

NASA Astrophysics Data System (ADS)

Melih Guleren, Kursad; Turk, Seyfettin; Mirza Demircan, Osman; Demir, Oguzhan

2018-03-01

Open-source flow solvers are getting more and more popular for the analysis of challenging flow problems in aeronautical and mechanical engineering applications. They are offered under the GNU General Public License and can be run, examined, shared and modified according to user’s requirements. SU2 and OpenFOAM are the two most popular open-source solvers in Computational Fluid Dynamics (CFD) community. In the present study, some passive control methods on the high-speed cavity flows are numerically simulated using these open-source flow solvers along with one commercial flow solver called ANSYS/Fluent. The results are compared with the available experimental data. The solver SU2 are seen to predict satisfactory the mean streamline velocity but not turbulent kinetic energy and overall averaged sound pressure level (OASPL). Whereas OpenFOAM predicts all these parameters nearly as the same levels of ANSYS/Fluent.

Is Open Science the Future of Drug Development?

PubMed

Shaw, Daniel L

2017-03-01

Traditional drug development models are widely perceived as opaque and inefficient, with the cost of research and development continuing to rise even as production of new drugs stays constant. Searching for strategies to improve the drug discovery process, the biomedical research field has begun to embrace open strategies. The resulting changes are starting to reshape the industry. Open science-an umbrella term for diverse strategies that seek external input and public engagement-has become an essential tool with researchers, who are increasingly turning to collaboration, crowdsourcing, data sharing, and open sourcing to tackle some of the most pressing problems in medicine. Notable examples of such open drug development include initiatives formed around malaria and tropical disease. Open practices have found their way into the drug discovery process, from target identification and compound screening to clinical trials. This perspective argues that while open science poses some risks-which include the management of collaboration and the protection of proprietary data-these strategies are, in many cases, the more efficient and ethical way to conduct biomedical research.

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

PubMed Central

Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

2008-01-01

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

Hubble, Jeremy; Demeter, Janos; Jin, Heng; Mao, Maria; Nitzberg, Michael; Reddy, T B K; Wymore, Farrell; Zachariah, Zachariah K; Sherlock, Gavin; Ball, Catherine A

2009-01-01

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

Bias in the exchange of arguments: the case of scientists' evaluation of lay viewpoints on GM food.

PubMed

Cuppen, Eefje; Hisschemøller, Matthijs; Midden, Cees

2009-09-01

Most perspectives on public participation share the notion that dialogues should be open, allowing participants to articulate and evaluate different views and knowledge claims. We hypothesize that participants' evaluation of claims may be biased because participants have a preference for a particular type or source of a claim. This would hamper an open dialogue. We tested the effect of three variables on scientists' evaluation of claims of the general public about GM food: the claim's favorability towards GM food, the phrasing, and the source of the claim. Results are based on a survey-experiment among 73 biotechnology-scientists. Biased processing occurred when scientists evaluated claims. Claims that were corresponding with the attitude of the scientists and that were phrased in a cognitive way were evaluated more positively than claims that were contrasting the attitude of the scientists and that were phrased in an affective way. Contrary to our expectation, scientists evaluated claims of the public more positively than claims of experts.

First Universities Allied for Essential Medicines (UAEM) Neglected Diseases and Innovation Symposium

PubMed Central

Musselwhite, Laura W.; Maciag, Karolina; Lankowski, Alex; Gretes, Michael C.; Wellems, Thomas E.; Tavera, Gloria; Goulding, Rebecca E.; Guillen, Ethan

2012-01-01

Universities Allied for Essential Medicines organized its first Neglected Diseases and Innovation Symposium to address expanding roles of public sector research institutions in innovation in research and development of biomedical technologies for treatment of diseases, particularly neglected tropical diseases. Universities and other public research institutions are increasingly integrated into the pharmaceutical innovation system. Academic entities now routinely undertake robust high-throughput screening and medicinal chemistry research programs to identify lead compounds for small molecule drugs and novel drug targets. Furthermore, product development partnerships are emerging between academic institutions, non-profit entities, and biotechnology and pharmaceutical companies to create diagnostics, therapies, and vaccines for diseases of the poor. With not for profit mission statements, open access publishing standards, open source platforms for data sharing and collaboration, and a shift in focus to more translational research, universities and other public research institutions are well-placed to accelerate development of medical technologies, particularly for neglected tropical diseases. PMID:22232453

Where civics meets science: building science for the public good through Civic Science.

PubMed

Garlick, J A; Levine, P

2017-09-01

Public understanding of science and civic engagement on science issues that impact contemporary life matter more today than ever. From the Planned Parenthood controversy, to the Flint water crisis and the fluoridation debate, societal polarization about science issues has reached dramatic levels that present significant obstacles to public discussion and problem solving. This is happening, in part, because systems built to support science do not often reward open-minded thinking, inclusive dialogue, and moral responsibility regarding science issues. As a result, public faith in science continues to erode. This review explores how the field of Civic Science can impact public work on science issues by building new understanding of the practices, influences, and cultures of science. Civic Science is defined as a discipline that considers science practice and knowledge as resources for civic engagement, democratic action, and political change. This review considers how Civic Science informs the roles that key participants-scientists, public citizens and institutions of higher education-play in our national science dialogue. Civic Science aspires to teach civic capacities, to inform the responsibilities of scientists engaged in public science issues and to inspire an open-minded, inclusive dialogue where all voices are heard and shared commitments are acknowledged. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Metadata management for high content screening in OMERO

PubMed Central

Li, Simon; Besson, Sébastien; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Lindner, Dominik; Linkert, Melissa; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Allan, Chris; Burel, Jean-Marie; Moore, Josh; Swedlow, Jason R.

2016-01-01

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org. PMID:26476368

Metadata management for high content screening in OMERO.

PubMed

Li, Simon; Besson, Sébastien; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Lindner, Dominik; Linkert, Melissa; Moore, William J; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Allan, Chris; Burel, Jean-Marie; Moore, Josh; Swedlow, Jason R

2016-03-01

High content screening (HCS) experiments create a classic data management challenge-multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of "final" results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Cultural carrying capacity: Organ donation advocacy, discursive framing, and social media engagement.

PubMed

Bail, Christopher A

2016-09-01

Social media sites such as Facebook have become a powerful tool for public health outreach because they enable advocacy organizations to influence the rapidly increasing number of people who frequent these forums. Yet the very open-ness of social media sites creates fierce competition for public attention. The vast majority of social media messages provoke little or no reaction because of the sheer volume of information that confronts the typical social media user each day. In this article, I present a theory of the "cultural carrying capacity" of social media messaging campaigns. I argue that advocacy organizations inspire more endorsements, comments, and shares by social media users if they diversify the discursive content of their messages. Yet too much diversification creates large, disconnected audiences that lack the sense of shared purpose necessary to sustain an online movement. To evaluate this theory, I created a Facebook application that collects social media posts produced by forty-two organ donation advocacy organizations over 1.5 years, as well as supplemental information about the organization, its audience, and the broader social context in which they interact. Time series models provide strong evidence for my theory net of demographic characteristics of social media users, the resources and tactics of each organization, and broader external factors. I conclude by discussing the implications of these findings for public health, cultural sociology, and the nascent field of computational social science. Copyright © 2016 Elsevier Ltd. All rights reserved.

Using Social Media to Discover Public Values, Interests, and Perceptions about Cattle Grazing on Park Lands

NASA Astrophysics Data System (ADS)

Barry, Sheila J.

2014-02-01

In the western United States, livestock grazing often co-exists with recreation, cultural resource management and biodiversity protection on federal and state protected rangelands as well as on many local government open space areas. While the value of livestock grazing for managing rangeland vegetation to reduce fire fuel loads and improve wildlife habitat is increasingly recognized by resource management professionals, public concerns, and conflict between recreationist and livestock have led to reductions in public land grazing. Traditional public input methods yield a constrained picture of people's attitudes toward cows and public land grazing. Public meetings, hearings, and surveys, the most commonly used mechanisms for public land managers to solicit public opinion, tend to foster participation of organized special interests or, in the case of surveys, focus on a specific topic. General public input is limited. This study explored the use of personal photography in social media to gain insight into public perceptions of livestock grazing in public spaces. Key findings of this study include that many recreationist in grazed San Francisco Bay Area parks shared views, interests, and concerns about cows and grazing on the photo-sharing website, FlickrTM that seldom show up at a public meeting or in surveys. Results suggest that social media analysis can help develop a more nuanced understanding of public viewpoints useful in making decisions and creating outreach and education programs for public grazing lands. This study demonstrates that using such media can be useful in gaining an understanding of public concerns about natural resource management.

Voices from the Field: Working Together for Safe and Secure Schools. Summary of Findings from Florida Education Commissioner Charlie Crist's School Safety and Security Summits.

ERIC Educational Resources Information Center

Florida State Dept. of Education, Tallahassee.

During summer and fall 2001, the Florida Commissioner of Education conducted eight regional meetings, open to the public, on school safety and security. The purpose of the meetings was to explore safety issues faced by districts and schools, share best safety practices, and generate local discussion on matters of school safety and security. This…

Workshop on the Development of the UNESCO Co-Action Learning Centre Programme (1st, Kuala Lumpur, Malaysia, November 12-18, 1992). Final Report.

ERIC Educational Resources Information Center

National Federation of UNESCO Associations in Japan, Tokyo.

This publication summarizes reports from a workshop to share the experience of UNESCO's literacy program and to learn about other effective experiences in literacy available in the region. The opening of the workshop and election of officers is reported. Summaries of the following reports are given: (1) the role of learning centers to achieve…

a Public Platform for Geospatial Data Sharing for Disaster Risk Management

NASA Astrophysics Data System (ADS)

Balbo, S.; Boccardo, P.; Dalmasso, S.; Pasquali, P.

2013-01-01

Several studies have been conducted in Africa to assist local governments in addressing the risk situation related to natural hazards. Geospatial data containing information on vulnerability, impacts, climate change, disaster risk reduction is usually part of the output of such studies and is valuable to national and international organizations to reduce the risks and mitigate the impacts of disasters. Nevertheless this data isn't efficiently widely distributed and often resides in remote storage solutions hardly reachable. Spatial Data Infrastructures are technical solutions capable to solve this issue, by storing geospatial data and making them widely available through the internet. Among these solutions, GeoNode, an open source online platform for geospatial data sharing, has been developed in recent years. GeoNode is a platform for the management and publication of geospatial data. It brings together mature and stable open-source software projects under a consistent and easy-to-use interface allowing users, with little training, to quickly and easily share data and create interactive maps. GeoNode data management tools allow for integrated creation of data, metadata, and map visualizations. Each dataset in the system can be shared publicly or restricted to allow access to only specific users. Social features like user profiles and commenting and rating systems allow for the development of communities around each platform to facilitate the use, management, and quality control of the data the GeoNode instance contains (http://geonode.org/). This paper presents a case study scenario of setting up a Web platform based on GeoNode. It is a public platform called MASDAP and promoted by the Government of Malawi in order to support development of the country and build resilience against natural disasters. A substantial amount of geospatial data has already been collected about hydrogeological risk, as well as several other-disasters related information. Moreover this platform will help to ensure that the data created by a number of past or ongoing projects is maintained and that this information remains accessible and useful. An Integrated Flood Risk Management Plan for a river basin has already been included in the platform and other data from future disaster risk management projects will be added as well.

Flutrack.org: Open-source and linked data for epidemiology.

PubMed

Chorianopoulos, Konstantinos; Talvis, Karolos

2016-12-01

Epidemiology has made advances, thanks to the availability of real-time surveillance data and by leveraging the geographic analysis of incidents. There are many health information systems that visualize the symptoms of influenza-like illness on a digital map, which is suitable for end-users, but it does not afford further processing and analysis. Existing systems have emphasized the collection, analysis, and visualization of surveillance data, but they have neglected a modular and interoperable design that integrates high-resolution geo-location with real-time data. As a remedy, we have built an open-source project and we have been operating an open service that detects flu-related symptoms and shares the data in real-time with anyone who wants to built upon this system. An analysis of a small number of precisely geo-located status updates (e.g. Twitter) correlates closely with the Google Flu Trends and the Centers for Disease Control and Prevention flu-positive reports. We suggest that public health information systems should embrace an open-source approach and offer linked data, in order to facilitate the development of an ecosystem of applications and services, and in order to be transparent to the general public interest. © The Author(s) 2015.

Secure open cloud in data transmission using reference pattern and identity with enhanced remote privacy checking

NASA Astrophysics Data System (ADS)

Vijay Singh, Ran; Agilandeeswari, L.

2017-11-01

To handle the large amount of client’s data in open cloud lots of security issues need to be address. Client’s privacy should not be known to other group members without data owner’s valid permission. Sometime clients are fended to have accessing with open cloud servers due to some restrictions. To overcome the security issues and these restrictions related to storing, data sharing in an inter domain network and privacy checking, we propose a model in this paper which is based on an identity based cryptography in data transmission and intermediate entity which have client’s reference with identity that will take control handling of data transmission in an open cloud environment and an extended remote privacy checking technique which will work at admin side. On behalf of data owner’s authority this proposed model will give best options to have secure cryptography in data transmission and remote privacy checking either as private or public or instructed. The hardness of Computational Diffie-Hellman assumption algorithm for key exchange makes this proposed model more secure than existing models which are being used for public cloud environment.

Resource sharing of online teaching materials: The lon-capa project

NASA Astrophysics Data System (ADS)

Bauer, Wolfgang

2004-03-01

The use of information technology resources in conventional lecture-based courses, in distance-learning offerings, as well as hybrid courses, is increasing. But this may put additional burden on faculty, who are now asked to deliver this new content. Additionally, it may require the installation of commercial courseware systems, putting the colleges and universities in new financial licensing dependencies. To address exactly these two problems, the lon-capa system was invented to provide an open-source, gnu public license based, courseware system that allows for sharing of educational resources across institutional and disciplinary boundaries. This presentation will focus on both aspects of the system, the courseware capabilities that allow for customized environments for individual students, and the educational resources library that enables teachers to take full advantages of the work of their colleagues. Research results on learning effectiveness, resource and system usage patterns, and customization for different learning styles will be shown. Institutional perceptions of and responses to open source courseware systems will be discussed.

Integration of a neuroimaging processing pipeline into a pan-canadian computing grid

NASA Astrophysics Data System (ADS)

Lavoie-Courchesne, S.; Rioux, P.; Chouinard-Decorte, F.; Sherif, T.; Rousseau, M.-E.; Das, S.; Adalat, R.; Doyon, J.; Craddock, C.; Margulies, D.; Chu, C.; Lyttelton, O.; Evans, A. C.; Bellec, P.

2012-02-01

The ethos of the neuroimaging field is quickly moving towards the open sharing of resources, including both imaging databases and processing tools. As a neuroimaging database represents a large volume of datasets and as neuroimaging processing pipelines are composed of heterogeneous, computationally intensive tools, such open sharing raises specific computational challenges. This motivates the design of novel dedicated computing infrastructures. This paper describes an interface between PSOM, a code-oriented pipeline development framework, and CBRAIN, a web-oriented platform for grid computing. This interface was used to integrate a PSOM-compliant pipeline for preprocessing of structural and functional magnetic resonance imaging into CBRAIN. We further tested the capacity of our infrastructure to handle a real large-scale project. A neuroimaging database including close to 1000 subjects was preprocessed using our interface and publicly released to help the participants of the ADHD-200 international competition. This successful experiment demonstrated that our integrated grid-computing platform is a powerful solution for high-throughput pipeline analysis in the field of neuroimaging.

The HydroServer Platform for Sharing Hydrologic Data

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Schreuders, K.; Maidment, D. R.; Zaslavsky, I.; Valentine, D. W.

2010-12-01

The CUAHSI Hydrologic Information System (HIS) is an internet based system that supports sharing of hydrologic data. HIS consists of databases connected using the Internet through Web services, as well as software for data discovery, access, and publication. The HIS system architecture is comprised of servers for publishing and sharing data, a centralized catalog to support cross server data discovery and a desktop client to access and analyze data. This paper focuses on HydroServer, the component developed for sharing and publishing space-time hydrologic datasets. A HydroServer is a computer server that contains a collection of databases, web services, tools, and software applications that allow data producers to store, publish, and manage the data from an experimental watershed or project site. HydroServer is designed to permit publication of data as part of a distributed national/international system, while still locally managing access to the data. We describe the HydroServer architecture and software stack, including tools for managing and publishing time series data for fixed point monitoring sites as well as spatially distributed, GIS datasets that describe a particular study area, watershed, or region. HydroServer adopts a standards based approach to data publication, relying on accepted and emerging standards for data storage and transfer. CUAHSI developed HydroServer code is free with community code development managed through the codeplex open source code repository and development system. There is some reliance on widely used commercial software for general purpose and standard data publication capability. The sharing of data in a common format is one way to stimulate interdisciplinary research and collaboration. It is anticipated that the growing, distributed network of HydroServers will facilitate cross-site comparisons and large scale studies that synthesize information from diverse settings, making the network as a whole greater than the sum of its parts in advancing hydrologic research. Details of the CUAHSI HIS can be found at http://his.cuahsi.org, and HydroServer codeplex site http://hydroserver.codeplex.com.

The Federal Geospatial Platform a shared infrastructure for publishing, discovering and exploiting public data and spatial applications.

NASA Astrophysics Data System (ADS)

Dabolt, T. O.

2016-12-01

The proliferation of open data and data services continues to thrive and is creating new challenges on how researchers, policy analysts and other decision makes can quickly discover and use relevant data. While traditional metadata catalog approaches used by applications such as data.gov prove to be useful starting points for data search they can quickly frustrate end users who are seeking ways to quickly find and then use data in machine to machine environs. The Geospatial Platform is overcoming these obstacles and providing end users and applications developers a richer more productive user experience. The Geospatial Platform leverages a collection of open source and commercial technology hosted on Amazon Web Services providing an ecosystem of services delivering trusted, consistent data in open formats to all users as well as a shared infrastructure for federal partners to serve their spatial data assets. It supports a diverse array of communities of practice ranging on topics from the 16 National Geospatial Data Assets Themes, to homeland security and climate adaptation. Come learn how you can contribute your data and leverage others or check it out on your own at https://www.geoplatform.gov/

Co-producing public involvement training with members of the public and research organisations in the East Midlands: creating, delivering and evaluating the lay assessor training programme.

PubMed

Horobin, Adele; Brown, George; Higton, Fred; Vanhegan, Stevie; Wragg, Andrew; Wray, Paula; Walker, Dawn-Marie

2017-01-01

Members of the public share their views with researchers to improve health and social care research. Lay assessing is one way of doing this. This is where people, drawing upon personal and general life experience, comment on material, such as grant applications and patient information, to highlight strengths and weaknesses and to suggest improvements. This paper reports on setting up a training programme for lay assessors. Meetings were held between interested public and staff from research organisations. People discussed what lay assessing is, why they want to do it, skills and support needed and if training was wanted. They were invited to form a group to develop the training together. Training was delivered in the East Midlands. People who attended gave their thoughts about it by completing questionnaires and joining a feedback event. The group developed the structure of the training programme together and it oversaw the development of the training content by individual members. People who attended training reported feeling more confident about lay assessing. This was particularly so for those who had not done lay assessing before. They indicated how valuable it was to talk with others at the training. Our findings support the National Institute for Health Research recommendations for improving learning and development for public involvement in research. This project has created a solid base for local research organisations to work together in public involvement training. Lay assessor training is now part of a wider programme of shared resources called the Sharebank. Background Involving members of the public in research can improve its quality and incorporate the needs and views of patients. One method for doing this is lay assessing, where members of the public are consulted to improve research materials. This paper documents the establishment of a pilot training programme for lay assessors. It describes a way of working that embodies a regional, cross-organisational approach to co-producing training with members of the public. Methods Open meetings, led by AH, were held for existing and aspiring lay assessors to define lay assessing, motivations for doing it, skills required, associated learning and development needs, and to gauge interest for training. Those who attended meetings, including members of the public and staff, were invited to form a working group to co-produce the training programme. Training was delivered in modules at two centres in the East Midlands and evaluated through participant feedback at the end of each module and at an evaluation event. Feedback was through a mix of Likert scale scoring, open text and verbal responses. Results Discussions from the open meetings informed the development of the training by the working group. Led by AH, the working group, as a whole, co-produced the structure and format of the training and oversaw training content development by individuals within the group. Training was well-received by participants. Feedback through Likert scoring ( n  = 14) indicated higher feelings of confidence in knowledge of relevant subject matter and in fulfilling the lay assessor role, particularly amongst those who had not done lay assessing before. Opportunities that the training afforded for interaction between participants - sharing of varied experiences and knowledge - and a 'learn by doing' approach was of particular value, as indicated by 10 responses to open-ended questions. Conclusions This project has created a solid foundation for collaboration between research organisations in the East Midlands in devising and delivering training in public involvement together. Our evaluation provides evidence in support of National Institute for Health Research (NIHR) recommendations on principles for learning and development for public involvement in research.

iBiology: communicating the process of science.

PubMed

Goodwin, Sarah S

2014-08-01

The Internet hosts an abundance of science video resources aimed at communicating scientific knowledge, including webinars, massive open online courses, and TED talks. Although these videos are efficient at disseminating information for diverse types of users, they often do not demonstrate the process of doing science, the excitement of scientific discovery, or how new scientific knowledge is developed. iBiology (www.ibiology.org), a project that creates open-access science videos about biology research and science-related topics, seeks to fill this need by producing videos by science leaders that make their ideas, stories, and experiences available to anyone with an Internet connection. © 2014 Goodwin. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Full and Open Access to Data in the Global Earth Observing System of Systems (GEOSS): Implementing the GEOSS Data Sharing Principles

NASA Astrophysics Data System (ADS)

Chen, R. S.; Uhlir, P. F.; Gabrinowicz, J. I.

2008-12-01

Full and open access to data from remote sensing platforms and other sources can facilitate not only scientific research but also the more widespread and effective use of scientific data for the benefit of society. The Global Earth Observing System of Systems (GEOSS) is a major international initiative of the Group on Earth Observations (GEO) to develop "coordinated, comprehensive and sustained Earth observations and information." In 2005, GEO adopted the GEOSS Data Sharing Principles, which call for the "full and open exchange of data, metadata, and products shared within GEOSS, recognizing relevant international instruments and national policies and legislation." These Principles also note that "All shared data, metadata, and products will be made available with minimum time delay and at minimum cost" and that "All shared data, metadata, and products being free of charge or no more than cost of reproduction will be encouraged for research and education." GEOSS Task DA-06-01, aimed at developing a set of recommended implementation guidelines for the Principles, was established in 2006 under the leadership of CODATA, the Committee on Data for Science and Technology of the International Council for Science (ICSU). An international team of authors has developed a draft White Paper on the GEOSS Data Sharing Principles and a proposed set of implementation guidelines. These have been carefully reviewed by independent reviewers, various GEO Committees, and GEO National Members and Participating Organizations. It is expected that the proposed implementation guidelines will be discussed at the GEO-V Plenary in Budapest in November 2008. The current version of the proposed implementation guidelines recognizes the importance of good faith, voluntary adherence to the Principles by GEO National Members and Participating Organizations. It underscores the value of reuse and re-dissemination of GEOSS data with minimum restrictions, not only within GEOSS itself but on the part of GEOSS users. Consistency with relevant international instruments and applicable policies and legislation is essential, and therefore clarification and coordination of applicable policies and procedures are needed. Pricing of GEOSS data, metadata, and products should be based on the premise that the data and information within GEOSS is a public good for public-interest use in the nine societal benefit areas. Time delays for data access from both operational and research systems should be kept to a minimum, reflecting the norms of the relevant scientific communities or data processing centers. The proposed guidelines also emphasize the need to better define research and education uses and to develop and collect usage metrics and indicators. The draft White Paper provides a more detailed review of past and current data policies related to space-based and spatial data, assesses the implications of the Data Sharing Principles for selected case studies, and discusses a number of other important implementation issues. Successful implementation of the GEOSS Data Sharing Principles is likely to be a critical element in the future effectiveness and value of GEOSS.

Collaborative Data Publication Utilizing the Open Data Repository's (ODR) Data Publisher

NASA Technical Reports Server (NTRS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R. M.; Downs, R. T.; Blake, D.; Fonda, M.; Dateo, C.; Pires, A.

2017-01-01

Introduction: For small communities in diverse fields such as astrobiology, publishing and sharing data can be a difficult challenge. While large, homogenous fields often have repositories and existing data standards, small groups of independent researchers have few options for publishing standards and data that can be utilized within their community. In conjunction with teams at NASA Ames and the University of Arizona, the Open Data Repository's (ODR) Data Publisher has been conducting ongoing pilots to assess the needs of diverse research groups and to develop software to allow them to publish and share their data collaboratively. Objectives: The ODR's Data Publisher aims to provide an easy-to-use and implement software tool that will allow researchers to create and publish database templates and related data. The end product will facilitate both human-readable interfaces (web-based with embedded images, files, and charts) and machine-readable interfaces utilizing semantic standards. Characteristics: The Data Publisher software runs on the standard LAMP (Linux, Apache, MySQL, PHP) stack to provide the widest server base available. The software is based on Symfony (www.symfony.com) which provides a robust framework for creating extensible, object-oriented software in PHP. The software interface consists of a template designer where individual or master database templates can be created. A master database template can be shared by many researchers to provide a common metadata standard that will set a compatibility standard for all derivative databases. Individual researchers can then extend their instance of the template with custom fields, file storage, or visualizations that may be unique to their studies. This allows groups to create compatible databases for data discovery and sharing purposes while still providing the flexibility needed to meet the needs of scientists in rapidly evolving areas of research. Research: As part of this effort, a number of ongoing pilot and test projects are currently in progress. The Astrobiology Habitable Environments Database Working Group is developing a shared database standard using the ODR's Data Publisher and has a number of example databases where astrobiology data are shared. Soon these databases will be integrated via the template-based standard. Work with this group helps determine what data researchers in these diverse fields need to share and archive. Additionally, this pilot helps determine what standards are viable for sharing these types of data from internally developed standards to existing open standards such as the Dublin Core (http://dublincore.org) and Darwin Core (http://rs.twdg.org) metadata standards. Further studies are ongoing with the University of Arizona Department of Geosciences where a number of mineralogy databases are being constructed within the ODR Data Publisher system. Conclusions: Through the ongoing pilots and discussions with individual researchers and small research teams, a definition of the tools desired by these groups is coming into focus. As the software development moves forward, the goal is to meet the publication and collaboration needs of these scientists in an unobtrusive and functional way.

Infrastructure Commons in Economic Perspective

NASA Astrophysics Data System (ADS)

Frischmann, Brett M.

This chapter briefly summarizes a theory (developed in substantial detail elsewhere)1 that explains why there are strong economic arguments for managing and sustaining infrastructure resources in an openly accessible manner. This theory facilitates a better understanding of two related issues: how society benefits from infrastructure resources and how decisions about how to manage or govern infrastructure resources affect a wide variety of public and private interests. The key insights from this analysis are that infrastructure resources generate value as inputs into a wide range of productive processes and that the outputs from these processes are often public goods and nonmarket goods that generate positive externalities that benefit society as a whole. Managing such resources in an openly accessible manner may be socially desirable from an economic perspective because doing so facilitates these downstream productive activities. For example, managing the Internet infrastructure in an openly accessible manner facilitates active citizen involvement in the production and sharing of many different public and nonmarket goods. Over the last decade, this has led to increased opportunities for a wide range of citizens to engage in entrepreneurship, political discourse, social network formation, and community building, among many other activities. The chapter applies these insights to the network neutrality debate and suggests how the debate might be reframed to better account for the wide range of private and public interests at stake.

Publishing priorities of biomedical research funders

PubMed Central

Collins, Ellen

2013-01-01

Objectives To understand the publishing priorities, especially in relation to open access, of 10 UK biomedical research funders. Design Semistructured interviews. Setting 10 UK biomedical research funders. Participants 12 employees with responsibility for research management at 10 UK biomedical research funders; a purposive sample to represent a range of backgrounds and organisation types. Conclusions Publicly funded and large biomedical research funders are committed to open access publishing and are pleased with recent developments which have stimulated growth in this area. Smaller charitable funders are supportive of the aims of open access, but are concerned about the practical implications for their budgets and their funded researchers. Across the board, biomedical research funders are turning their attention to other priorities for sharing research outputs, including data, protocols and negative results. Further work is required to understand how smaller funders, including charitable funders, can support open access. PMID:24154520

Social Medicine: Twitter in Healthcare.

PubMed

Pershad, Yash; Hangge, Patrick T; Albadawi, Hassan; Oklu, Rahmi

2018-05-28

Social media enables the public sharing of information. With the recent emphasis on transparency and the open sharing of information between doctors and patients, the intersection of social media and healthcare is of particular interest. Twitter is currently the most popular form of social media used for healthcare communication; here, we examine the use of Twitter in medicine and specifically explore in what capacity using Twitter to share information on treatments and research has the potential to improve care. The sharing of information on Twitter can create a communicative and collaborative atmosphere for patients, physicians, and researchers and even improve quality of care. However, risks involved with using Twitter for healthcare discourse include high rates of misinformation, difficulties in verifying the credibility of sources, overwhelmingly high volumes of information available on Twitter, concerns about professionalism, and the opportunity cost of using physician time. Ultimately, the use of Twitter in healthcare can allow patients, healthcare professionals, and researchers to be more informed, but specific guidelines for appropriate use are necessary.

Librarians, Publishers, and Vendors Revisit E-Books: OeBF-Sponsored Gathering Tackles Content, Delivery, Usage, Economics, and the Dire Need for Standards

ERIC Educational Resources Information Center

Rogers, Michael

2004-01-01

The resurgence of interest in e-books, who uses them, and where the technology is headed were among the issues discussed March 16 at the eBooks in the Public Library Conference in New York, sponsored by the Open eBook Forum (OeBF). Roughly 200 librarians, publishers, and vendors braved a winter squall to share their expertise and experiences.…

NDEx - the Network Data Exchange, A Network Commons for Biologists | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Network models of biology, whether curated or derived from large-scale data analysis, are critical tools in the understanding of cancer mechanisms and in the design and personalization of therapies. The NDEx Project (Network Data Exchange) will create, deploy, and maintain an open-source, web-based software platform and public website to enable scientists, organizations, and software applications to share, store, manipulate, and publish biological networks.

Ontology-driven data integration and visualization for exploring regional geologic time and paleontological information

NASA Astrophysics Data System (ADS)

Wang, Chengbin; Ma, Xiaogang; Chen, Jianguo

2018-06-01

Initiatives of open data promote the online publication and sharing of large amounts of geologic data. How to retrieve information and discover knowledge from the big data is an ongoing challenge. In this paper, we developed an ontology-driven data integration and visualization pilot system for exploring information of regional geologic time, paleontology, and fundamental geology. The pilot system (http://www2.cs.uidaho.edu/%7Emax/gts/)

Commercial Development Plan for the International Space Station

NASA Technical Reports Server (NTRS)

1998-01-01

The long term objective is to establish the foundation for a marketplace and stimulate a national economy for space products and services in low-Earth orbit, where both demand and supply are dominated by the private sector. The short term objective is to begin the transition to private investment and offset a share of the public cost for operating the space shuttle fleet and space station through commercial enterprise in open markets.

Open research practices: unintended consequences and suggestions for averting them. (Commentary on the Peer Reviewers' Openness Initiative)

PubMed Central

2016-01-01

The Peer Reviewers' Openness Initiative (PROI) is a move to enlist reviewers in the promotion of data-sharing. In this commentary, I discuss objections that can be raised, first to the specific proposals in the PROI, and second to data-sharing in general. I argue that although many objections have strong counter-arguments, others merit more serious consideration. Regarding the PROI, I suggest that it could backfire if editors and authors feel coerced into data-sharing and so may not be the most pragmatic way of encouraging greater openness. More generally, while promoting data-sharing, we need to be sensitive to cases where sharing of data from human participants could create ethical problems. Furthermore, those interested in promoting reproducible science need to defend against an increased risk of data-dredging when large, multivariable datasets are shared. I end with some suggestions to avoid these unintended consequences. PMID:27152225

Do It Yourself (DIY) Earth Science Collaboratories Using Best Practices and Breakthrough Technologies

NASA Astrophysics Data System (ADS)

Stephan, E.

2017-12-01

The objective of published earth science study data results and literature on the Web should be to provide a means to integrate discoverable science resources through an open collaborative-Web. At the core of any open science collaborative infrastructure is the ability to discover, manage and ultimately use relevant data accessible to the collaboration. Equally important are the relationships between people, applications, services, and publications, which capture critical contextual knowledge that enable their effective use. While contributions of either irreproducible or costly data can be a great asset the inability of users being able to use the data intelligently or make sense of it, makes these investments not usable. An ability to describe ad-hoc discoverable usage methodologies, provide feedback to data producers, and identify and cite data in a systematic way by leveraging existing Web-enabled off the shelf technology is needed. Fortunately many break-through advancements in data publication best practices and government, open source, and commercial investments support consumers who can provide feedback, share experiences, and contribute back to the earth science ecosystem.

Hidden concerns of sharing research data by low/middle-income country scientists.

PubMed

Bezuidenhout, Louise; Chakauya, Ereck

2018-01-01

There has considerable interest in bringing low/middle-income countries (LMIC) scientists into discussions on Open Data - both as contributors and users. The establishment of in situ data sharing practices within LMIC research institutions is vital for the development of an Open Data landscape in the Global South. Nonetheless, many LMICs have significant challenges - resource provision, research support and extra-laboratory infrastructures. These low-resourced environments shape data sharing activities, but are rarely examined within Open Data discourse. In particular, little attention is given to how these research environments shape scientists' perceptions of data sharing (dis)incentives. This paper expands on these issues of incentivizing data sharing, using data from a quantitative survey disseminated to life scientists in 13 countries in sub-Saharan Africa. This interrogated not only perceptions of data sharing amongst LMIC scientists, but also how these are connected to the research environments and daily challenges experienced by them. The paper offers a series of analysis around commonly cited (dis)incentives such as data sharing as a means of improving research visibility; sharing and funding; and online connectivity. It identifies key areas that the Open Data community need to consider if true openness in research is to be established in the Global South.

Strategies and Exemplars for Public Outreach Events: Planning, Implementation, Evaluation

NASA Astrophysics Data System (ADS)

Cobb, W. H.; Buxner, S.; Shipp, S. S.; Shebby, S.

2015-12-01

IntroductionEach year the National Aeronautics and Space Administration (NASA) sponsors a variety of public outreach events to share information with educators, students, and the general public. These events are designed to increase interest in and awareness of the mission and goals of NASA. Planning and implementation best practices gleaned from the NASA SMD Education's review of large-scale events, "Best Practices in Outreach Events" will be shared. Outcomes from an event, i C Ceres, celebrating the Dawn mission's arrival at dwarf planet Ceres that utilized these strategies will be shared. Best practices included can be pertinent for all event organizers and evaluators regardless of event size. BackgroundThe literature review focused on identifying evaluations of large-scale public outreach events—and, within these evaluations, identifying best practices. The following criteria for identifying journal articles and reports to potentially include: Public, science-related events open to adults and children. Events with more than 1,000 attendees. Events that occurred during the last 5 years. Evaluations that included information on data collected from visitors and/or volunteers. Evaluations that specified the type of data collected, methodology, and associated results. Planning and Implementation Best PracticesThe literature review revealed key considerations for planning and of large-scale events implementing events. A summary of related best practices is presented below. 1) Advertise the event 2) Use and advertise access to scientists 3) Recruit scientists using these findings 4) Ensure that the event is group and particularly child friendly 5) Target specific event outcomes Best Practices Informing Real-world Planning, Implementation and EvaluationDawn mission's collaborative design of a series of events, i C Ceres, including in-person, interactive events geared to families and live presentations will be shared. Outcomes and lessons learned will be imparted rising from these events and their evaluation. There will be a focus on the family event, in particular the evidence that scientist participation was a particular driver for the event's impact and success.

The Open Data Repository's Data Publisher

NASA Astrophysics Data System (ADS)

Stone, N.; Lafuente, B.; Downs, R. T.; Bristow, T.; Blake, D. F.; Fonda, M.; Pires, A.

2015-12-01

Data management and data publication are becoming increasingly important components of research workflows. The complexity of managing data, publishing data online, and archiving data has not decreased significantly even as computing access and power has greatly increased. The Open Data Repository's Data Publisher software (http://www.opendatarepository.org) strives to make data archiving, management, and publication a standard part of a researcher's workflow using simple, web-based tools and commodity server hardware. The publication engine allows for uploading, searching, and display of data with graphing capabilities and downloadable files. Access is controlled through a robust permissions system that can control publication at the field level and can be granted to the general public or protected so that only registered users at various permission levels receive access. Data Publisher also allows researchers to subscribe to meta-data standards through a plugin system, embargo data publication at their discretion, and collaborate with other researchers through various levels of data sharing. As the software matures, semantic data standards will be implemented to facilitate machine reading of data and each database will provide a REST application programming interface for programmatic access. Additionally, a citation system will allow snapshots of any data set to be archived and cited for publication while the data itself can remain living and continuously evolve beyond the snapshot date. The software runs on a traditional LAMP (Linux, Apache, MySQL, PHP) server and is available on GitHub (http://github.com/opendatarepository) under a GPLv2 open source license. The goal of the Open Data Repository is to lower the cost and training barrier to entry so that any researcher can easily publish their data and ensure it is archived for posterity. We gratefully acknowledge the support for this study by the Science-Enabling Research Activity (SERA), and NASA NNX11AP82A, Mars Science Laboratory Investigations and University of Arizona Geosciences.

Is Biblioleaks Inevitable?

PubMed Central

Coiera, Enrico; Mandl, Kenneth D

2014-01-01

In 2014, the vast majority of published biomedical research is still hidden behind paywalls rather than open access. For more than a decade, similar restrictions over other digitally available content have engendered illegal activity. Music file sharing became rampant in the late 1990s as communities formed around new ways to share. The frequency and scale of cyber-attacks against commercial and government interests has increased dramatically. Massive troves of classified government documents have become public through the actions of a few. Yet we have not seen significant growth in the illegal sharing of peer-reviewed academic articles. Should we truly expect that biomedical publishing is somehow at less risk than other content-generating industries? What of the larger threat—a “Biblioleaks” event—a database breach and public leak of the substantial archives of biomedical literature? As the expectation that all research should be available to everyone becomes the norm for a younger generation of researchers and the broader community, the motivations for such a leak are likely to grow. We explore the feasibility and consequences of a Biblioleaks event for researchers, journals, publishers, and the broader communities of doctors and the patients they serve. PMID:24755534

Health Information–Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease

PubMed Central

Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-01-01

Background People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician’s Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs’ queries, and what causes possible differences in behavior. Objective The aim of our study was to evaluate how the general public’s and HCPs’ information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public’s information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Methods Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician’s Databases, were used. We compared the general public’s article openings on Lyme disease from Health Library to HCPs’ article openings on Lyme disease from Physician’s Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Results Both databases, Health Library and Physician’s Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Conclusions Lyme disease–related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public’s article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public’s access to Health Library. PMID:29109071

Is Open Science the Future of Drug Development?

PubMed Central

Shaw, Daniel L.

2017-01-01

Traditional drug development models are widely perceived as opaque and inefficient, with the cost of research and development continuing to rise even as production of new drugs stays constant. Searching for strategies to improve the drug discovery process, the biomedical research field has begun to embrace open strategies. The resulting changes are starting to reshape the industry. Open science—an umbrella term for diverse strategies that seek external input and public engagement—has become an essential tool with researchers, who are increasingly turning to collaboration, crowdsourcing, data sharing, and open sourcing to tackle some of the most pressing problems in medicine. Notable examples of such open drug development include initiatives formed around malaria and tropical disease. Open practices have found their way into the drug discovery process, from target identification and compound screening to clinical trials. This perspective argues that while open science poses some risks—which include the management of collaboration and the protection of proprietary data—these strategies are, in many cases, the more efficient and ethical way to conduct biomedical research. PMID:28356902

OpenAQ: A Platform to Aggregate and Freely Share Global Air Quality Data

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.; Flasher, J. C.; Veerman, O.; DeWitt, H. L.

2015-12-01

Thousands of ground-based air quality monitors around the world publicly publish real-time air quality data; however, researchers and the public do not have access to this information in the ways most useful to them. Often, air quality data are posted on obscure websites showing only current values, are programmatically inaccessible, and/or are in inconsistent data formats across sites. Yet, historical and programmatic access to such a global dataset would be transformative to several scientific fields, from epidemiology to low-cost sensor technologies to estimates of ground-level aerosol by satellite retrievals. To increase accessibility and standardize this disparate dataset, we have built OpenAQ, an innovative, open platform created by a group of scientists and open data programmers. The source code for the platform is viewable at github.com/openaq. Currently, we are aggregating, storing, and making publicly available real-time air quality data (PM2.5, PM10, SO2, NO2, and O3) via an Application Program Interface (API). We will present the OpenAQ platform, which currently has the following specific capabilities: A continuous ingest mechanism for some of the most polluted cities, generalizable to more sources An API providing data-querying, including ability to filter by location, measurement type and value and date, as well as custom sort options A generalized, chart-based visualization tool to explore data accessible via the API At this stage, we are seeking wider participation and input from multiple research communities in expanding our data retrieval sites, standardizing our protocols, receiving feedback on quality issues, and creating tools that can be built on top of this open platform.

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience.

PubMed

Hodge, Victoria; Jessop, Mark; Fletcher, Martyn; Weeks, Michael; Turner, Aaron; Jackson, Tom; Ingram, Colin; Smith, Leslie; Austin, Jim

2016-01-01

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met.

Supporting diverse data providers in the open water data initiative: Communicating water data quality and fitness of use

USGS Publications Warehouse

Larsen, Sara; Hamilton, Stuart; Lucido, Jessica M.; Garner, Bradley D.; Young, Dwane

2016-01-01

Shared, trusted, timely data are essential elements for the cooperation needed to optimize economic, ecologic, and public safety concerns related to water. The Open Water Data Initiative (OWDI) will provide a fully scalable platform that can support a wide variety of data from many diverse providers. Many of these will be larger, well-established, and trusted agencies with a history of providing well-documented, standardized, and archive-ready products. However, some potential partners may be smaller, distributed, and relatively unknown or untested as data providers. The data these partners will provide are valuable and can be used to fill in many data gaps, but can also be variable in quality or supplied in nonstandardized formats. They may also reflect the smaller partners' variable budgets and missions, be intermittent, or of unknown provenance. A challenge for the OWDI will be to convey the quality and the contextual “fitness” of data from providers other than the most trusted brands. This article reviews past and current methods for documenting data quality. Three case studies are provided that describe processes and pathways for effective data-sharing and publication initiatives. They also illustrate how partners may work together to find a metadata reporting threshold that encourages participation while maintaining high data integrity. And lastly, potential governance is proposed that may assist smaller partners with short- and long-term participation in the OWDI.

A Learned Society's Perspective on Publishing.

PubMed

Suzuki, Kunihiko; Edelson, Alan; Iversen, Leslie L; Hausmann, Laura; Schulz, Jörg B; Turner, Anthony J

2016-10-01

Scientific journals that are owned by a learned society, like the Journal of Neurochemistry (JNC), which is owned by the International Society for Neurochemistry (ISN), benefit the scientific community in that a large proportion of the income is returned to support the scientific mission of the Society. The income generated by the JNC enables the ISN to organize conferences as a platform for members and non-members alike to share their research, supporting researchers particularly in developing countries by travel grants and other funds, and promoting education in student schools. These direct benefits and initiatives for ISN members and non-members distinguish a society journal from pure commerce. However, the world of scholarly publishing is changing rapidly. Open access models have challenged the business model of traditional journal subscription and hence provided free access to publicly funded scientific research. In these models, the manuscript authors pay a publication cost after peer review and acceptance of the manuscript. Over the last decade, numerous new open access journals have been launched and traditional subscription journals have started to offer open access (hybrid journals). However, open access journals follow the general scheme that, of all participating parties, the publisher receives the highest financial benefit. The income is generated by researchers whose positions and research are mostly financed by taxpayers' or funders' money, and by reviewers and editors, who frequently are not reimbursed. Last but not least, the authors pay for the publication of their work after a rigorous and sometimes painful review process. JNC itself has an open access option, at a significantly reduced cost for Society members as an additional benefit. This article provides first-hand insights from two former Editors-in-Chief, Kunihiko Suzuki and Leslie Iversen, about the history of JNC's ownership and about the difficulties and battles fought along the way to its current success and reputation. Scientific journals that are owned by a learned society, like the Journal of Neurochemistry (JNC) which is owned by the International Society for Neurochemistry (ISN), benefit the scientific community in that a large proportion of the income is returned to support the scientific mission of the Society. The income generated by the JNC enables the ISN to organize conferences as a platform for members and non-members alike to share their research, supporting researchers particularly in developing countries by travel grants and other funds, and to promote education in student schools. These direct benefits and initiatives for ISN members and non-members distinguish a society journal from pure commerce. However, the world of scholarly publishing is changing rapidly. Open access models have challenged the business model of traditional journal subscription and hence provide free access to publicly funded scientific research. In these models, the manuscript authors pay a publication cost after peer review and acceptance of the manuscript. Over the last decade, numerous new open access journals have been launched and traditional subscription journals have started to offer open access (hybrid journals). However, open access journals pertain to the general scheme that, of all participating parties, the publisher receives the highest financial benefit. The income is generated by researchers whose positions and research are mostly financed by tax payers' or funders' money, reviewers and editors, who frequently are not reimbursed. Last but not least, the authors pay for the publication of their work after a rigorous and sometimes painful review process. JNC itself has an open access option, at a significantly reduced cost for Society members as an additional benefit. This article provides first-hand insights from a long-standing Editor-in-Chief, Kunihiko Suzuki, about the history of JNC's ownership and about difficulties and battles fought on the way to its current success and reputation today. This article is part of the 60th Anniversary special issue. © 2016 International Society for Neurochemistry.

Does Personality Have a Different Impact on Self-Rated Distraction, Job Satisfaction, and Job Performance in Different Office Types?

PubMed

Seddigh, Aram; Berntson, Erik; Platts, Loretta G; Westerlund, Hugo

2016-01-01

This study investigates the joint effect of office type (cell, shared room, open-plan, and flex) and personality, measured by the Big Five personality traits, on self-rated measures of distraction, job satisfaction, and job performance (measured by professional efficacy). Regression analyses with interactions between personality and office type were conducted on 1205 participants working in 5 organizations from both the private and public sectors. While few interactions were observed in the cases of professional efficacy and job satisfaction, several were observed between personality traits and office type on the level of distraction reported. Specifically, more emotionally stable participants reported lower distraction, particularly those working in flex offices. Both agreeableness and openness to experience were associated with higher levels of distraction among participants in open-plan compared to cell offices.

Does Personality Have a Different Impact on Self-Rated Distraction, Job Satisfaction, and Job Performance in Different Office Types?

PubMed Central

Seddigh, Aram; Berntson, Erik; Platts, Loretta G.; Westerlund, Hugo

2016-01-01

This study investigates the joint effect of office type (cell, shared room, open-plan, and flex) and personality, measured by the Big Five personality traits, on self-rated measures of distraction, job satisfaction, and job performance (measured by professional efficacy). Regression analyses with interactions between personality and office type were conducted on 1205 participants working in 5 organizations from both the private and public sectors. While few interactions were observed in the cases of professional efficacy and job satisfaction, several were observed between personality traits and office type on the level of distraction reported. Specifically, more emotionally stable participants reported lower distraction, particularly those working in flex offices. Both agreeableness and openness to experience were associated with higher levels of distraction among participants in open-plan compared to cell offices. PMID:27223898

Isfahan MISP Dataset.

PubMed

Kashefpur, Masoud; Kafieh, Rahele; Jorjandi, Sahar; Golmohammadi, Hadis; Khodabande, Zahra; Abbasi, Mohammadreza; Teifuri, Nilufar; Fakharzadeh, Ali Akbar; Kashefpoor, Maryam; Rabbani, Hossein

2017-01-01

An online depository was introduced to share clinical ground truth with the public and provide open access for researchers to evaluate their computer-aided algorithms. PHP was used for web programming and MySQL for database managing. The website was entitled "biosigdata.com." It was a fast, secure, and easy-to-use online database for medical signals and images. Freely registered users could download the datasets and could also share their own supplementary materials while maintaining their privacies (citation and fee). Commenting was also available for all datasets, and automatic sitemap and semi-automatic SEO indexing have been set for the site. A comprehensive list of available websites for medical datasets is also presented as a Supplementary (http://journalonweb.com/tempaccess/4800.584.JMSS_55_16I3253.pdf).

A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication.

PubMed

Hrynaszkiewicz, Iain

2010-09-02

BMC Research Notes aims to ensure that data files underlying published articles are made available in standard, reusable formats, and the journal is calling for contributions from the scientific community to achieve this goal. Educational Data Notes included in this special series should describe a domain-specific data standard and provide an example data set with the article, or a link to data that are permanently hosted elsewhere. The contributions should also provide some evidence of the data standard's application and preparation guidance that could be used by others wishing to conduct similar experiments. The journal is also keen to receive contributions on broader aspects of scientific data sharing, archiving, and open data.

Stakeholders' perspectives on biobank-based genomic research: systematic review of the literature

PubMed Central

Husedzinovic, Alma; Ose, Dominik; Schickhardt, Christoph; Fröhling, Stefan; Winkler, Eva C

2015-01-01

The success of biobank-based genomic research is widely dependent on people's willingness to donate their tissue. Thus, stakeholders' opinions should be considered in the development of best practice guidelines for research and recruiting participants. We systematically analyzed the empirical literature describing different stakeholders' views towards ethical questions with regard to type of consent, data sharing and return of incidental findings. Patients are more open to one-time general consent than the public. Only a small proportion desires recontact if the research aim changed. A broad consent model would prevent only a small proportion of patients from participating in research. Although professionals are concerned about a risk of reidentification, patients and the public support data sharing and find that the benefit of research outweighs the potential risk of reidentification. However, they desire detailed information about the privacy protection measures. Regarding the return of incidental findings, the public and professionals focus on clinically actionable results, whereas patients are interested in receiving as much information as possible. For professionals, concrete guidelines that help managing the return of incidental findings should be warranted. For this it would be helpful addressing the different categories – actionable, untreatable and inheritable diseases – upfront with patients and public. PMID:25735479

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

PubMed

Clark, Alex M; Dole, Krishna; Coulon-Spektor, Anna; McNutt, Andrew; Grass, George; Freundlich, Joel S; Reynolds, Robert C; Ekins, Sean

2015-06-22

On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, and the ability to share such models still remains a major challenge limiting drug discovery. We describe the creation of a reference implementation of a Bayesian model-building software module, which we have released as an open source component that is now included in the Chemistry Development Kit (CDK) project, as well as implemented in the CDD Vault and in several mobile apps. We use this implementation to build an array of Bayesian models for ADME/Tox, in vitro and in vivo bioactivity, and other physicochemical properties. We show that these models possess cross-validation receiver operator curve values comparable to those generated previously in prior publications using alternative tools. We have now described how the implementation of Bayesian models with FCFP6 descriptors generated in the CDD Vault enables the rapid production of robust machine learning models from public data or the user's own datasets. The current study sets the stage for generating models in proprietary software (such as CDD) and exporting these models in a format that could be run in open source software using CDK components. This work also demonstrates that we can enable biocomputation across distributed private or public datasets to enhance drug discovery.

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets

PubMed Central

2015-01-01

On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, and the ability to share such models still remains a major challenge limiting drug discovery. We describe the creation of a reference implementation of a Bayesian model-building software module, which we have released as an open source component that is now included in the Chemistry Development Kit (CDK) project, as well as implemented in the CDD Vault and in several mobile apps. We use this implementation to build an array of Bayesian models for ADME/Tox, in vitro and in vivo bioactivity, and other physicochemical properties. We show that these models possess cross-validation receiver operator curve values comparable to those generated previously in prior publications using alternative tools. We have now described how the implementation of Bayesian models with FCFP6 descriptors generated in the CDD Vault enables the rapid production of robust machine learning models from public data or the user’s own datasets. The current study sets the stage for generating models in proprietary software (such as CDD) and exporting these models in a format that could be run in open source software using CDK components. This work also demonstrates that we can enable biocomputation across distributed private or public datasets to enhance drug discovery. PMID:25994950

Data Management Challenges in a National Scientific Program of 55 Diverse Research Projects

NASA Astrophysics Data System (ADS)

De Bruin, T.

2016-12-01

In 2007-2015, the Dutch funding agency NWO funded the National Ocean and Coastal Research Program (in Dutch: ZKO). This program focused on `the scientific analysis of five societal challenges related to a sustainable use of the sea and coastal zones'. These five challenges were safety, economic yield, nature, spatial planning & development and water quality. The ZKO program was `set up to strengthen the cohesion and collaboration within Dutch marine research'. From the start of the program, data management was addressed, to allow data to be shared amongst the, diverse, research projects. The ZKO program was divided in 4 different themes (or regions). The `Carrying Capacity' theme was subdivided into 3 `research lines': Carrying capacity (Wadden Sea) - Policy-relevant Research - Monitoring - Hypothesis-driven Research Oceans North Sea Transnational Wadden Sea Research 56 Projects were funded, ranging from studies on the governance of the Wadden Sea to expeditions studying trace elements in the Atlantic Ocean. One of the first projects to be funded was the data management project. Its objectives were to allow data exchange between projects, to archive all relevant data from all ZKO projects and to make the data and publications publicly available, following the ZKO Data Policy. This project was carried out by the NIOZ Data Management Group. It turned out that the research projects had hardly any interest in sharing data between projects and had good (?) arguments not to share data at all until the end of the projects. A data portal was built, to host and make available all ZKO data and publications. When it came to submitting the data to this portal, most projects obliged willingly, though found it occasionally difficult to find time to do so. However, some projects refused to submit data to an open data portal, despite the rules set up by the funding agency and agreed by all. The take-home message of this presentation is that data sharing is a cultural and psychological issue, not a technical one. The presentation will explain how the data portal was set up and is embedded in national and international data access infrastructures. The focus of the presentation will be on the roles of research funders, researchers and their institutions, politics and society in achieving truly open data, using the ZKO program as a real-life example.

Complete data lifecycles and citizen science integration via The Public Laboratory

NASA Astrophysics Data System (ADS)

Griffith, A.; Dosemagen, S.; Warren, J.

2012-04-01

The collection, communication, and sharing of data relating to the 2010 Deepwater Horizon oil spill proved to be a case study in the lack of data transparency and poor collaboration on a variety of levels. British Petroleum and the government worked together to keep the public out of the spill area while collecting over 31,000 water and sediment samples from the Gulf of Mexico after the initial explosion in April, 2010. Although thousands of images were immediately collected by the National Oceanic and Atmospheric Administration and the US Geological Survey, some of those raw data sets still remain inaccessible, are in difficult to use formats, or have been modified for public release. The lack of sharing of information by federal agencies and BP was particularly frustrating given the use of publicly funded resources. Discrepancies between information posted on federal and state websites and conditions in the field were apparent and a key factor in the poor relations between authorities and local residents. The conditions under which data is collected, the affiliation of the authors, and the intended use, vastly impacts how well we trust those data. The solution, we believe, is for local communities to produce their own high-quality data through collaboration with organizations such as The Public Laboratory for Open Technology and Science. The Public Laboratory community worked with Gulf Coast residents in the field to document the effects of oil on shorelines with do-it-yourself aerial photography. For less than 100 in parts, we used helium balloons and kites to send cameras to over a thousand feet, and stitched the resulting images into high-resolution maps using our free, open-source software. Over a hundred volunteers hit the beaches to take tens of thousands of photos, depicting slicks, oiled wetlands, and the birds, fish, and plants threatened by the disaster. Our efforts resulted in the largest repository of publicly archived oil spill data to date and it is for use without restriction. Public Laboratory techniques are cheaper, more temporally relevant, more portable, and more accurate than other methods of remote sensing. In some cases, our spatial resolutions were 20 times better than those of Google Earth. Our integration of community members represents a bottom up approach in data collection, management, and literacy. The Public Laboratory data archives are maintained on-line with public access and all our software is open source with the source code publicly available. We believe this approach to be the new paradigm in data transparency, whether privately or publicly funded. The Public Laboratory has even initiated discussions with lawyers familiar with environmental laws to increase possible uses in litigation. But the data are collected for the public, by the public. By involving the public and any interested parties in the collection of data and tracking that data horizontally from collection to publication, we engage a larger number of people making transparency inherent in the process. We have found greater levels of interest and comprehension by citizens when they are involved in the inclusive process.

An analysis of ophthalmology services in Finland - has the time come for a Public-Private Partnership?

PubMed Central

Tynkkynen, Liina-Kaisa; Lehto, Juhani

2009-01-01

Background We studied the prerequisites for Public-Private Partnership (PPP) in the context of the Finnish health care system and more specifically in the field of ophthalmology. PPP can be defined as a more or less permanent cooperation between public and private actors, through which the joint products or services are developed and in which the risks, costs and profits are shared. The Finnish eye care services system is heterogeneous with several different providers and can be regarded as sub-optimal in terms of overall resource use. What is more, the public sector is suffering from a shortage of ophthalmologists, which further decreases its possibilities to meet the present needs. As ophthalmology has traditionally been a medical specialty with a substantial private sector involvement in service provision, PPP could be a feasible policy to be used in the field. We thus ask the following research question: Is there, and to what extent, an open window of opportunity for PPP? Methods In addition to the previously published literature, the research data consisted of 17 thematic interviews with public and private experts in the field of ophthalmology. The analysis was conducted in two stages. First, a literature-based content analysis was used to explore the prerequisites for PPP. Second, Kingdon's (1995) multiple streams theory was used to study the opening of the window of opportunity for PPP. Results Public and private parties reported similar problems in the current situation but defined them differently. Also, there is no consensus on policy alternatives. Public opinion seems to be somewhat uncertain as to the attitudes towards private service providers. The analysis thus showed that although there are prerequisites for PPP, the time has not yet come for a Public-Private Partnership. Conclusion Should the window open fully, the emergence of policy entrepreneurs and an opportunity for a win-win situation between public and private organizations are required. PMID:19900293

45 CFR 304.30 - Public sources of State's share.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 2 2011-10-01 2011-10-01 false Public sources of State's share. 304.30 Section 304.30 Public Welfare Regulations Relating to Public Welfare OFFICE OF CHILD SUPPORT ENFORCEMENT... HUMAN SERVICES FEDERAL FINANCIAL PARTICIPATION § 304.30 Public sources of State's share. (a) Public...

Commercial Development Plan for the International Space Station

NASA Technical Reports Server (NTRS)

1998-01-01

The long term objective of the development plan for the International Space Station (ISS) is to establish the foundation for a marketplace and stimulate a national economy for space products and services in low-Earth orbit, where both demand and supply are dominated by the private sector. The short term objective is to begin the transition to private investment and offset a share of the public cost for operating the space shuttle fleet and space station through commercial enterprise in open markets.

UC Berkeley's Celebration of the International Year of Astronomy 2009

NASA Astrophysics Data System (ADS)

Cobb, B. E.; Croft, S.; Silverman, J. M.; Klein, C.; Modjaz, M.

2010-08-01

We present the astronomy outreach efforts undertaken for the International Year of Astronomy 2009 at the University of California, Berkeley. Our department-wide endeavors included a monthly public lecture series by UC Berkeley astronomers and a major astronomy outreach event during a campus-wide university "open house," which included solar observing and a Starlab Planetarium. In addition to sharing our outreach techniques and outcomes, we discuss some of our unique strategies for advertising our events to the local community.

Final Report for Project FG02-05ER25685

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiaosong Ma

2009-05-07

In this report, the PI summarizes the results and achievements obtained in the sponsored project. Overall, the project has been very successful and produced both research results in massive data-intensive computing and data management for large scale supercomputers today, and in open-source software products. During the project period, 14 conference/journal publications, as well as two PhD students, have been produced due to exclusive or shared support from this award. In addition, the PI has recently been granted tenure from NC State University.

Publishing SNP genotypes of human embryonic stem cell lines: policy statement of the International Stem Cell Forum Ethics Working Party.

PubMed

Knoppers, Bartha M; Isasi, Rosario; Benvenisty, Nissim; Kim, Ock-Joo; Lomax, Geoffrey; Morris, Clive; Murray, Thomas H; Lee, Eng Hin; Perry, Margery; Richardson, Genevra; Sipp, Douglas; Tanner, Klaus; Wahlström, Jan; de Wert, Guido; Zeng, Fanyi

2011-09-01

Novel methods and associated tools permitting individual identification in publicly accessible SNP databases have become a debatable issue. There is growing concern that current technical and ethical safeguards to protect the identities of donors could be insufficient. In the context of human embryonic stem cell research, there are no studies focusing on the probability that an hESC line donor could be identified by analyzing published SNP profiles and associated genotypic and phenotypic information. We present the International Stem Cell Forum (ISCF) Ethics Working Party's Policy Statement on "Publishing SNP Genotypes of Human Embryonic Stem Cell Lines (hESC)". The Statement prospectively addresses issues surrounding the publication of genotypic data and associated annotations of hESC lines in open access databases. It proposes a balanced approach between the goals of open science and data sharing with the respect for fundamental bioethical principles (autonomy, privacy, beneficence, justice and research merit and integrity).

Transforming Education Research through Open Video Data Sharing

ERIC Educational Resources Information Center

Gilmore, Rick O.; Adolph, Karen E.; Millman, David S.; Gordon, Andrew

2016-01-01

Open data sharing promises to accelerate the pace of discovery in the developmental and learning sciences, but significant technical, policy, and cultural barriers have limited its adoption. As a result, most research on learning and development remains shrouded in a culture of isolation. Data sharing is the rare exception (Gilmore, 2016). Many…

Opening education.

PubMed

Smith, Marshall S

2009-01-02

Spurred by the publication of Massachusetts Institute of Technology OpenCourseWare in 2002, the open educational resources (OER) movement, which has rapidly expanded and captured the imagination and energy of millions of creators and users throughout the world, now faces many opportunities and substantial challenges as it moves to become an integral part of the world's educational environment. The confluence of the Web and a spirit of sharing intellectual property have fueled a worldwide movement to make knowledge and education materials open to all for use. OER are content (courses, books, lesson plans, articles, etc.), tools (virtual laboratories, simulations, and games), and software that support learning and educational practice. OER are free on the Web, and most have licenses that allow copyright holders to retain ownership while providing specified rights for use in original and modified forms. At the least, OER have helped to level the distribution of knowledge across the world. A second promise of OER is to help transform educational practices. This article explores the history of and promises and challenges for OER.

xiSPEC: web-based visualization, analysis and sharing of proteomics data.

PubMed

Kolbowski, Lars; Combe, Colin; Rappsilber, Juri

2018-05-08

We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments. Highlighting or selecting data points in any view is represented in all other views. Views are interactive scalable vector graphic elements, which can be exported, e.g. for use in publication. xiSPEC allows for re-annotation of spectra for easy hypothesis testing by modifying input data. xiSPEC is freely accessible at http://spectrumviewer.org and the source code is openly available on https://github.com/Rappsilber-Laboratory/xiSPEC.

DCO-VIVO: A Collaborative Data Platform for the Deep Carbon Science Communities

NASA Astrophysics Data System (ADS)

Wang, H.; Chen, Y.; West, P.; Erickson, J. S.; Ma, X.; Fox, P. A.

2014-12-01

Deep Carbon Observatory (DCO) is a decade-long scientific endeavor to understand carbon in the complex deep Earth system. Thousands of DCO scientists from institutions across the globe are organized into communities representing four domains of exploration: Extreme Physics and Chemistry, Reservoirs and Fluxes, Deep Energy, and Deep Life. Cross-community and cross-disciplinary collaboration is one of the most distinctive features in DCO's flexible research framework. VIVO is an open-source Semantic Web platform that facilitates cross-institutional researcher and research discovery. it includes a number of standard ontologies that interconnect people, organizations, publications, activities, locations, and other entities of research interest to enable browsing, searching, visualizing, and generating Linked Open (research) Data. The DCO-VIVO solution expedites research collaboration between DCO scientists and communities. Based on DCO's specific requirements, the DCO Data Science team developed a series of extensions to the VIVO platform including extending the VIVO information model, extended query over the semantic information within VIVO, integration with other open source collaborative environments and data management systems, using single sign-on, assigning of unique Handles to DCO objects, and publication and dataset ingesting extensions using existing publication systems. We present here the iterative development of these requirements that are now in daily use by the DCO community of scientists for research reporting, information sharing, and resource discovery in support of research activities and program management.

Web-based GIS for spatial pattern detection: application to malaria incidence in Vietnam.

PubMed

Bui, Thanh Quang; Pham, Hai Minh

2016-01-01

There is a great concern on how to build up an interoperable health information system of public health and health information technology within the development of public information and health surveillance programme. Technically, some major issues remain regarding to health data visualization, spatial processing of health data, health information dissemination, data sharing and the access of local communities to health information. In combination with GIS, we propose a technical framework for web-based health data visualization and spatial analysis. Data was collected from open map-servers and geocoded by open data kit package and data geocoding tools. The Web-based system is designed based on Open-source frameworks and libraries. The system provides Web-based analyst tool for pattern detection through three spatial tests: Nearest neighbour, K function, and Spatial Autocorrelation. The result is a web-based GIS, through which end users can detect disease patterns via selecting area, spatial test parameters and contribute to managers and decision makers. The end users can be health practitioners, educators, local communities, health sector authorities and decision makers. This web-based system allows for the improvement of health related services to public sector users as well as citizens in a secure manner. The combination of spatial statistics and web-based GIS can be a solution that helps empower health practitioners in direct and specific intersectional actions, thus provide for better analysis, control and decision-making.

Automatic page composition with nested sub-layouts

NASA Astrophysics Data System (ADS)

Hunter, Andrew

2013-03-01

This paper provides an overview of a system for the automatic composition of publications. The system first composes nested hierarchies of contents, then applies layout engines at branch points in the hierarchies to explore layout options, and finally selects the best overall options for the finished publications. Although the system has been developed as a general platform for automated publishing, this paper describes its application to the composition and layout of a magazine-like publication for social content from Facebook. The composition process works by assembling design fragments that have been populated with text and images from the Facebook social network. The fragments constitute a design language for a publication. Each design fragment is a nested mutable sub-layout that has no specific size or shape until after it has been laid-out. The layout process balances the space requirements of the fragment's internal contents with its external context in the publication. The mutability of sub-layouts requires that their layout options must be kept open until all the other contents that share the same space have been considered. Coping with large numbers of options is one of the greatest challenges in layout automation. Most existing layout methods work by rapidly elimination design options rather than by keeping options open. A further goal of this publishing system is to confirm that a custom publication can be generated quickly by the described methods. In general, the faster that publications can be created, the greater the opportunities for the technology.

The national drug abuse treatment clinical trials network data share project: website design, usage, challenges, and future directions.

PubMed

Shmueli-Blumberg, Dikla; Hu, Lian; Allen, Colleen; Frasketi, Michael; Wu, Li-Tzy; Vanveldhuisen, Paul

2013-01-01

There are many benefits of data sharing, including the promotion of new research from effective use of existing data, replication of findings through re-analysis of pooled data files, meta-analysis using individual patient data, and reinforcement of open scientific inquiry. A randomized controlled trial is considered as the 'gold standard' for establishing treatment effectiveness, but clinical trial research is very costly, and sharing data is an opportunity to expand the investment of the clinical trial beyond its original goals at minimal costs. We describe the goals, developments, and usage of the Data Share website (http://www.ctndatashare.org) for the National Drug Abuse Treatment Clinical Trials Network (CTN) in the United States, including lessons learned, limitations, and major revisions, and considerations for future directions to improve data sharing. Data management and programming procedures were conducted to produce uniform and Health Insurance Portability and Accountability Act (HIPAA)-compliant de-identified research data files from the completed trials of the CTN for archiving, managing, and sharing on the Data Share website. Since its inception in 2006 and through October 2012, nearly 1700 downloads from 27 clinical trials have been accessed from the Data Share website, with the use increasing over the years. Individuals from 31 countries have downloaded data from the website, and there have been at least 13 publications derived from analyzing data through the public Data Share website. Minimal control over data requests and usage has resulted in little information and lack of control regarding how the data from the website are used. Lack of uniformity in data elements collected across CTN trials has limited cross-study analyses. The Data Share website offers researchers easy access to de-identified data files with the goal to promote additional research and identify new findings from completed CTN studies. To maximize the utility of the website, ongoing collaborative efforts are needed to standardize the core measures used for data collection in the CTN studies with the goal to increase their comparability and to facilitate the ability to pool data files for cross-study analyses.

The National Drug Abuse Treatment Clinical Trials Network Data Share Project: Website Design, Usage, Challenges and Future Directions

PubMed Central

Shmueli-Blumberg, Dikla; Hu, Lian; Allen, Colleen; Frasketi, Michael; Wu, Li-Tzy; VanVeldhuisen, Paul

2014-01-01

Background The are many benefits of data sharing, including the promotion of new research from effective use of existing data, replication of findings through re-analysis of pooled data files, meta-analysis using individual patient data, and reinforcement of open scientific inquiry. A randomized controlled trial is considered as the “gold standard” for establishing treatment effectiveness, but clinical trial research is very costly and sharing data is an opportunity to expand the investment of the clinical trial beyond its original goals at minimal costs. Purpose We describe the goals, developments, and usage of the Data Share website (www.ctndatashare.org) for the National Drug Abuse Treatment Clinical Trials Network (CTN) in the US, including lessons learned, limitations and major revisions and considerations for future directions to improve data sharing. Methods Data management and programming procedures were conducted to produce uniform and Health Insurance Portability and Accountability Act (HIPAA)-compliant de-identified research data files from the completed trials of the CTN for archiving, managing, and sharing on the Data Share website. Results Since its inception in 2006 and through October 2012, nearly 1700 downloads from 27 clinical trials have been accessed from the Data Share website, with the use increasing over the years. Individuals from 31 countries have downloaded data from the website, and there have been at least 13 publications derived from analyzing data through the public Data Share website. Limitations Minimal control over data requests and usage has resulted in little information and lack of control regarding how the data from the website are used. Lack of uniformity in data elements collected across CTN trials has limited cross-study analyses. Conclusions The Data Share website offers researchers easy access to deidentified data files with the goal to promote additional research and identify new findings from completed CTN studies. To maximize the utility of the website, on-going collaborative efforts are needed to standardize the core measures used for data collection in the CTN studies with the goal to increase their comparability and to facilitate the ability to pool data files for cross-study analyses. PMID:24085772

Open resource metagenomics: a model for sharing metagenomic libraries.

PubMed

Neufeld, J D; Engel, K; Cheng, J; Moreno-Hagelsieb, G; Rose, D R; Charles, T C

2011-11-30

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM(2)BL [1]). The CM(2)BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.

Open resource metagenomics: a model for sharing metagenomic libraries

PubMed Central

Neufeld, J.D.; Engel, K.; Cheng, J.; Moreno-Hagelsieb, G.; Rose, D.R.; Charles, T.C.

2011-01-01

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM2BL [1]). The CM2BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project. PMID:22180823

The biometric imaginary: (Dis)trust in a policy vacuum.

PubMed

Gunnarsdóttir, Kristrún; Rommetveit, Kjetil

2017-02-01

The decision in Europe to implement biometric passports, visas and residence permits was made at the highest levels without much consultation, checks and balances. Council regulation came into force relatively unnoticed in January 2005, as part of wider securitization policies urging systems interoperability and data sharing across borders. This article examines the biometric imaginary that characterizes this European Union decision, dictated by executive powers in the policy vacuum after 9/11 - a depiction of mobility governance, technological necessity and whom/what to trust or distrust, calling upon phantom publics to justify decisions rather than test their grounding. We consult an online blog we operated in 2010 to unravel this imaginary years on. Drawing on Dewey's problem of the public, we discuss this temporary opening of a public space in which the imaginary could be reframed and contested, and how such activities may shape, if at all, relations between politics, publics, policy intervention and societal development.

PhysioNet: physiologic signals, time series and related open source software for basic, clinical, and applied research.

PubMed

Moody, George B; Mark, Roger G; Goldberger, Ary L

2011-01-01

PhysioNet provides free web access to over 50 collections of recorded physiologic signals and time series, and related open-source software, in support of basic, clinical, and applied research in medicine, physiology, public health, biomedical engineering and computing, and medical instrument design and evaluation. Its three components (PhysioBank, the archive of signals; PhysioToolkit, the software library; and PhysioNetWorks, the virtual laboratory for collaborative development of future PhysioBank data collections and PhysioToolkit software components) connect researchers and students who need physiologic signals and relevant software with researchers who have data and software to share. PhysioNet's annual open engineering challenges stimulate rapid progress on unsolved or poorly solved questions of basic or clinical interest, by focusing attention on achievable solutions that can be evaluated and compared objectively using freely available reference data.

Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

PubMed Central

2016-01-01

The development of new antimalarial compounds remains a pivotal part of the strategy for malaria elimination. Recent large-scale phenotypic screens have provided a wealth of potential starting points for hit-to-lead campaigns. One such public set is explored, employing an open source research mechanism in which all data and ideas were shared in real time, anyone was able to participate, and patents were not sought. One chemical subseries was found to exhibit oral activity but contained a labile ester that could not be replaced without loss of activity, and the original hit exhibited remarkable sensitivity to minor structural change. A second subseries displayed high potency, including activity within gametocyte and liver stage assays, but at the cost of low solubility. As an open source research project, unexplored avenues are clearly identified and may be explored further by the community; new findings may be cumulatively added to the present work. PMID:27800551

Las Cumbres Observatory Partners With Local Museums In “Experience The Eclipse” Community Program

NASA Astrophysics Data System (ADS)

Greenstreet, Sarah; Seale, Sandy; Rivera, Javier; Skinner, Ron

2017-10-01

Las Cumbres Observatory (LCO) in Goleta, California, together with the Santa Barbara Museum of Natural History (SBMNH) and the Wolf Museum of Exploration & Innovation (MOXI) put together a community program called “Experience the Eclipse” for the month of August.The greater Santa Barbara community includes over 200,000 people and the city is known for its vibrant cultural life. Events featuring science, physics, and astronomy are very popular. In 2016, Javier Rivera, the Astronomy Program Manager of the SBMNH, and Ron Skinner, the Director of Education at MOXI, met with LCO to discuss planning a month of activities to educate the public about the Great American Eclipse. The vision was to capitalize on the strength of each organization and to share information and events.The events included daily planetarium shows and open houses at the observatory of the SBMNH. All three organizations gave parties at public venues with presentations by astronomers. Together the group purchased 6,000 pairs of eclipse viewer glasses and they shared the responsibility of distributing these to local schools and community groups. A master calendar of the events was published in local press outlets and a document describing the eclipse and safe viewing practices was distributed widely. Preparation of these materials was a joint effort among the three institutions.“Experience the Eclipse” was a great success. The open houses at SBMNH were well attended and all public events sold out very quickly. On August 21, the SBMNH presented a live feed of the eclipse taken from their own observatory.We will present photos and videos from these events, along with data on the attendance and quotes from enthusiastic participants.

OpenTopography: Enabling Online Access to High-Resolution Lidar Topography Data and Processing Tools

NASA Astrophysics Data System (ADS)

Crosby, Christopher; Nandigam, Viswanath; Baru, Chaitan; Arrowsmith, J. Ramon

2013-04-01

High-resolution topography data acquired with lidar (light detection and ranging) technology are revolutionizing the way we study the Earth's surface and overlying vegetation. These data, collected from airborne, tripod, or mobile-mounted scanners have emerged as a fundamental tool for research on topics ranging from earthquake hazards to hillslope processes. Lidar data provide a digital representation of the earth's surface at a resolution sufficient to appropriately capture the processes that contribute to landscape evolution. The U.S. National Science Foundation-funded OpenTopography Facility (http://www.opentopography.org) is a web-based system designed to democratize access to earth science-oriented lidar topography data. OpenTopography provides free, online access to lidar data in a number of forms, including the raw point cloud and associated geospatial-processing tools for customized analysis. The point cloud data are co-located with on-demand processing tools to generate digital elevation models, and derived products and visualizations which allow users to quickly access data in a format appropriate for their scientific application. The OpenTopography system is built using a service-oriented architecture (SOA) that leverages cyberinfrastructure resources at the San Diego Supercomputer Center at the University of California San Diego to allow users, regardless of expertise level, to access these massive lidar datasets and derived products for use in research and teaching. OpenTopography hosts over 500 billion lidar returns covering 85,000 km2. These data are all in the public domain and are provided by a variety of partners under joint agreements and memoranda of understanding with OpenTopography. Partners include national facilities such as the NSF-funded National Center for Airborne Lidar Mapping (NCALM), as well as non-governmental organizations and local, state, and federal agencies. OpenTopography has become a hub for high-resolution topography resources. Datasets hosted by other organizations, as well as lidar-specific software, can be registered into the OpenTopography catalog, providing users a "one-stop shop" for such information. With several thousand active users, OpenTopography is an excellent example of a mature Spatial Data Infrastructure system that is enabling access to challenging data for research, education and outreach. Ongoing OpenTopography design and development work includes the archive and publication of datasets using digital object identifiers (DOIs); creation of a more flexible and scalable high-performance environment for processing of large datasets; expanded support for satellite and terrestrial lidar; and creation of a "pluggable" infrastructure for third-party programs and algorithms. OpenTopography has successfully created a facility for sharing lidar data. In the project's next phase, we are working to enable equally easy and successful sharing of services for processing and analysis of these data.

Privacy-Preserving and Secure Sharing of PHR in the Cloud.

PubMed

Zhang, Leyou; Wu, Qing; Mu, Yi; Zhang, Jingxia

2016-12-01

As a new summarized record of an individual's medical data and information, Personal Health Record (PHR) can be accessible online. The owner can control fully his/her PHR files to be shared with different users such as doctors, clinic agents, and friends. However, in an open network environment like in the Cloud, these sensitive privacy information may be gotten by those unauthorized parties and users. In this paper, we consider how to achieve PHR data confidentiality and provide fine-grained access control of PHR files in the public Cloud based on Attribute Based Encryption(ABE). Differing from previous works, we also consider the privacy preserving of the receivers since the attributes of the receivers relate to their identity or medical information, which would make some sensitive data exposed to third services. Anonymous ABE(AABE) not only enforces the security of PHR of the owners but also preserves the privacy of the receivers. But a normal AABE with a single private key generation(PKG) center may not match a PHR system in the hierarchical architecture. Therefore, we discuss not only the construction of the PHR sharing system base on AABE but also how to construct the PHR sharing system based on the hierarchical AABE. The proposed schemes(especially based on hierarchical AABE) have many advantages over the available such as short public keys, constant-size private keys, which overcome the weaknesses in the existing works. In the standard model, the introduced schemes achieve compact security in the prime order groups.

Measuring the Value of Research Data: A Citation Analysis of Oceanographic Data Sets

PubMed Central

Belter, Christopher W.

2014-01-01

Evaluation of scientific research is becoming increasingly reliant on publication-based bibliometric indicators, which may result in the devaluation of other scientific activities - such as data curation – that do not necessarily result in the production of scientific publications. This issue may undermine the movement to openly share and cite data sets in scientific publications because researchers are unlikely to devote the effort necessary to curate their research data if they are unlikely to receive credit for doing so. This analysis attempts to demonstrate the bibliometric impact of properly curated and openly accessible data sets by attempting to generate citation counts for three data sets archived at the National Oceanographic Data Center. My findings suggest that all three data sets are highly cited, with estimated citation counts in most cases higher than 99% of all the journal articles published in Oceanography during the same years. I also find that methods of citing and referring to these data sets in scientific publications are highly inconsistent, despite the fact that a formal citation format is suggested for each data set. These findings have important implications for developing a data citation format, encouraging researchers to properly curate their research data, and evaluating the bibliometric impact of individuals and institutions. PMID:24671177

Measuring the value of research data: a citation analysis of oceanographic data sets.

PubMed

Belter, Christopher W

2014-01-01

Evaluation of scientific research is becoming increasingly reliant on publication-based bibliometric indicators, which may result in the devaluation of other scientific activities--such as data curation--that do not necessarily result in the production of scientific publications. This issue may undermine the movement to openly share and cite data sets in scientific publications because researchers are unlikely to devote the effort necessary to curate their research data if they are unlikely to receive credit for doing so. This analysis attempts to demonstrate the bibliometric impact of properly curated and openly accessible data sets by attempting to generate citation counts for three data sets archived at the National Oceanographic Data Center. My findings suggest that all three data sets are highly cited, with estimated citation counts in most cases higher than 99% of all the journal articles published in Oceanography during the same years. I also find that methods of citing and referring to these data sets in scientific publications are highly inconsistent, despite the fact that a formal citation format is suggested for each data set. These findings have important implications for developing a data citation format, encouraging researchers to properly curate their research data, and evaluating the bibliometric impact of individuals and institutions.

Four disruptive strategies for removing drug discovery bottlenecks.

PubMed

Ekins, Sean; Waller, Chris L; Bradley, Mary P; Clark, Alex M; Williams, Antony J

2013-03-01

Drug discovery is shifting focus from industry to outside partners and, in the process, creating new bottlenecks. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the USA, with little coordination or consideration of the outputs and creating a translational gap. Although there have been collaborative public-private partnerships in Europe to share pharmaceutical data, the USA has seemingly lagged behind and this may hold it back. Sharing precompetitive data and models may accelerate discovery across the board, while finding the best collaborators, mining social media and mobile approaches to open drug discovery should be evaluated in our efforts to remove drug discovery bottlenecks. We describe four strategies to rectify the current unsustainable situation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Isfahan MISP Dataset

PubMed Central

Kashefpur, Masoud; Kafieh, Rahele; Jorjandi, Sahar; Golmohammadi, Hadis; Khodabande, Zahra; Abbasi, Mohammadreza; Teifuri, Nilufar; Fakharzadeh, Ali Akbar; Kashefpoor, Maryam; Rabbani, Hossein

2017-01-01

An online depository was introduced to share clinical ground truth with the public and provide open access for researchers to evaluate their computer-aided algorithms. PHP was used for web programming and MySQL for database managing. The website was entitled “biosigdata.com.” It was a fast, secure, and easy-to-use online database for medical signals and images. Freely registered users could download the datasets and could also share their own supplementary materials while maintaining their privacies (citation and fee). Commenting was also available for all datasets, and automatic sitemap and semi-automatic SEO indexing have been set for the site. A comprehensive list of available websites for medical datasets is also presented as a Supplementary (http://journalonweb.com/tempaccess/4800.584.JMSS_55_16I3253.pdf). PMID:28487832

Communicating Your Science

NASA Astrophysics Data System (ADS)

Young, C. A.

2016-12-01

Effective science communication can open doors, accelerate your career and even make you a better scientist. Part of being an effective and productive scientist means being an effective science communicator. The scientist must communicate their work in talks, posters, peer-reviewed papers, internal reports, proposals as well as to the broader public (including law makers). Despite the importance of communication, it has traditionally not been part of our core training as scientists. Today's science students are beginning to have more opportunities to formally develop their science communication skills. Fortunately, new and even more established scientists have a range of tools and resources at their disposal. In this presentation, we will share some of these resources, share our own experiences utilizing them, and provide some practical tools to improve your own science communication skills.

Open Data in Global Environmental Research: The Belmont Forum's Open Data Survey.

PubMed

Schmidt, Birgit; Gemeinholzer, Birgit; Treloar, Andrew

2016-01-01

This paper presents the findings of the Belmont Forum's survey on Open Data which targeted the global environmental research and data infrastructure community. It highlights users' perceptions of the term "open data", expectations of infrastructure functionalities, and barriers and enablers for the sharing of data. A wide range of good practice examples was pointed out by the respondents which demonstrates a substantial uptake of data sharing through e-infrastructures and a further need for enhancement and consolidation. Among all policy responses, funder policies seem to be the most important motivator. This supports the conclusion that stronger mandates will strengthen the case for data sharing.

Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

NASA Astrophysics Data System (ADS)

Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

2015-12-01

Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical models.

Balancing Benefits and Risks of Immortal Data: Participants' Views of Open Consent in the Personal Genome Project.

PubMed

Zarate, Oscar A; Brody, Julia Green; Brown, Phil; Ramirez-Andreotta, Mónica D; Perovich, Laura; Matz, Jacob

2016-01-01

An individual's health, genetic, or environmental-exposure data, placed in an online repository, creates a valuable shared resource that can accelerate biomedical research and even open opportunities for crowd-sourcing discoveries by members of the public. But these data become "immortalized" in ways that may create lasting risk as well as benefit. Once shared on the Internet, the data are difficult or impossible to redact, and identities may be revealed by a process called data linkage, in which online data sets are matched to each other. Reidentification (re-ID), the process of associating an individual's name with data that were considered deidentified, poses risks such as insurance or employment discrimination, social stigma, and breach of the promises often made in informed-consent documents. At the same time, re-ID poses risks to researchers and indeed to the future of science, should re-ID end up undermining the trust and participation of potential research participants. The ethical challenges of online data sharing are heightened as so-called big data becomes an increasingly important research tool and driver of new research structures. Big data is shifting research to include large numbers of researchers and institutions as well as large numbers of participants providing diverse types of data, so the participants' consent relationship is no longer with a person or even a research institution. In addition, consent is further transformed because big data analysis often begins with descriptive inquiry and generation of a hypothesis, and the research questions cannot be clearly defined at the outset and may be unforeseeable over the long term. In this article, we consider how expanded data sharing poses new challenges, illustrated by genomics and the transition to new models of consent. We draw on the experiences of participants in an open data platform-the Personal Genome Project-to allow study participants to contribute their voices to inform ethical consent practices and protocol reviews for big-data research. © 2015 The Hastings Center.

Wireless Shared Resources: Sharing Right-Of-Way For Wireless Telecommunications, Guidance On Legal And Institutional Issues

DOT National Transportation Integrated Search

1997-06-06

PUBLIC-PRIVATE PARTNERSHIPS SHARED RESOURCE PROJECTS ARE PUBLIC-PRIVATE ARRANGEMENTS THAT INVOLVE SHARING PUBLIC PROPERTY SUCH AS RIGHTS-OF-WAY AND PRIVATE RESOURCES SUCH AS TELECOMMUNICATIONS CAPACITY AND EXPERTISE. TYPICALLY, PRIVATE TELECOMMUNI...

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications.

PubMed

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu.

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications

PubMed Central

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu PMID:24131510

Openness Versus Obstruction: The Importance of Protecting Open Data and Transparency, While Guarding Against Obstruction and Interference

NASA Astrophysics Data System (ADS)

Rosenthal, S.; Kurtz, L.

2017-12-01

Open data plays an important role in facilitating scientific progress and developing sound public policies. However, sometimes important scientific initiatives can be subverted by those seeking to politicize science and attack scientists. There is a critical distinction between data openness, and forcing scientists to live in a fishbowl by demanding disclosure of traditionally confidential materials, such as peer review correspondence or preliminary drafts. The former is intended to promote scientific advances (which may well involve criticisms and disagreements), while the latter is an attempt to chill and disrupt research. Agenda-driven groups have sought to obtain scientists' private emails, preliminary drafts, and peer critiques - which may include technical jargon and "what if" debates that can easily be taken out of context - in an effort to intimidate researchers and disrupt their work. Fostering true transparency requires an understanding of what should be shared to advance scientific research, including disclosing information that might expose potential biases (such as funding information), while also protecting the candid debate, open collaboration, and academic freedom that is integral to the scientific process.

To share or not to share? Expected pros and cons of data sharing in radiological research.

PubMed

Sardanelli, Francesco; Alì, Marco; Hunink, Myriam G; Houssami, Nehmat; Sconfienza, Luca M; Di Leo, Giovanni

2018-06-01

The aims of this paper are to illustrate the trend towards data sharing, i.e. the regulated availability of the original patient-level data obtained during a study, and to discuss the expected advantages (pros) and disadvantages (cons) of data sharing in radiological research. Expected pros include the potential for verification of original results with alternative or supplementary analyses (including estimation of reproducibility), advancement of knowledge by providing new results by testing new hypotheses (not explored by the original authors) on pre-existing databases, larger scale analyses based on individual-patient data, enhanced multidisciplinary cooperation, reduced publication of false studies, improved clinical practice, and reduced cost and time for clinical research. Expected cons are outlined as the risk that the original authors could not exploit the entire potential of the data they obtained, possible failures in patients' privacy protection, technical barriers such as the lack of standard formats, and possible data misinterpretation. Finally, open issues regarding data ownership, the role of individual patients, advocacy groups and funding institutions in decision making about sharing of data and images are discussed. • Regulated availability of patient-level data of published clinical studies (data-sharing) is expected. • Expected benefits include verification/advancement of knowledge, reduced cost/time of research, clinical improvement. • Potential drawbacks include faults in patients' identity protection and data misinterpretation.

Towards Networked Knowledge: The Learning Registry, an Infrastructure for Sharing Online Learning Resources

ERIC Educational Resources Information Center

Lee, Ashley; Hobson, Joe; Bienkowski, Marie; Midgley, Steve; Currier, Sarah; Campbell, Lorna M.; Novoselova, Tatiana

2012-01-01

In this article, the authors describe an open-source, open-data digital infrastructure for sharing information about open educational resources (OERs) across disparate systems and platforms. The Learning Registry, which began as a project funded by the U.S. Departments of Education and Defense, currently has an active international community…

Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks.

PubMed

Rosenberg, David M; Horn, Charles C

2016-08-01

Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus-a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software-an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research. Copyright © 2016 the American Physiological Society.

Neurophysiological analytics for all! Free open-source software tools for documenting, analyzing, visualizing, and sharing using electronic notebooks

PubMed Central

2016-01-01

Neurophysiology requires an extensive workflow of information analysis routines, which often includes incompatible proprietary software, introducing limitations based on financial costs, transfer of data between platforms, and the ability to share. An ecosystem of free open-source software exists to fill these gaps, including thousands of analysis and plotting packages written in Python and R, which can be implemented in a sharable and reproducible format, such as the Jupyter electronic notebook. This tool chain can largely replace current routines by importing data, producing analyses, and generating publication-quality graphics. An electronic notebook like Jupyter allows these analyses, along with documentation of procedures, to display locally or remotely in an internet browser, which can be saved as an HTML, PDF, or other file format for sharing with team members and the scientific community. The present report illustrates these methods using data from electrophysiological recordings of the musk shrew vagus—a model system to investigate gut-brain communication, for example, in cancer chemotherapy-induced emesis. We show methods for spike sorting (including statistical validation), spike train analysis, and analysis of compound action potentials in notebooks. Raw data and code are available from notebooks in data supplements or from an executable online version, which replicates all analyses without installing software—an implementation of reproducible research. This demonstrates the promise of combining disparate analyses into one platform, along with the ease of sharing this work. In an age of diverse, high-throughput computational workflows, this methodology can increase efficiency, transparency, and the collaborative potential of neurophysiological research. PMID:27098025

Public engagement workshop: how to improve medicines for older people?

PubMed

Orlu-Gul, Mine; Raimi-Abraham, Bahijja; Jamieson, Elizabeth; Wei, Li; Murray, Macey; Stawarz, Katarzyna; Stegemann, Sven; Tuleu, Catherine; Smith, Felicity J

2014-01-01

Public engagement in medication management has become more and more important in promoting population health. A public engagement workshop attended by 78 members of the geriatric community, family carers as well as professionals from academic research, industry and regulatory agencies entitled 'How to improve medicines for older people?' took place on the 2nd July 2013 at the University College London (UCL) School of Pharmacy. The main aim of the event was to provide a dynamic environment for information exchange and to identify ways of improving current and future geriatric drug therapy. The day opened with presentations from UCL School of Pharmacy researchers on the use of medicines at home, formulations, administration devices and multi-component compliance aids (MCAs) whilst a representative from UCL Interaction Centre gave an insightful presentation on human errors and resilience strategies regarding medication use. These opening presentations encouraged participants to share their own experiences as well as initiating a lively debate. Following the plenary presentations, the workshop was divided into 8 groups for parallel discussion session. These opinion sharing sessions witnessed fruitful discussions between patients, carers and researchers. The day closed with a panel session of representatives from the European Medicines Agency (EMA), the Medicines and Healthcare products Regulatory Agency (MHRA), the Geriatric Medicines Society and Guy's and St. Thomas' NHS Foundation Trust (GSTT). Participants were encouraged to voice their questions, concerns and recommendations about medications. The main concern expressed by both patients and carers from the workshop were (but are not limited to) formulation changes, MCA accessibility difficulties, interactions of different medicines, carers' concerns with the administration of medicines and not having enough knowledge of services provided by community pharmacists i.e. medicines use reviews (MURs) or new medicine service (NMS). Overall, this workshop created a useful forum for members of the geriatric community, their carers as well as research and industrial professionals to have an input in the improvement and management of geriatric drug therapy and this event also provided an excellent opportunity for the researchers to share the latest research innovations with attendees. Copyright © 2013 Elsevier B.V. All rights reserved.

NASA Plan for Increasing Access to the Results of Scientific Research

NASA Technical Reports Server (NTRS)

2014-01-01

This plan is issued in response to the Executive Office of the President's February 22, 2013, Office of Science and Technology Policy (OSTP) Memorandum for the Heads of Executive Departments and Agencies, "Increasing Access to the Results of Federally Funded Scientific Research." Through this memorandum, OSTP directed all agencies with more than $100 million in annual research and development expenditures to prepare a plan for improving the public's access to the results of federally funded research. The National Aeronautics and Space Administration (NASA) invests on the order of $3 billion annually in fundamental and applied research and technology development1 across a broad range of topics, including space and Earth sciences, life and physical sciences, human health, aeronautics, and technology. Promoting the full and open sharing of data with research communities, private industry, academia, and the general public is one of NASA's longstanding core values. For example, NASA's space and suborbital mission personnel routinely process, archive, and distribute their data to researchers around the globe. This plan expands the breadth of NASA's open-access culture to include data and publications for all of the scientific research that the Agency sponsors.

Meta4: a web application for sharing and annotating metagenomic gene predictions using web services.

PubMed

Richardson, Emily J; Escalettes, Franck; Fotheringham, Ian; Wallace, Robert J; Watson, Mick

2013-01-01

Whole-genome shotgun metagenomics experiments produce DNA sequence data from entire ecosystems, and provide a huge amount of novel information. Gene discovery projects require up-to-date information about sequence homology and domain structure for millions of predicted proteins to be presented in a simple, easy-to-use system. There is a lack of simple, open, flexible tools that allow the rapid sharing of metagenomics datasets with collaborators in a format they can easily interrogate. We present Meta4, a flexible and extensible web application that can be used to share and annotate metagenomic gene predictions. Proteins and predicted domains are stored in a simple relational database, with a dynamic front-end which displays the results in an internet browser. Web services are used to provide up-to-date information about the proteins from homology searches against public databases. Information about Meta4 can be found on the project website, code is available on Github, a cloud image is available, and an example implementation can be seen at.

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

PubMed Central

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V.; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-01-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfra­structure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities. PMID:22514186

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology.

PubMed

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-05-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

Seabird databases and the new paradigm for scientific publication and attribution

USGS Publications Warehouse

Hatch, Scott A.

2010-01-01

For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

WWOSC 2014: research needs for better health resilience to weather hazards.

PubMed

Jancloes, Michel; Anderson, Vidya; Gosselin, Pierre; Mee, Carol; Chong, Nicholas J

2015-03-05

The first World Weather Open Science Conference (WWOSC, held from 17-21 August 2014 in Montreal, Québec), provided an open forum where the experience and perspective of a variety of weather information providers and users was combined with the latest application advances in social sciences. A special session devoted to health focused on how best the most recent weather information and communication technologies (ICT) could improve the health emergency responses to disasters resulting from natural hazards. Speakers from a plenary presentation and its corresponding panel shared lessons learnt from different international multidisciplinary initiatives against weather-related epidemics, such as malaria, leptospirosis and meningitis and from public health responses to floods and heat waves such as in Ontario and Quebec, Canada. Participants could bear witness to recent progress made in the use of forecasting tools and in the application of increased spatiotemporal resolutions in the management of weather related health risks through anticipative interventions, early alert and warning and early responses especially by vulnerable groups. There was an agreement that resilience to weather hazards is best developed based on evidence of their health impact and when, at local level, there is a close interaction between health care providers, epidemiologists, climate services, public health authorities and communities. Using near real time health data (such as hospital admission, disease incidence monitoring…) combined with weather information has been recommended to appraise the relevance of decisions and the effectiveness of interventions and to make adjustments when needed. It also helps appraising how people may be more or less vulnerable to a particular hazard depending on the resilience infrastructures and services. This session was mainly attended by climate, environment and social scientists from North American and European countries. Producing a commentary appears to be an effective way to share this session's conclusions to research institutions and public health experts worldwide. It also advocates for better linking operational research and decision making and for appraising the impact of ICT and public health interventions on health.

Engaging the Public to Identify Opportunities to Improve Critical Care: A Qualitative Analysis of an Open Community Forum

PubMed Central

Potestio, Melissa L.; Boyd, Jamie M.; Bagshaw, Sean M.; Heyland, Daren; Oxland, Peter; Doig, Christopher J.; Zygun, Dave; Stelfox, Henry T.

2015-01-01

Objective To engage the public to understand how to improve the care of critically ill patients. Design A qualitative content analysis of an open community forum (Café Scientifique). Setting Public venue in Calgary, Alberta, Canada. Participants Members of the general public including patients, families of patients, health care providers, and members of the community at large. Methods A panel of researchers, decision-makers, and a family member led a Café Scientifique, an informal dialogue between the populace and experts, over three-hours to engage the public to understand how to improve the care of critically ill patients. Conventional qualitative content analysis was used to analyze the data. The inductive analysis occurred in three phases: coding, categorizing, and developing themes. Results Thirty-eight members of the public (former ICU patients, family members of patients, providers, community members) attended. Participants focused the discussion and provided concrete suggestions for improvement around communication (family as surrogate voice, timing of conversations, decision tools) and provider well-being and engagement, as opposed to medical interventions in critical care. Conclusions Café participants believe patient and family centered care is important to ensure high-quality care in the ICU. A Café Scientifique is a valuable forum to engage the public to contribute to priority setting areas for research in critical care, as well as a platform to share lived experience. Research stakeholders including health care organizations, governments, and funding organizations should provide more opportunities for the public to engage in meaningful conversations about how to best improve healthcare. PMID:26580406

Engaging the Public to Identify Opportunities to Improve Critical Care: A Qualitative Analysis of an Open Community Forum.

PubMed

Potestio, Melissa L; Boyd, Jamie M; Bagshaw, Sean M; Heyland, Daren; Oxland, Peter; Doig, Christopher J; Zygun, Dave; Stelfox, Henry T

2015-01-01

To engage the public to understand how to improve the care of critically ill patients. A qualitative content analysis of an open community forum (Café Scientifique). Public venue in Calgary, Alberta, Canada. Members of the general public including patients, families of patients, health care providers, and members of the community at large. A panel of researchers, decision-makers, and a family member led a Café Scientifique, an informal dialogue between the populace and experts, over three-hours to engage the public to understand how to improve the care of critically ill patients. Conventional qualitative content analysis was used to analyze the data. The inductive analysis occurred in three phases: coding, categorizing, and developing themes. Thirty-eight members of the public (former ICU patients, family members of patients, providers, community members) attended. Participants focused the discussion and provided concrete suggestions for improvement around communication (family as surrogate voice, timing of conversations, decision tools) and provider well-being and engagement, as opposed to medical interventions in critical care. Café participants believe patient and family centered care is important to ensure high-quality care in the ICU. A Café Scientifique is a valuable forum to engage the public to contribute to priority setting areas for research in critical care, as well as a platform to share lived experience. Research stakeholders including health care organizations, governments, and funding organizations should provide more opportunities for the public to engage in meaningful conversations about how to best improve healthcare.

Driving towards ecotechnologies.

PubMed

Najjar, Devora A; Normandin, Avery M; Strait, Elizabeth A; Esvelt, Kevin M

2017-12-01

The prospect of using genetic methods to target vector, parasite, and reservoir species offers tremendous potential benefits to public health, but the use of genome editing to alter the shared environment will require special attention to public perception and community governance in order to benefit the world. Public skepticism combined with the media scrutiny of gene drive systems could easily derail unpopular projects entirely, especially given the potential for trade barriers to be raised against countries that employ self-propagating gene drives. Hence, open and community-guided development of thoughtfully chosen applications is not only the most ethical approach, but also the most likely to overcome the economic, social, and diplomatic barriers. Here we review current and past attempts to alter ecosystems using biological methods, identify key determinants of social acceptance, and chart a stepwise path for developers towards safe and widely supported use.

Changes in mode of travel to work: a natural experimental study of new transport infrastructure.

PubMed

Heinen, Eva; Panter, Jenna; Mackett, Roger; Ogilvie, David

2015-06-20

New transport infrastructure may promote a shift towards active travel, thereby improving population health. The purpose of this study was to determine the effect of a major transport infrastructure project on commuters' mode of travel, trip frequency and distance travelled to work. Quasi-experimental analysis nested within a cohort study of 470 adults working in Cambridge, UK. The intervention consisted of the opening of a guided busway with a path for walking and cycling in 2011. Exposure to the intervention was defined as the negative of the square root of the shortest distance from home to busway. The outcome measures were changes in commute mode share and number of commute trips - both based on a seven-day travel-to-work record collected before (2009) and after (2012) the intervention - and change in objective commute distance. The mode share outcomes were changes in the proportions of trips (i) involving any active travel, (ii) involving any public transport, and (iii) made entirely by car. Separate multinomial regression models were estimated adjusting for commute and sociodemographic characteristics, residential settlement size and life events. Proximity to the busway predicted an increased likelihood of a large (>30 %) increase in the share of commute trips involving any active travel (relative risk ratio [RRR] 1.80, 95 % CI 1.27, 2.55) and a large decrease in the share of trips made entirely by car (RRR 2.09, 95 % CI 1.35, 3.21), as well as a lower likelihood of a small (<30 %) reduction in the share of trips involving any active travel (RRR 0.47, 95 % CI 0.28, 0.81). It was not associated with changes in the share of commute trips involving any public transport, the number of commute trips, or commute distance. The new infrastructure promoted an increase in the share of commuting trips involving active travel and a decrease in the share made entirely by car. Further analysis will show the extent to which the changes in commute mode share were translated into an increase in time spent in active commuting and consequent health gain.

'Predatory' open access: a longitudinal study of article volumes and market characteristics.

PubMed

Shen, Cenyu; Björk, Bo-Christer

2015-10-01

A negative consequence of the rapid growth of scholarly open access publishing funded by article processing charges is the emergence of publishers and journals with highly questionable marketing and peer review practices. These so-called predatory publishers are causing unfounded negative publicity for open access publishing in general. Reports about this branch of e-business have so far mainly concentrated on exposing lacking peer review and scandals involving publishers and journals. There is a lack of comprehensive studies about several aspects of this phenomenon, including extent and regional distribution. After an initial scan of all predatory publishers and journals included in the so-called Beall's list, a sample of 613 journals was constructed using a stratified sampling method from the total of over 11,000 journals identified. Information about the subject field, country of publisher, article processing charge and article volumes published between 2010 and 2014 were manually collected from the journal websites. For a subset of journals, individual articles were sampled in order to study the country affiliation of authors and the publication delays. Over the studied period, predatory journals have rapidly increased their publication volumes from 53,000 in 2010 to an estimated 420,000 articles in 2014, published by around 8,000 active journals. Early on, publishers with more than 100 journals dominated the market, but since 2012 publishers in the 10-99 journal size category have captured the largest market share. The regional distribution of both the publisher's country and authorship is highly skewed, in particular Asia and Africa contributed three quarters of authors. Authors paid an average article processing charge of 178 USD per article for articles typically published within 2 to 3 months of submission. Despite a total number of journals and publishing volumes comparable to respectable (indexed by the Directory of Open Access Journals) open access journals, the problem of predatory open access seems highly contained to just a few countries, where the academic evaluation practices strongly favor international publication, but without further quality checks.

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework

PubMed Central

Grigis, Antoine; Goyard, David; Cherbonnier, Robin; Gareau, Thomas; Papadopoulos Orfanos, Dimitri; Chauvat, Nicolas; Di Mascio, Adrien; Schumann, Gunter; Spooren, Will; Murphy, Declan; Frouin, Vincent

2017-01-01

In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts. PMID:28360851

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework.

PubMed

Grigis, Antoine; Goyard, David; Cherbonnier, Robin; Gareau, Thomas; Papadopoulos Orfanos, Dimitri; Chauvat, Nicolas; Di Mascio, Adrien; Schumann, Gunter; Spooren, Will; Murphy, Declan; Frouin, Vincent

2017-01-01

In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts.

Open Data in Global Environmental Research: The Belmont Forum’s Open Data Survey

PubMed Central

Schmidt, Birgit; Gemeinholzer, Birgit; Treloar, Andrew

2016-01-01

This paper presents the findings of the Belmont Forum’s survey on Open Data which targeted the global environmental research and data infrastructure community. It highlights users’ perceptions of the term “open data”, expectations of infrastructure functionalities, and barriers and enablers for the sharing of data. A wide range of good practice examples was pointed out by the respondents which demonstrates a substantial uptake of data sharing through e-infrastructures and a further need for enhancement and consolidation. Among all policy responses, funder policies seem to be the most important motivator. This supports the conclusion that stronger mandates will strengthen the case for data sharing. PMID:26771577

The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data

PubMed Central

Berman, Jules J; Edgerton, Mary E; Friedman, Bruce A

2003-01-01

Background Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone using the data exchange specification can validate their TMA files using a software implementation written in Perl and distributed as a supplemental file with this publication. Conclusion The TMA data exchange specification is now available in a draft form with community-approved Common Data Elements and a community-approved general file format and data structure. The specification can be freely used by the scientific community. Efforts sponsored by the Association for Pathology Informatics to refine the draft TMA data exchange specification are expected to continue for at least two more years. The interested public is invited to participate in these open efforts. Information on future workshops will be posted at (API we site). PMID:12769826

Using Co-authorship Networks to Map and Analyse Global Neglected Tropical Disease Research with an Affiliation to Germany

PubMed Central

Bender, Max Ernst; Edwards, Suzanne; von Philipsborn, Peter; Steinbeis, Fridolin; Keil, Thomas; Tinnemann, Peter

2015-01-01

Background Research on Neglected Tropical Diseases (NTDs) has increased in recent decades, and significant need-gaps in diagnostic and treatment tools remain. Analysing bibliometric data from published research is a powerful method for revealing research efforts, partnerships and expertise. We aim to identify and map NTD research networks in Germany and their partners abroad to enable an informed and transparent evaluation of German contributions to NTD research. Methodology/Principal Findings A SCOPUS database search for articles with German author affiliations that were published between 2002 and 2012 was conducted for kinetoplastid and helminth diseases. Open-access tools were used for data cleaning and scientometrics (OpenRefine), geocoding (OpenStreetMaps) and to create (Table2Net), visualise and analyse co-authorship networks (Gephi). From 26,833 publications from around the world that addressed 11 diseases, we identified 1,187 (4.4%) with at least one German author affiliation, and we processed 972 publications for the five most published-about diseases. Of those, we extracted 4,007 individual authors and 863 research institutions to construct co-author networks. The majority of co-authors outside Germany were from high-income countries and Brazil. Collaborations with partners on the African continent remain scattered. NTD research within Germany was distributed among 220 research institutions. We identified strong performers on an individual level by using classic parameters (number of publications, h-index) and social network analysis parameters (betweenness centrality). The research network characteristics varied strongly between diseases. Conclusions/Significance The share of NTD publications with German affiliations is approximately half of its share in other fields of medical research. This finding underlines the need to identify barriers and expand Germany’s otherwise strong research activities towards NTDs. A geospatial analysis of research collaborations with partners abroad can support decisions to strengthen research capacity, particularly in low- and middle-income countries, which were less involved in collaborations than high-income countries. Identifying knowledge hubs within individual researcher networks complements traditional scientometric indicators that are used to identify opportunities for collaboration. Using free tools to analyse research processes and output could facilitate data-driven health policies. Our findings contribute to the prioritisation of efforts in German NTD research at a time of impending local and global policy decisions. PMID:26719978

Researcher Perspectives on Publication and Peer Review of Data

PubMed Central

Kratz, John Ernest; Strasser, Carly

2015-01-01

Data “publication” seeks to appropriate the prestige of authorship in the peer-reviewed literature to reward researchers who create useful and well-documented datasets. The scholarly communication community has embraced data publication as an incentive to document and share data. But, numerous new and ongoing experiments in implementation have not yet resolved what a data publication should be, when data should be peer-reviewed, or how data peer review should work. While researchers have been surveyed extensively regarding data management and sharing, their perceptions and expectations of data publication are largely unknown. To bring this important yet neglected perspective into the conversation, we surveyed ∼ 250 researchers across the sciences and social sciences– asking what expectations“data publication” raises and what features would be useful to evaluate the trustworthiness, evaluate the impact, and enhance the prestige of a data publication. We found that researcher expectations of data publication center on availability, generally through an open database or repository. Few respondents expected published data to be peer-reviewed, but peer-reviewed data enjoyed much greater trust and prestige. The importance of adequate metadata was acknowledged, in that almost all respondents expected data peer review to include evaluation of the data’s documentation. Formal citation in the reference list was affirmed by most respondents as the proper way to credit dataset creators. Citation count was viewed as the most useful measure of impact, but download count was seen as nearly as valuable. These results offer practical guidance for data publishers seeking to meet researcher expectations and enhance the value of published data. PMID:25706992

So you want to be a science writer.

PubMed

Fleischman, John; Szalinski, Christina

2014-07-01

The Internet destroyed the ecology of traditional science journalism, drying up ad revenues and pushing "old school" mass media toward extinction. But the new technology opened a wider landscape for digital science writers, online "content curators," and scientists to chronicle the wonders and worries of modern science. For those thinking of a career in science writing, here is a flash history, a quick overview, some advice, and a few cautions. © 2014 Fleischman and Szalinski. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Social Media as a New Vital Sign: Commentary

PubMed Central

2018-01-01

Mobile technologies, such as wireless glucometers and mobile health apps, are increasingly being integrated into health and medical care. Because patients openly share real-time information about their health behaviors and outcomes on social media, social media data may also be used as a tool for monitoring patient care. This commentary describes how recent advances in computer science, psychology, and medicine enable social media data to become a new health “vital sign,” as well as actionable steps that public health officials, health systems, and clinics can take to integrate social data into both public and population health as well as into individual patient care. Barriers that first need to be addressed, including privacy concerns, legal and ethical responsibilities, and infrastructure support, are discussed. PMID:29712631

42: An Open-Source Simulation Tool for Study and Design of Spacecraft Attitude Control Systems

NASA Technical Reports Server (NTRS)

Stoneking, Eric

2018-01-01

Simulation is an important tool in the analysis and design of spacecraft attitude control systems. The speaker will discuss the simulation tool, called simply 42, that he has developed over the years to support his own work as an engineer in the Attitude Control Systems Engineering Branch at NASA Goddard Space Flight Center. 42 was intended from the outset to be high-fidelity and powerful, but also fast and easy to use. 42 is publicly available as open source since 2014. The speaker will describe some of 42's models and features, and discuss its applicability to studies ranging from early concept studies through the design cycle, integration, and operations. He will outline 42's architecture and share some thoughts on simulation development as a long-term project.

Exposing the QCD Splitting Function with CMS Open Data.

PubMed

Larkoski, Andrew; Marzani, Simone; Thaler, Jesse; Tripathee, Aashish; Xue, Wei

2017-09-29

The splitting function is a universal property of quantum chromodynamics (QCD) which describes how energy is shared between partons. Despite its ubiquitous appearance in many QCD calculations, the splitting function cannot be measured directly, since it always appears multiplied by a collinear singularity factor. Recently, however, a new jet substructure observable was introduced which asymptotes to the splitting function for sufficiently high jet energies. This provides a way to expose the splitting function through jet substructure measurements at the Large Hadron Collider. In this Letter, we use public data released by the CMS experiment to study the two-prong substructure of jets and test the 1→2 splitting function of QCD. To our knowledge, this is the first ever physics analysis based on the CMS Open Data.

12 CFR 701.32 - Payment on shares by public units and nonmembers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... needs, sources and intended uses of public unit and nonmember shares; (ii) Provision for matching maturities of public unit and nonmember shares with corresponding assets, or justification for any mismatch...

12 CFR 701.32 - Payment on shares by public units and nonmembers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... needs, sources and intended uses of public unit and nonmember shares; (ii) Provision for matching maturities of public unit and nonmember shares with corresponding assets, or justification for any mismatch...

easyDAS: Automatic creation of DAS servers

PubMed Central

2011-01-01

Background The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. Results Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. Conclusions easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community. PMID:21244646

The TimeStudio Project: An open source scientific workflow system for the behavioral and brain sciences.

PubMed

Nyström, Pär; Falck-Ytter, Terje; Gredebäck, Gustaf

2016-06-01

This article describes a new open source scientific workflow system, the TimeStudio Project, dedicated to the behavioral and brain sciences. The program is written in MATLAB and features a graphical user interface for the dynamic pipelining of computer algorithms developed as TimeStudio plugins. TimeStudio includes both a set of general plugins (for reading data files, modifying data structures, visualizing data structures, etc.) and a set of plugins specifically developed for the analysis of event-related eyetracking data as a proof of concept. It is possible to create custom plugins to integrate new or existing MATLAB code anywhere in a workflow, making TimeStudio a flexible workbench for organizing and performing a wide range of analyses. The system also features an integrated sharing and archiving tool for TimeStudio workflows, which can be used to share workflows both during the data analysis phase and after scientific publication. TimeStudio thus facilitates the reproduction and replication of scientific studies, increases the transparency of analyses, and reduces individual researchers' analysis workload. The project website ( http://timestudioproject.com ) contains the latest releases of TimeStudio, together with documentation and user forums.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruegg, Janine; Gries, Corinna; Bond-Lamberty, Benjamin

An important goal of macrosystems ecology research is to advance understanding of ecological systems at both fine and broad temporal and spatial scales. Our premise in this paper is that such projects require information management that is integrated into projects from their inception. Such efforts will lead to improved communication and sharing of knowledge among diverse project participants, better science outcomes, and more open science. We promote "closing the data life cycle" by publishing well-documented data sets, which allows for re-use of data to answer new and different questions from the ones conceived by the original projects. The practice ofmore » documenting and submitting data sets to publicly accessible data repositories ensures that research results and data are accessible to and useable by other researchers, thus fostering open science. Ecologists are often not familiar with the information management tools and requirements to effectively preserve data, however, and receive little institutional or professional incentive to do so. This paper describes recommended steps to these ends, and gives examples from current macrosystem ecology projects of why information management is so critical to ensuring that scientific results can be both reproduced and data shared for future use.« less

The Open AUC Project.

PubMed

Cölfen, Helmut; Laue, Thomas M; Wohlleben, Wendel; Schilling, Kristian; Karabudak, Engin; Langhorst, Bradley W; Brookes, Emre; Dubbs, Bruce; Zollars, Dan; Rocco, Mattia; Demeler, Borries

2010-02-01

Progress in analytical ultracentrifugation (AUC) has been hindered by obstructions to hardware innovation and by software incompatibility. In this paper, we announce and outline the Open AUC Project. The goals of the Open AUC Project are to stimulate AUC innovation by improving instrumentation, detectors, acquisition and analysis software, and collaborative tools. These improvements are needed for the next generation of AUC-based research. The Open AUC Project combines on-going work from several different groups. A new base instrument is described, one that is designed from the ground up to be an analytical ultracentrifuge. This machine offers an open architecture, hardware standards, and application programming interfaces for detector developers. All software will use the GNU Public License to assure that intellectual property is available in open source format. The Open AUC strategy facilitates collaborations, encourages sharing, and eliminates the chronic impediments that have plagued AUC innovation for the last 20 years. This ultracentrifuge will be equipped with multiple and interchangeable optical tracks so that state-of-the-art electronics and improved detectors will be available for a variety of optical systems. The instrument will be complemented by a new rotor, enhanced data acquisition and analysis software, as well as collaboration software. Described here are the instrument, the modular software components, and a standardized database that will encourage and ease integration of data analysis and interpretation software.

GRIIDC: A Data Repository for Gulf of Mexico Science

NASA Astrophysics Data System (ADS)

Ellis, S.; Gibeaut, J. C.

2017-12-01

The Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) system is a data management solution appropriate for any researcher sharing Gulf of Mexico and oil spill science data. Our mission is to ensure a data and information legacy that promotes continual scientific discovery and public awareness of the Gulf of Mexico ecosystem. GRIIDC developed an open-source software solution to manage data from the Gulf of Mexico Research Initiative (GoMRI). The GoMRI program has over 2500 researchers from diverse fields of study with a variety of attitudes, experiences, and capacities for data sharing. The success of this solution is apparent through new partnerships to share data generated by RESTORE Act Centers of Excellence Programs, the National Academies of Science, and others. The GRIIDC data management system integrates dataset management planning, metadata creation, persistent identification, and data discoverability into an easy-to-use web application. No specialized software or program installations are required to support dataset submission or discovery. Furthermore, no data transformations are needed to submit data to GRIIDC; common file formats such as Excel, csv, and text are all acceptable for submissions. To ensure data are properly documented using the GRIIDC implementation of the ISO 19115-2 metadata standard, researchers submit detailed descriptive information through a series of interactive forms and no knowledge of metadata or xml formats are required. Once a dataset is documented and submitted the GRIIDC team performs a review of the dataset package. This review ensures that files can be opened and contain data, and that data are completely and accurately described. This review does not include performing quality assurance or control of data points, as GRIIDC expects scientists to perform these steps during the course of their work. Once approved, data are made public and searchable through the GRIIDC data discovery portal and the DataONE network.

Intoxigenic digital spaces? Youth, social networking sites and alcohol marketing.

PubMed

Griffiths, Richard; Casswell, Sally

2010-09-01

To examine how young people in New Zealand engage with alcohol and reproduce alcohol marketing messages and alcohol-related branding in 'Bebo', a popular social networking site (SNS) on the Internet. Data are drawn from information posted on approximately 150 Bebo Web pages and analysed by way of textual analysis and cyberspace ethnography. Social networking sites, such as Bebo, provide young people with a digital space in which to share a range of alcohol marketing messages via peer-to-peer transmission. Bebo also enables youth to communicate to one another how they consume alcohol and their views of alcohol marketing messages. The information being shared by young people who use Bebo is openly provided in the form of personal information, forum comments, digital photographs and answering quizzes about their engagement with alcohol. Through this sharing of information in the digital Internet environment, young people are creating 'intoxigenic social identities' as well as 'intoxigenic digital spaces' that further contribute towards the normalisation of youth consumption of alcohol. A better understanding of how youth are using the Internet to share their experiences with alcohol and engagement with alcohol-related messages is crucial to public health research as alcohol marketing practices rapidly evolve.

Citizen science as seen by scientists: Methodological, epistemological and ethical dimensions.

PubMed

Riesch, Hauke; Potter, Clive

2014-01-01

Citizen science as a way of communicating science and doing public engagement has over the past decade become the focus of considerable hopes and expectations. It can be seen as a win-win situation, where scientists get help from the public and the participants get a public engagement experience that involves them in real and meaningful scientific research. In this paper we present the results of a series of qualitative interviews with scientists who participated in the 'OPAL' portfolio of citizen science projects that has been running in England since 2007: What were their experiences of participating in citizen science? We highlight two particular sets of issues that our participants have voiced, methodological/epistemological and ethical issues. While we share the general enthusiasm over citizen science, we hope that the research in this paper opens up more debate over the potential pitfalls of citizen science as seen by the scientists themselves.

NOAA Inter-Agency Networking for Open Data and Research Results

NASA Astrophysics Data System (ADS)

de la Beaujardiere, J.

2015-12-01

The US National Oceanic and Atmospheric Administration (NOAA) generates tens of terabytes of data per day from hundreds of sensors on satellites, radars, aircraft, ships, and buoys, and from numerical models. With rare exceptions, all of these data should be made publicly accessible in a usable fashion. NOAA has long been both an advocate and a practitioner of open data, and has observations going back 150 years in its archives. The NOAA data management community therefore welcomed the White House mandates on Open Data and Open Research, and has striven to improve standardization internally and in collaboration with other organizations. This paper will summarize the state of inter-agency networking by NOAA, and will discuss future perspectives, in particular the need to achieve a state where the appropriate technology choices for particular classes of geospatial data are obvious and beyond discussion, and where data sharing and metadata creation are built into agency workflows for project planning, approval, and execution, so that instead of writing and enforcing mandates we can focus on actually using data from multiple sources to improve understanding and decision-making.

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.

PubMed

Procacci, Piero

2016-06-27

We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .

The Role of Hospital Information Systems in Universal Health Coverage Monitoring in Rwanda.

PubMed

Karara, Gustave; Verbeke, Frank; Nyssen, Marc

2015-01-01

In this retrospective study, the authors monitored the patient health coverage in 6 Rwandan hospitals in the period between 2011 and 2014. Among the 6 hospitals, 2 are third level hospitals, 2 district hospitals and 2 private hospitals. Patient insurance and financial data were extracted and analyzed from OpenClinic GA, an open source hospital information system (HIS) used in those 6 hospitals. The percentage of patients who had no health insurer globally decreased from 35% in 2011 to 15% in 2014. The rate of health insurance coverage in hospitals varied between 75% in private hospitals and 84% in public hospitals. The amounts paid by the patients for health services decreased in private hospitals to 25% of the total costs in 2014 (-7.4%) and vary between 14% and 19% in public hospitals. Although the number of insured patients has increased and the patient share decreased over the four years of study, the patients' out-of-pocket payments increased especially for in-patients. This study emphasizes the value of integrated hospital information systems for this kind of health economics research in developing countries.

MiMiR – an integrated platform for microarray data sharing, mining and analysis

PubMed Central

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-01-01

Background Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. Results A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. Conclusion The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies. PMID:18801157

MiMiR--an integrated platform for microarray data sharing, mining and analysis.

PubMed

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-09-18

Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

Removing a barrier to computer-based outbreak and disease surveillance--the RODS Open Source Project.

PubMed

Espino, Jeremy U; Wagner, M; Szczepaniak, C; Tsui, F C; Su, H; Olszewski, R; Liu, Z; Chapman, W; Zeng, X; Ma, L; Lu, Z; Dara, J

2004-09-24

Computer-based outbreak and disease surveillance requires high-quality software that is well-supported and affordable. Developing software in an open-source framework, which entails free distribution and use of software and continuous, community-based software development, can produce software with such characteristics, and can do so rapidly. The objective of the Real-Time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate the deployment of computer-based outbreak and disease surveillance systems by writing software and catalyzing the formation of a community of users, developers, consultants, and scientists who support its use. The University of Pittsburgh seeded the Open Source Project by releasing the RODS software under the GNU General Public License. An infrastructure was created, consisting of a website, mailing lists for developers and users, designated software developers, and shared code-development tools. These resources are intended to encourage growth of the Open Source Project community. Progress is measured by assessing website usage, number of software downloads, number of inquiries, number of system deployments, and number of new features or modules added to the code base. During September--November 2003, users generated 5,370 page views of the project website, 59 software downloads, 20 inquiries, one new deployment, and addition of four features. Thus far, health departments and companies have been more interested in using the software as is than in customizing or developing new features. The RODS laboratory anticipates that after initial installation has been completed, health departments and companies will begin to customize the software and contribute their enhancements to the public code base.

The NKI-Rockland Sample: A Model for Accelerating the Pace of Discovery Science in Psychiatry

PubMed Central

Nooner, Kate Brody; Colcombe, Stanley J.; Tobe, Russell H.; Mennes, Maarten; Benedict, Melissa M.; Moreno, Alexis L.; Panek, Laura J.; Brown, Shaquanna; Zavitz, Stephen T.; Li, Qingyang; Sikka, Sharad; Gutman, David; Bangaru, Saroja; Schlachter, Rochelle Tziona; Kamiel, Stephanie M.; Anwar, Ayesha R.; Hinz, Caitlin M.; Kaplan, Michelle S.; Rachlin, Anna B.; Adelsberg, Samantha; Cheung, Brian; Khanuja, Ranjit; Yan, Chaogan; Craddock, Cameron C.; Calhoun, Vincent; Courtney, William; King, Margaret; Wood, Dylan; Cox, Christine L.; Kelly, A. M. Clare; Di Martino, Adriana; Petkova, Eva; Reiss, Philip T.; Duan, Nancy; Thomsen, Dawn; Biswal, Bharat; Coffey, Barbara; Hoptman, Matthew J.; Javitt, Daniel C.; Pomara, Nunzio; Sidtis, John J.; Koplewicz, Harold S.; Castellanos, Francisco Xavier; Leventhal, Bennett L.; Milham, Michael P.

2012-01-01

The National Institute of Mental Health strategic plan for advancing psychiatric neuroscience calls for an acceleration of discovery and the delineation of developmental trajectories for risk and resilience across the lifespan. To attain these objectives, sufficiently powered datasets with broad and deep phenotypic characterization, state-of-the-art neuroimaging, and genetic samples must be generated and made openly available to the scientific community. The enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) is a response to this need. NKI-RS is an ongoing, institutionally centered endeavor aimed at creating a large-scale (N > 1000), deeply phenotyped, community-ascertained, lifespan sample (ages 6–85 years old) with advanced neuroimaging and genetics. These data will be publically shared, openly, and prospectively (i.e., on a weekly basis). Herein, we describe the conceptual basis of the NKI-RS, including study design, sampling considerations, and steps to synchronize phenotypic and neuroimaging assessment. Additionally, we describe our process for sharing the data with the scientific community while protecting participant confidentiality, maintaining an adequate database, and certifying data integrity. The pilot phase of the NKI-RS, including challenges in recruiting, characterizing, imaging, and sharing data, is discussed while also explaining how this experience informed the final design of the enhanced NKI-RS. It is our hope that familiarity with the conceptual underpinnings of the enhanced NKI-RS will facilitate harmonization with future data collection efforts aimed at advancing psychiatric neuroscience and nosology. PMID:23087608

Using Data Maturity Metrics to Help Insure Scientific Integrity

NASA Astrophysics Data System (ADS)

Bates, J. J.

2016-12-01

In the past few years, the full and open sharing of data and other artifacts of research in the geophysics have become mandatory. These include commitments from scientific societies, calls from international organizations, and in the United States, Executive Orders and legislation for open data. Unfortunately, these calls for open data have had, at best, mixed results. Audits by publishers indicate most who do not comply with are unaware of the policies or simply ignore them. A recent high profile publication on global warming resulted in repeated demands of `all data' from Congress and a prolonged back and forth on what `all data' meant. The emerging field of Data Management Maturity is making substantial progress on quantifying the elements needed to fully document, and making open and accessible, geophysical data sets. The proposed metrics have been culled from best practices for observational data sets and these metrics have been applied to a number of geophysical disciplines. A case study applying this metric to climate change indicators will be presented. It is recommended that U.S. Agencies and scientific societies formally adopt data maturity metrics to help ensure a consistent approach to ensure open data and scientific integrity.

Catalogue of extreme wave events in Ireland: revised and updated for 14 680 BP to 2017

NASA Astrophysics Data System (ADS)

O'Brien, Laura; Renzi, Emiliano; Dudley, John M.; Clancy, Colm; Dias, Frédéric

2018-03-01

This paper aims to extend and update the survey of extreme wave events in Ireland that was previously carried out by O'Brien et al. (2013). The original catalogue highlighted the frequency of such events dating back as far as the turn of the last ice age and as recent as 2012. Ireland's marine territory extends far beyond its coastline and is one of the largest seabed territories in Europe. It is therefore not surprising that extreme waves have continued to occur regularly since 2012, particularly considering the severity of weather during the winters of 2013-2014 and 2015-2016. In addition, a large number of storm surges have been identified since the publication of the original catalogue. This paper updates the O'Brien et al. (2013) catalogue to include events up to the end of 2017. Storm surges are included as a new category and events are categorised into long waves (tsunamis and storm surges) and short waves (storm and rogue waves). New results prior to 2012 are also included and some of the events previously documented are reclassified. Important questions regarding public safety, services and the influence of climate change are also highlighted. An interactive map has been created to allow the reader to navigate through events: https://drive.google.com/open?id=19cZ59pDHfDnXKYIziYAVWV6AfoE&usp=sharing.

Key Lessons in Building "Data Commons": The Open Science Data Cloud Ecosystem

NASA Astrophysics Data System (ADS)

Patterson, M.; Grossman, R.; Heath, A.; Murphy, M.; Wells, W.

2015-12-01

Cloud computing technology has created a shift around data and data analysis by allowing researchers to push computation to data as opposed to having to pull data to an individual researcher's computer. Subsequently, cloud-based resources can provide unique opportunities to capture computing environments used both to access raw data in its original form and also to create analysis products which may be the source of data for tables and figures presented in research publications. Since 2008, the Open Cloud Consortium (OCC) has operated the Open Science Data Cloud (OSDC), which provides scientific researchers with computational resources for storing, sharing, and analyzing large (terabyte and petabyte-scale) scientific datasets. OSDC has provided compute and storage services to over 750 researchers in a wide variety of data intensive disciplines. Recently, internal users have logged about 2 million core hours each month. The OSDC also serves the research community by colocating these resources with access to nearly a petabyte of public scientific datasets in a variety of fields also accessible for download externally by the public. In our experience operating these resources, researchers are well served by "data commons," meaning cyberinfrastructure that colocates data archives, computing, and storage infrastructure and supports essential tools and services for working with scientific data. In addition to the OSDC public data commons, the OCC operates a data commons in collaboration with NASA and is developing a data commons for NOAA datasets. As cloud-based infrastructures for distributing and computing over data become more pervasive, we ask, "What does it mean to publish data in a data commons?" Here we present the OSDC perspective and discuss several services that are key in architecting data commons, including digital identifier services.

Intercultural Competency in Public Health: A Call for Action to Incorporate Training into Public Health Education

PubMed Central

Fleckman, Julia M.; Dal Corso, Mark; Ramirez, Shokufeh; Begalieva, Maya; Johnson, Carolyn C.

2015-01-01

Due to increasing national diversity, programs addressing cultural competence have multiplied in U.S. medical training institutions. Although these programs share common goals for improving clinical care for patients and reducing health disparities, there is little standardization across programs. Furthermore, little progress has been made to translate cultural competency training from the clinical setting into the public health setting where the focus is on population-based health, preventative programming, and epidemiological and behavioral research. The need for culturally relevant public health programming and culturally sensitive public health research is more critical than ever. Awareness of differing cultures needs to be included in all processes of planning, implementation and evaluation. By focusing on community-based health program planning and research, cultural competence implies that it is possible for public health professionals to completely know another culture, whereas intercultural competence implies it is a dual-sided process. Public health professionals need a commitment toward intercultural competence and skills that demonstrate flexibility, openness, and self-reflection so that cultural learning is possible. In this article, the authors recommend a number of elements to develop, adapt, and strengthen intercultural competence education in public health educational institutions. PMID:26389109

Intercultural Competency in Public Health: A Call for Action to Incorporate Training into Public Health Education.

PubMed

Fleckman, Julia M; Dal Corso, Mark; Ramirez, Shokufeh; Begalieva, Maya; Johnson, Carolyn C

2015-01-01

Due to increasing national diversity, programs addressing cultural competence have multiplied in U.S. medical training institutions. Although these programs share common goals for improving clinical care for patients and reducing health disparities, there is little standardization across programs. Furthermore, little progress has been made to translate cultural competency training from the clinical setting into the public health setting where the focus is on population-based health, preventative programming, and epidemiological and behavioral research. The need for culturally relevant public health programming and culturally sensitive public health research is more critical than ever. Awareness of differing cultures needs to be included in all processes of planning, implementation and evaluation. By focusing on community-based health program planning and research, cultural competence implies that it is possible for public health professionals to completely know another culture, whereas intercultural competence implies it is a dual-sided process. Public health professionals need a commitment toward intercultural competence and skills that demonstrate flexibility, openness, and self-reflection so that cultural learning is possible. In this article, the authors recommend a number of elements to develop, adapt, and strengthen intercultural competence education in public health educational institutions.

How the World Trade Organisation is shaping domestic policies in health care.

PubMed

Price, D; Pollock, A M; Shaoul, J

1999-11-27

High up on the agenda of the World Trade Organisation (WTO) is the privatisation of education, health, welfare, social housing and transport. The WTO's aim is to extend the free market in the provision of traditional public services. Governments in Europe and the US link the expansion of trade in public services to economic success, and with the backing of powerful medico-pharmaceutical, insurance, and service corporations, the race is on to capture the share of gross domestic product that governments currently spend on public services. They will open domestic European services and domestic markets to global competition by government procurement agreements, dispute-settlement procedures, and the investment rules of global financial institutions. The UK has already set up the necessary mechanisms: the introduction of private-sector accounting rules to public services; the funding of public-sector investment via private-public partnerships or the private finance initiative; and the change to capitation funding streams, which allows the substitution of private for public funds and services. We explain the implications of these changes for European public-health-care systems and the threat they pose to universal coverage, solidarity through risk-pooling, equity, comprehensive care, and democratic accountability.

Towards an open science publishing platform.

PubMed

Tracz, Vitek; Lawrence, Rebecca

2016-01-01

The way science and research is done is rapidly becoming more open and collaborative. The traditional way of publishing new findings in journals is becoming increasingly outdated and no longer serves the needs of much of science. Whilst preprints can bring significant benefits of removing delay and selection, they do not go far enough if simply implemented alongside the existing journal system. We propose that we need a new approach, an Open Science Platform, that takes the benefits of preprints but adds formal, invited, and transparent post-publication peer review. This bypasses the problems of the current journal system and, in doing so, moves the evaluation of research and researchers away from the journal-based Impact Factor and towards a fairer system of article-based qualitative and quantitative indicators. In the long term, it should be irrelevant where a researcher publishes their findings. What is important is that research is shared and made available without delay within a framework that encourages quality standards and requires all players in the research community to work as collaborators.

A text-mining analysis of the public's reactions to the opioid crisis.

PubMed

Glowacki, Elizabeth M; Glowacki, Joseph B; Wilcox, Gary B

2017-07-19

Opioid abuse has become an epidemic in the United States. On August 25, 2016, the former Surgeon General of the United States sent an open letter to care providers asking for their help with combatting this growing health crisis. Social media forums such as Twitter allow for open discussions among the public and up-to-date exchanges of information about timely topics such as opioids. Therefore, the goal of the current study is to identify the public's reactions to the opioid epidemic by identifying the most popular topics tweeted by users. A text miner, algorithmic-driven statistical program was used to capture 73,235 original tweets and retweets posted within a 2-month time span 15 (August 15, 2016, through October 15, 2016). All tweets contained references to "opioids," "turnthetide," or similar keywords. The sets of tweets were then analyzed to identify the most prevalent topics. The most discussed topics had to do with public figures addressing opioid abuse, creating better treatment options for teen addicts, using marijuana as an alternative for managing pain, holding foreign and domestic drug makers accountable for the epidemic, promoting the "Rx for Change" campaign, addressing double standards in the perceptions and treatment of black and white opioid users, and advertising opioid recovery programs. Twitter allows users to find current information, voice their concerns, and share calls for action in response to the opioid epidemic. Monitoring the conversations about opioids that are taking place on social media forums such as Twitter can help public health officials and care providers better understand how the public is responding to this health crisis.

Enabling Interoperable and Selective Data Sharing among Social Networking Sites

NASA Astrophysics Data System (ADS)

Shin, Dongwan; Lopes, Rodrigo

With the widespread use of social networking (SN) sites and even introduction of a social component in non-social oriented services, there is a growing concern over user privacy in general, how to handle and share user profiles across SN sites in particular. Although there have been several proprietary or open source-based approaches to unifying the creation of third party applications, the availability and retrieval of user profile information are still limited to the site where the third party application is run, mostly devoid of the support for data interoperability. In this paper we propose an approach to enabling interopearable and selective data sharing among SN sites. To support selective data sharing, we discuss an authenticated dictionary (ADT)-based credential which enables a user to share only a subset of her information certified by external SN sites with applications running on an SN site. For interoperable data sharing, we propose an extension to the OpenSocial API so that it can provide an open source-based framework for allowing the ADT-based credential to be used seamlessly among different SN sites.

Department of Energy ALARA implementation guide. Response to the Health Physics Society

DOE Office of Scientific and Technical Information (OSTI.GOV)

Connelly, J.M.

1995-03-01

In the August 1993 Health Physics Society (HPS) newsletter, the HPS Scientific and Public Issues Committee published a Position Statement entitled {open_quotes}Radiation Protection of the Public and the Environment.{close_quotes}. In this article, this HPS committee made the statement that they were deeply concerned by the trend for agencies to incorporate the ALARA concept as a regulatory requirements, without providing specific guidance as to what it means and how to implement it consistently. The HPS position paper was in response to the DOE notice on proposed rulemaking for Title 10 Code of Federal Regulations Part 834, {open_quotes}Radiation Protection of the Publicmore » and the Environment{close_quotes} (10 CFR 834). In the notice of proposed rulemaking for 10 CFR 834, the Department of Energy (DOE) defined ALARA as follows: {open_quotes}As used in this part, ALARA is not a dose limit, but rather a process which has the objective of attaining doses as far below the applicable limit of this part as is reasonably achievable{close_quotes} (10 CFR 834.2, p. 16283 of the Federal Register). The HPS position paper continues, {open_quotes}The section goes on to elaborate on what is meant by a process without providing sufficient guidance to assure uniform applicability of the process.{close_quotes}. Although this concern is directed towards the ALARA process as it relates to the environment, the Office of Health, which is responsible for occupational workers, shares the same definition for ALARA.« less

Open Energy Info (OpenEI) (Fact Sheet)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2010-12-01

The Open Energy Information (OpenEI.org) initiative is a free, open-source, knowledge-sharing platform. OpenEI was created to provide access to data, models, tools, and information that accelerate the transition to clean energy systems through informed decisions.

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

Data Sharing Reveals Complexity in the Westward Spread of Domestic Animals across Neolithic Turkey

PubMed Central

Arbuckle, Benjamin S.; Kansa, Sarah Whitcher; Kansa, Eric; Orton, David; Çakırlar, Canan; Gourichon, Lionel; Atici, Levent; Galik, Alfred; Marciniak, Arkadiusz; Mulville, Jacqui; Buitenhuis, Hijlke; Carruthers, Denise; De Cupere, Bea; Demirergi, Arzu; Frame, Sheelagh; Helmer, Daniel; Martin, Louise; Peters, Joris; Pöllath, Nadja; Pawłowska, Kamilla; Russell, Nerissa; Twiss, Katheryn; Würtenberger, Doris

2014-01-01

This study presents the results of a major data integration project bringing together primary archaeozoological data for over 200,000 faunal specimens excavated from seventeen sites in Turkey spanning the Epipaleolithic through Chalcolithic periods, c. 18,000-4,000 cal BC, in order to document the initial westward spread of domestic livestock across Neolithic central and western Turkey. From these shared datasets we demonstrate that the westward expansion of Neolithic subsistence technologies combined multiple routes and pulses but did not involve a set ‘package’ comprising all four livestock species including sheep, goat, cattle and pig. Instead, Neolithic animal economies in the study regions are shown to be more diverse than deduced previously using quantitatively more limited datasets. Moreover, during the transition to agro-pastoral economies interactions between domestic stock and local wild fauna continued. Through publication of datasets with Open Context (opencontext.org), this project emphasizes the benefits of data sharing and web-based dissemination of large primary data sets for exploring major questions in archaeology (Alternative Language Abstract S1). PMID:24927173

78 FR 45565 - Notice Pursuant to the National Cooperative Research and Production Act of 1993 -- tranSMART...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-29

... activities are to enable effective sharing, integration, standardization, and analysis of heterogeneous data from collaborative translational research by mobilizing the tranSMART open- source and open-data...: (a) Establish and sustain tranSMART as the preferred data sharing and analytics platform for...

Sharing Resources in Open Educational Communities

ERIC Educational Resources Information Center

Tosato, Paolo; Arranz, Beatriz Carramolino; Avi, Bartolomé Rubia

2014-01-01

The spread of Internet and the latest Web developments have promoted the relationships between teachers, learners and institutions, as well as the creation and sharing of new Open Educational Resources (OERs). Despite this fact, many projects and research efforts paid more attention to content distribution focusing on their format and description,…

Finding Services for an Open Architecture: A Review of Existing Applications and Programs in PEO C4I

DTIC Science & Technology

2011-01-01

2004) Two key SOA success factors listed were as follows: 1. Shared Services Strategy: Existence of a strategy to identify overlapping business and...model Architectural pattern 22 Finding Services for an Open Architecture or eliminating redundancies and overlaps through use of shared services 2...Funding Model: Existence of an IT funding model aligned with and supportive of a shared services strategy. (Sun Micro- systems, 2004) Become Data

Transforming Education Research Through Open Video Data Sharing.

PubMed

Gilmore, Rick O; Adolph, Karen E; Millman, David S; Gordon, Andrew

2016-01-01

Open data sharing promises to accelerate the pace of discovery in the developmental and learning sciences, but significant technical, policy, and cultural barriers have limited its adoption. As a result, most research on learning and development remains shrouded in a culture of isolation. Data sharing is the rare exception (Gilmore, 2016). Many researchers who study teaching and learning in classroom, laboratory, museum, and home contexts use video as a primary source of raw research data. Unlike other measures, video captures the complexity, richness, and diversity of behavior. Moreover, because video is self-documenting, it presents significant potential for reuse. However, the potential for reuse goes largely unrealized because videos are rarely shared. Research videos contain information about participants' identities making the materials challenging to share. The large size of video files, diversity of formats, and incompatible software tools pose technical challenges. The Databrary (databrary.org) digital library enables researchers who study learning and development to store, share, stream, and annotate videos. In this article, we describe how Databrary has overcome barriers to sharing research videos and associated data and metadata. Databrary has developed solutions for respecting participants' privacy; for storing, streaming, and sharing videos; and for managing videos and associated metadata. The Databrary experience suggests ways that videos and other identifiable data collected in the context of educational research might be shared. Open data sharing enabled by Databrary can serve as a catalyst for a truly multidisciplinary science of learning.

Transforming Education Research Through Open Video Data Sharing

PubMed Central

Gilmore, Rick O.; Adolph, Karen E.; Millman, David S.; Gordon, Andrew

2016-01-01

Open data sharing promises to accelerate the pace of discovery in the developmental and learning sciences, but significant technical, policy, and cultural barriers have limited its adoption. As a result, most research on learning and development remains shrouded in a culture of isolation. Data sharing is the rare exception (Gilmore, 2016). Many researchers who study teaching and learning in classroom, laboratory, museum, and home contexts use video as a primary source of raw research data. Unlike other measures, video captures the complexity, richness, and diversity of behavior. Moreover, because video is self-documenting, it presents significant potential for reuse. However, the potential for reuse goes largely unrealized because videos are rarely shared. Research videos contain information about participants’ identities making the materials challenging to share. The large size of video files, diversity of formats, and incompatible software tools pose technical challenges. The Databrary (databrary.org) digital library enables researchers who study learning and development to store, share, stream, and annotate videos. In this article, we describe how Databrary has overcome barriers to sharing research videos and associated data and metadata. Databrary has developed solutions for respecting participants’ privacy; for storing, streaming, and sharing videos; and for managing videos and associated metadata. The Databrary experience suggests ways that videos and other identifiable data collected in the context of educational research might be shared. Open data sharing enabled by Databrary can serve as a catalyst for a truly multidisciplinary science of learning. PMID:28042361

78 FR 32487 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing of Proposed Rule Change Relating...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-30

... and trade the shares of the following under NYSE Arca Equities Rule 8.600 (``Managed Fund Shares... proposes to list and trade the shares (``Shares'') of the PowerShares China A-Share Portfolio (``Fund... with the Commission as an open-end management investment company.\\6\\ \\4\\ A Managed Fund Share is a...

45 CFR 304.26 - Determination of Federal share of collections.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 2 2011-10-01 2011-10-01 false Determination of Federal share of collections. 304.26 Section 304.26 Public Welfare Regulations Relating to Public Welfare OFFICE OF CHILD SUPPORT... HEALTH AND HUMAN SERVICES FEDERAL FINANCIAL PARTICIPATION § 304.26 Determination of Federal share of...

Open Availability of Patient Medical Photographs in Google Images Search Results: Cross-Sectional Study of Transgender Research

PubMed Central

Brunger, Fern; Welch, Vivian; Asghari, Shabnam; Kaposy, Chris

2018-01-01

Background This paper focuses on the collision of three factors: a growing emphasis on sharing research through open access publication, an increasing awareness of big data and its potential uses, and an engaged public interested in the privacy and confidentiality of their personal health information. One conceptual space where this collision is brought into sharp relief is with the open availability of patient medical photographs from peer-reviewed journal articles in the search results of online image databases such as Google Images. Objective The aim of this study was to assess the availability of patient medical photographs from published journal articles in Google Images search results and the factors impacting this availability. Methods We conducted a cross-sectional study using data from an evidence map of research with transgender, gender non-binary, and other gender diverse (trans) participants. For the original evidence map, a comprehensive search of 15 academic databases was developed in collaboration with a health sciences librarian. Initial search results produced 25,230 references after duplicates were removed. Eligibility criteria were established to include empirical research of any design that included trans participants or their personal information and that was published in English in peer-reviewed journals. We identified all articles published between 2008 and 2015 with medical photographs of trans participants. For each reference, images were individually numbered in order to track the total number of medical photographs. We used odds ratios (OR) to assess the association between availability of the clinical photograph on Google Images and the following factors: whether the article was openly available online (open access, Researchgate.net, or Academia.edu), whether the article included genital images, if the photographs were published in color, and whether the photographs were located on the journal article landing page. Results We identified 94 articles with medical photographs of trans participants, including a total of 605 photographs. Of the 94 publications, 35 (37%) included at least one medical photograph that was found on Google Images. The ability to locate the article freely online contributes to the availability of at least one image from the article on Google Images (OR 2.99, 95% CI 1.20-7.45). Conclusions This is the first study to document the existence of medical photographs from peer-reviewed journals appearing in Google Images search results. Almost all of the images we searched for included sensitive photographs of patient genitals, chests, or breasts. Given that it is unlikely that patients consented to sharing their personal health information in these ways, this constitutes a risk to patient privacy. Based on the impact of current practices, revisions to informed consent policies and guidelines are required. PMID:29483069

Public Performance

NASA Astrophysics Data System (ADS)

Krupp, E. C.

2013-01-01

America’s first planetaria all opened in the 1930s, and each was the distinctive product of local circumstances. In Los Angeles, the populist sensibilities of Griffith J. Griffith prompted him to value the transformative power of a personal encounter with a telescope, and he quickly embraced the idea of a public observatory with free access to all. Griffith Observatory and its planetarium emerged from that intent. Authenticity, intelligibility, and theatricality were fundamental principles in Griffith’s thinking, and they were transformed into solid and enduring scientific and astronomical values by those who actually guided the Observatory’s design, construction, and programming. That said, the public profile of Griffith Observatory was most defined by its inspired hilltop location, its distinctive, commanding architecture, and its felicitous proximity to Hollywood. The Observatory is theatric in placement and in appearance, and before the Observatory even opened, it was used as a motion picture set. That continuing vocation turned Griffith Observatory into a Hollywood star. Because entertainment industry objectives and resources were part of the Los Angeles landscape, they influenced Observatory programming throughout the Observatory’s history. Public astronomy in Los Angeles has largely been framed by the Observatory’s fundamental nature. It has exhibits, but it is not a museum. It has a planetarium, but it is essentially an observatory. As a public observatory, it is filled with instruments that transform visitors into observers. This role emphasized the importance of personal experience and established the perception of Griffith Observatory as a place for public gathering and shared contact with the cosmos. The Observatory’s close and continuous link with amateur astronomers made amateurs influential partners in the public enterprise. In full accord with Griffith J. Griffith’s original intent, Griffith Observatory has all been about putting people eyeball to the universe with authenticity, showmanship, and style.

Individual- and area-level disparities in access to the road network, subway system and a public bicycle share program on the Island of Montreal, Canada.

PubMed

Fuller, Daniel; Gauvin, Lise; Kestens, Yan

2013-02-01

Few studies have examined potential disparities in access to transportation infrastructures, an important determinant of population health. To examine individual- and area-level disparities in access to the road network, public transportation system, and a public bicycle share program in Montreal, Canada. Examining associations between sociodemographic variables and access to the road network, public transportation system, and a public bicycle share program, 6,495 adult respondents (mean age, 48.7 years; 59.0 % female) nested in 33 areas were included in a multilevel analysis. Individuals with lower incomes lived significantly closer to public transportation and the bicycle share program. At the area level, the interaction between low-education and low-income neighborhoods showed that these areas were significantly closer to public transportation and the bicycle share program controlling for individual and urbanicity variables. More deprived areas of the Island of Montreal have better access to transportation infrastructure than less-deprived areas.

The Materials Data Facility: Data Services to Advance Materials Science Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blaiszik, B.; Chard, K.; Pruyne, J.

2016-07-06

With increasingly strict data management requirements from funding agencies and institutions, expanding focus on the challenges of research replicability, and growing data sizes and heterogeneity, new data needs are emerging in the materials community. The materials data facility (MDF) operates two cloudhosted services, data publication and data discovery, with features to promote open data sharing, self-service data publication and curation, and encourage data reuse, layered with powerful data discovery tools. The data publication service simplifies the process of copying data to a secure storage location, assigning data a citable persistent identifier, and recording custom (e.g., material, technique, or instrument specific)andmore » automatically-extractedmetadata in a registrywhile the data discovery service will provide advanced search capabilities (e.g., faceting, free text range querying, and full text search) against the registered data and metadata. TheMDF services empower individual researchers, research projects, and institutions to (I) publish research datasets, regardless of size, from local storage, institutional data stores, or cloud storage, without involvement of thirdparty publishers; (II) build, share, and enforce extensible domain-specific custom metadata schemas; (III) interact with published data and metadata via representational state transfer (REST) application program interfaces (APIs) to facilitate automation, analysis, and feedback; and (IV) access a data discovery model that allows researchers to search, interrogate, and eventually build on existing published data. We describe MDF’s design, current status, and future plans.« less

The Materials Data Facility: Data Services to Advance Materials Science Research

NASA Astrophysics Data System (ADS)

Blaiszik, B.; Chard, K.; Pruyne, J.; Ananthakrishnan, R.; Tuecke, S.; Foster, I.

2016-08-01

With increasingly strict data management requirements from funding agencies and institutions, expanding focus on the challenges of research replicability, and growing data sizes and heterogeneity, new data needs are emerging in the materials community. The materials data facility (MDF) operates two cloud-hosted services, data publication and data discovery, with features to promote open data sharing, self-service data publication and curation, and encourage data reuse, layered with powerful data discovery tools. The data publication service simplifies the process of copying data to a secure storage location, assigning data a citable persistent identifier, and recording custom (e.g., material, technique, or instrument specific) and automatically-extracted metadata in a registry while the data discovery service will provide advanced search capabilities (e.g., faceting, free text range querying, and full text search) against the registered data and metadata. The MDF services empower individual researchers, research projects, and institutions to (I) publish research datasets, regardless of size, from local storage, institutional data stores, or cloud storage, without involvement of third-party publishers; (II) build, share, and enforce extensible domain-specific custom metadata schemas; (III) interact with published data and metadata via representational state transfer (REST) application program interfaces (APIs) to facilitate automation, analysis, and feedback; and (IV) access a data discovery model that allows researchers to search, interrogate, and eventually build on existing published data. We describe MDF's design, current status, and future plans.

Perceived Nurse-Physician Communication in Patient Care and Associated Factors in Public Hospitals of Jimma Zone, South West Ethiopia: Cross Sectional Study.

PubMed

Hailu, Fikadu Balcha; Kassahun, Chanyalew Worku; Kerie, Mirkuzie Woldie

2016-01-01

Nurse-physician communication has been shown to have a significant impact on the job satisfaction and retention of staff. In areas where it has been studied, communication failure between nurses and physicians was found to be one of the leading causes of preventable patient injuries, complications, death and medical malpractice claims. The objective of this study is to determine perception of nurses and physicians towards nurse-physician communication in patient care and associated factors in public hospitals of Jimma zone, southwest Ethiopia. Institution based cross-sectional survey was conducted from March 10 to April 16, 2014 among 341 nurses and 168 physicians working in public hospitals in Jimma zone. Data was collected using a pre-tested self-administered questionnaire; entered into EpiData version 3.1 and exported to Statistical Package for Social Sciences (SPSS) version 16.0 for analysis. Factor analysis was carried out. Descriptive statistics, independent sample t-test, linear regression and one way analysis of variance were used. Variables with P-value < 0.05 were considered as statistically significant. The response rate of the study was 91.55%. The mean perceived nurse-physician communication scores were 50.88±19.7% for perceived professional respect and satisfaction, and 48.52±19.7% for perceived openness and sharing of patient information on nurse-physician communication. Age, salary and organizational factors were statistically significant predictors for perceived respect and satisfaction. Whereas sex, working hospital, work attitude individual factors and organizational factors were significant predictors of perceived openness and sharing of patient information in nurse-physician communication during patient care. Perceived level of nurse-physician communication mean score was low among nurses than physicians and it is attention seeking gap. Hence, the finding of our study suggests the need for developing and implementing nurse-physician communication improvement strategies to solve communication mishaps in patient care.

Perceived Nurse—Physician Communication in Patient Care and Associated Factors in Public Hospitals of Jimma Zone, South West Ethiopia: Cross Sectional Study

PubMed Central

Hailu, Fikadu Balcha; Kassahun, Chanyalew Worku; Kerie, Mirkuzie Woldie

2016-01-01

Background Nurse–physician communication has been shown to have a significant impact on the job satisfaction and retention of staff. In areas where it has been studied, communication failure between nurses and physicians was found to be one of the leading causes of preventable patient injuries, complications, death and medical malpractice claims. Objective The objective of this study is to determine perception of nurses and physicians towards nurse-physician communication in patient care and associated factors in public hospitals of Jimma zone, southwest Ethiopia. Methods Institution based cross-sectional survey was conducted from March 10 to April 16, 2014 among 341 nurses and 168 physicians working in public hospitals in Jimma zone. Data was collected using a pre-tested self-administered questionnaire; entered into EpiData version 3.1 and exported to Statistical Package for Social Sciences (SPSS) version 16.0 for analysis. Factor analysis was carried out. Descriptive statistics, independent sample t-test, linear regression and one way analysis of variance were used. Variables with P-value < 0.05 were considered as statistically significant. Results The response rate of the study was 91.55%. The mean perceived nurse-physician communication scores were 50.88±19.7% for perceived professional respect and satisfaction, and 48.52±19.7% for perceived openness and sharing of patient information on nurse-physician communication. Age, salary and organizational factors were statistically significant predictors for perceived respect and satisfaction. Whereas sex, working hospital, work attitude individual factors and organizational factors were significant predictors of perceived openness and sharing of patient information in nurse-physician communication during patient care. Conclusion Perceived level of nurse-physician communication mean score was low among nurses than physicians and it is attention seeking gap. Hence, the finding of our study suggests the need for developing and implementing nurse-physician communication improvement strategies to solve communication mishaps in patient care. PMID:27632162

What Multilevel Parallel Programs do when you are not Watching: A Performance Analysis Case Study Comparing MPI/OpenMP, MLP, and Nested OpenMP

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors, parallel programming techniques have evolved that support parallelism beyond a single level. When comparing the performance of applications based on different programming paradigms, it is important to differentiate between the influence of the programming model itself and other factors, such as implementation specific behavior of the operating system (OS) or architectural issues. Rewriting-a large scientific application in order to employ a new programming paradigms is usually a time consuming and error prone task. Before embarking on such an endeavor it is important to determine that there is really a gain that would not be possible with the current implementation. A detailed performance analysis is crucial to clarify these issues. The multilevel programming paradigms considered in this study are hybrid MPI/OpenMP, MLP, and nested OpenMP. The hybrid MPI/OpenMP approach is based on using MPI [7] for the coarse grained parallelization and OpenMP [9] for fine grained loop level parallelism. The MPI programming paradigm assumes a private address space for each process. Data is transferred by explicitly exchanging messages via calls to the MPI library. This model was originally designed for distributed memory architectures but is also suitable for shared memory systems. The second paradigm under consideration is MLP which was developed by Taft. The approach is similar to MPi/OpenMP, using a mix of coarse grain process level parallelization and loop level OpenMP parallelization. As it is the case with MPI, a private address space is assumed for each process. The MLP approach was developed for ccNUMA architectures and explicitly takes advantage of the availability of shared memory. A shared memory arena which is accessible by all processes is required. Communication is done by reading from and writing to the shared memory.

linkedISA: semantic representation of ISA-Tab experimental metadata.

PubMed

González-Beltrán, Alejandra; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2014-01-01

Reporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that datasets are comprehensible and, in principle, reproducible, comparable and reusable. Furthermore, sharing datasets in formats designed for consumption by humans and machines will also maximize their use. The Investigation/Study/Assay (ISA) open source metadata tracking framework facilitates standards-compliant collection, curation, visualization, storage and sharing of datasets, leveraging on other platforms to enable analysis and publication. The ISA software suite includes several components used in increasingly diverse set of life science and biomedical domains; it is underpinned by a general-purpose format, ISA-Tab, and conversions exist into formats required by public repositories. While ISA-Tab works well mainly as a human readable format, we have also implemented a linked data approach to semantically define the ISA-Tab syntax. We present a semantic web representation of the ISA-Tab syntax that complements ISA-Tab's syntactic interoperability with semantic interoperability. We introduce the linkedISA conversion tool from ISA-Tab to the Resource Description Framework (RDF), supporting mappings from the ISA syntax to multiple community-defined, open ontologies and capitalising on user-provided ontology annotations in the experimental metadata. We describe insights of the implementation and how annotations can be expanded driven by the metadata. We applied the conversion tool as part of Bio-GraphIIn, a web-based application supporting integration of the semantically-rich experimental descriptions. Designed in a user-friendly manner, the Bio-GraphIIn interface hides most of the complexities to the users, exposing a familiar tabular view of the experimental description to allow seamless interaction with the RDF representation, and visualising descriptors to drive the query over the semantic representation of the experimental design. In addition, we defined queries over the linkedISA RDF representation and demonstrated its use over the linkedISA conversion of datasets from Nature' Scientific Data online publication. Our linked data approach has allowed us to: 1) make the ISA-Tab semantics explicit and machine-processable, 2) exploit the existing ontology-based annotations in the ISA-Tab experimental descriptions, 3) augment the ISA-Tab syntax with new descriptive elements, 4) visualise and query elements related to the experimental design. Reasoning over ISA-Tab metadata and associated data will facilitate data integration and knowledge discovery.

An Open Data Platform in the framework of the EGI-LifeWatch Competence Center

NASA Astrophysics Data System (ADS)

Aguilar Gómez, Fernando; de Lucas, Jesús Marco; Yaiza Rodríguez Marrero, Ana

2016-04-01

The working pilot of an Open Data Platform supporting the full data cycle in research is presented. It aims to preserve knowledge explicitly, starting with the description of the Case Studies, and integrating data and software management and preservation on equal basis. The uninterrupted support in the chain starts at the data acquisition level and covers up to the support for reuse and publication in an open framework, providing integrity and provenance controls. The Lifewatch Open Science Framework is a pilot web portal developed in collaboration with different commercial companies that tries to enrich and integrate different data lifecycle-related tools in order to address the management of the different steps: data planning, gathering, storing, curation, preservation, sharing, discovering, etc. To achieve this goal, the platform includes the following features: -Data Management Planning. Tool to set up an structure of the data, including what data will be generated, how it will be exploited, re-used, curated, preserved, etc. It has a semantic approach: includes reference to ontologies in order to express what data will be gathered. -Close to instrumentation. The portal includes a distributed storage system that can be used both for storing data from instruments and output data from analysis. All that data can be shared -Analysis. Resources from EGI Federated Cloud are accessible within the portal, so that users can exploit computing resources to perform analysis and other processes, including workflows. -Preservation. Data can be preserved in different systems and DOIs can be minted not only for datasets but also for software, DMPs, etc. The presentation will show the different components of the framework as well as how it can be extrapolated to other communities.

Integration of DICOM and openEHR standards

NASA Astrophysics Data System (ADS)

Wang, Ying; Yao, Zhihong; Liu, Lei

2011-03-01

The standard format for medical imaging storage and transmission is DICOM. openEHR is an open standard specification in health informatics that describes the management and storage, retrieval and exchange of health data in electronic health records. Considering that the integration of DICOM and openEHR is beneficial to information sharing, on the basis of XML-based DICOM format, we developed a method of creating a DICOM Imaging Archetype in openEHR to enable the integration of DICOM and openEHR. Each DICOM file contains abundant imaging information. However, because reading a DICOM involves looking up the DICOM Data Dictionary, the readability of a DICOM file has been limited. openEHR has innovatively adopted two level modeling method, making clinical information divided into lower level, the information model, and upper level, archetypes and templates. But one critical challenge posed to the development of openEHR is the information sharing problem, especially in imaging information sharing. For example, some important imaging information cannot be displayed in an openEHR file. In this paper, to enhance the readability of a DICOM file and semantic interoperability of an openEHR file, we developed a method of mapping a DICOM file to an openEHR file by adopting the form of archetype defined in openEHR. Because an archetype has a tree structure, after mapping a DICOM file to an openEHR file, the converted information is structuralized in conformance with openEHR format. This method enables the integration of DICOM and openEHR and data exchange without losing imaging information between two standards.

Shared resources : sharing right-of-way for telecommunications : identification, review and analysis of legal and institutional issues

DOT National Transportation Integrated Search

1996-04-01

This report presents the results of research on the institutional and non-technical issues related to shared resource projects. Shared resource projects are a particular form of public-private partnering that may help public agencies underwrite their...

State Support for Open Educational Resources: Key Findings from Achieve's OER Institute

ERIC Educational Resources Information Center

Achieve, Inc., 2013

2013-01-01

Open Educational Resources (OER) offer unique new opportunities for educators to share quality learning resources, especially in an increasingly digital world. Forty-six states and the District of Columbia have adopted the Common Core State Standards (CCSS), providing them with the unprecedented advantage of being able to share resources that are…

Copyright and Collaborative Spaces: Open Licensing and Wikis

ERIC Educational Resources Information Center

Botterbusch, Hope R.; Parker, Preston

2008-01-01

As recently as ten years ago, it may have seemed like science fiction to imagine collaborative spaces on the Internet. Today, collaborative websites have proliferated: (1) blogs; (2) social networking; (3) image sharing; (4) video sharing; (5) open educational resources; and (6) popularity websites. Another type is called a wiki, an online…

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

Alaoui, Adil; Ingeholm, Mary Lou; Padh, Shilpa; Dorobantu, Mihai; Desai, Mihir; Cleary, Kevin; Mun, Seong K.

2008-03-01

The Information Management Toolkit (ImTK) Consortium is an open source initiative to develop robust, freely available tools related to the information management needs of basic, clinical, and translational research. An open source framework and agile programming methodology can enable distributed software development while an open architecture will encourage interoperability across different environments. The ISIS Center has conceptualized a prototype data sharing network that simulates a multi-center environment based on a federated data access model. This model includes the development of software tools to enable efficient exchange, sharing, management, and analysis of multimedia medical information such as clinical information, images, and bioinformatics data from multiple data sources. The envisioned ImTK data environment will include an open architecture and data model implementation that complies with existing standards such as Digital Imaging and Communications (DICOM), Health Level 7 (HL7), and the technical framework and workflow defined by the Integrating the Healthcare Enterprise (IHE) Information Technology Infrastructure initiative, mainly the Cross Enterprise Document Sharing (XDS) specifications.

WWOSC 2014: Research Needs for Better Health Resilience to Weather Hazards

PubMed Central

Jancloes, Michel; Anderson, Vidya; Gosselin, Pierre; Mee, Carol; Chong, Nicholas J.

2015-01-01

The first World Weather Open Science Conference (WWOSC, held from 17–21 August 2014 in Montreal, Québec), provided an open forum where the experience and perspective of a variety of weather information providers and users was combined with the latest application advances in social sciences. A special session devoted to health focused on how best the most recent weather information and communication technologies (ICT) could improve the health emergency responses to disasters resulting from natural hazards. Speakers from a plenary presentation and its corresponding panel shared lessons learnt from different international multidisciplinary initiatives against weather-related epidemics, such as malaria, leptospirosis and meningitis and from public health responses to floods and heat waves such as in Ontario and Quebec, Canada. Participants could bear witness to recent progress made in the use of forecasting tools and in the application of increased spatiotemporal resolutions in the management of weather related health risks through anticipative interventions, early alert and warning and early responses especially by vulnerable groups. There was an agreement that resilience to weather hazards is best developed based on evidence of their health impact and when, at local level, there is a close interaction between health care providers, epidemiologists, climate services, public health authorities and communities. Using near real time health data (such as hospital admission, disease incidence monitoring…) combined with weather information has been recommended to appraise the relevance of decisions and the effectiveness of interventions and to make adjustments when needed. It also helps appraising how people may be more or less vulnerable to a particular hazard depending on the resilience infrastructures and services. This session was mainly attended by climate, environment and social scientists from North American and European countries. Producing a commentary appears to be an effective way to share this session’s conclusions to research institutions and public health experts worldwide. It also advocates for better linking operational research and decision making and for appraising the impact of ICT and public health interventions on health. PMID:25809508

AgShare Open Knowledge: Improving Rural Communities through University Student Action Research

ERIC Educational Resources Information Center

Geith, Christine; Vignare, Karen

2013-01-01

The aim of AgShare is to create a scalable and sustainable collaboration of existing organizations for African publishing, localizing, and sharing of science-based teaching and learning materials that fill critical resource gaps in African MSc agriculture curriculum. Shared innovative practices are emerging through the AgShare projects, not only…

A data management and publication workflow for a large-scale, heterogeneous sensor network.

PubMed

Jones, Amber Spackman; Horsburgh, Jeffery S; Reeder, Stephanie L; Ramírez, Maurier; Caraballo, Juan

2015-06-01

It is common for hydrology researchers to collect data using in situ sensors at high frequencies, for extended durations, and with spatial distributions that produce data volumes requiring infrastructure for data storage, management, and sharing. The availability and utility of these data in addressing scientific questions related to water availability, water quality, and natural disasters relies on effective cyberinfrastructure that facilitates transformation of raw sensor data into usable data products. It also depends on the ability of researchers to share and access the data in useable formats. In this paper, we describe a data management and publication workflow and software tools for research groups and sites conducting long-term monitoring using in situ sensors. Functionality includes the ability to track monitoring equipment inventory and events related to field maintenance. Linking this information to the observational data is imperative in ensuring the quality of sensor-based data products. We present these tools in the context of a case study for the innovative Urban Transitions and Aridregion Hydrosustainability (iUTAH) sensor network. The iUTAH monitoring network includes sensors at aquatic and terrestrial sites for continuous monitoring of common meteorological variables, snow accumulation and melt, soil moisture, surface water flow, and surface water quality. We present the overall workflow we have developed for effectively transferring data from field monitoring sites to ultimate end-users and describe the software tools we have deployed for storing, managing, and sharing the sensor data. These tools are all open source and available for others to use.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

PubMed

Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Pocock, Matthew; Flanagan, Keith; Hallinan, Jennifer; Wipat, Anil

2016-06-17

Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.

Creating demand for foreign brands in a 'home run' market: tobacco company tactics in South Korea following market liberalisation.

PubMed

Lee, Sungkyu; Lee, Kelley; Holden, Chris

2014-05-01

To analyse the tactics transnational tobacco companies (TTCs) used to increase market share in South Korea after market liberalisation in 1988, and the subsequent impact of TTCs' activities on the domestic industry and ultimately public health. Internal tobacco industry documents were searched iteratively and analysed by keyword related to strategies for increasing market share in Korea since liberalisation. Following market liberalisation, TTCs faced entrenched cultural and institutional barriers in Korea which hindered increased sales of cigarette imports. TTCs identified population groups more favourably inclined towards imported brands, developed new distribution channels and used promotional activities targeting these groups. The growth in market share by TTCs suggests that these activities were successful at challenging the Korea Tobacco & Ginseng Corporation (KTGC) monopoly. In response, KTGC shifted to a proactive marketing approach and adopted strategies similar to TTCs. This, in turn, made the Korean market highly competitive. Findings show that, after market liberalisation, there was an upward trend in cigarette consumption and smoking prevalence among the targeted population groups, notably youth and young women. Governments engaging in trade negotiations that may lead to the opening of domestic tobacco markets need a fuller understanding of previous industry activities for expanding into emerging markets as well as how the domestic industry can change accordingly. To protect public health, the adoption of comprehensive tobacco control measures, guided by WHO Framework Convention on Tobacco Control, are needed as part of such negotiations.

Toward Enhancing OpenMP's Work-Sharing Directives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapman, B M; Huang, L; Jin, H

2006-05-17

OpenMP provides a portable programming interface for shared memory parallel computers (SMPs). Although this interface has proven successful for small SMPs, it requires greater flexibility in light of the steadily growing size of individual SMPs and the recent advent of multithreaded chips. In this paper, we describe two application development experiences that exposed these expressivity problems in the current OpenMP specification. We then propose mechanisms to overcome these limitations, including thread subteams and thread topologies. Thus, we identify language features that improve OpenMP application performance on emerging and large-scale platforms while preserving ease of programming.

Social amplification of risk in the Internet environment.

PubMed

Chung, Ik Jae

2011-12-01

This article analyzes the dynamic process of risk amplification in the Internet environment with special emphasis on public concern for environmental risks from a high-speed railway tunnel construction project in South Korea. Environmental organizations and activists serving as social stations collected information about the project and its ecological impact, and communicated this with the general public, social groups, and institutions. The Internet provides social stations and the public with an efficient means for interactive communication and an open space for active information sharing and public participation. For example, while the website of an organization such as an environmental activist group can initially trigger local interest, the Internet allows this information to be disseminated to a much wider audience in a manner unavailable to the traditional media. Interaction among social stations demonstrates an amplifying process of public attention to the risk. Analyses of the volume of readers' comments to online newspaper articles and public opinions posted on message board of public and nonprofit organizations show the ripple effects of the amplification process as measured along temporal, geographical, and sectoral dimensions. Public attention is also influenced by the symbolic connotations of risk information. Interpretations of risk in religious, political, or legal terms intensify public concern for the environmental risk. © 2011 Society for Risk Analysis.

A FairShare Scheduling Service for OpenNebula

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Vallero, S.; Zaccolo, V.

2017-10-01

In the ideal limit of infinite resources, multi-tenant applications are able to scale in/out on a Cloud driven only by their functional requirements. While a large Public Cloud may be a reasonable approximation of this condition, small scientific computing centres usually work in a saturated regime. In this case, an advanced resource allocation policy is needed in order to optimize the use of the data centre. The general topic of advanced resource scheduling is addressed by several components of the EU-funded INDIGO-DataCloud project. In this contribution, we describe the FairShare Scheduler Service (FaSS) for OpenNebula (ONE). The service must satisfy resource requests according to an algorithm which prioritizes tasks according to an initial weight and to the historical resource usage of the project. The software was designed to be less intrusive as possible in the ONE code. We keep the original ONE scheduler implementation to match requests to available resources, but the queue of pending jobs to be processed is the one ordered according to priorities as delivered by the FaSS. The FaSS implementation is still being finalized and in this contribution we describe the functional and design requirements the module should satisfy, as well as its high-level architecture.

Open Governance in Higher Education: Extending the Past to the Future

ERIC Educational Resources Information Center

Masson, Patrick

2011-01-01

Open educational resources, open content, open access, open research, open courseware--all of these open initiatives share, and benefit from, a vision of access and a collaborative framework that often result in improved outcomes. Many of these open initiatives have gained adoption within higher education and are now serving in mission-critical…

Public Health Workforce Self-Identified Training Needs by Jurisdiction and Job Type.

PubMed

Yeager, Valerie A; Wisniewski, Janna M; Chapple-McGruder, Theresa; Castrucci, Brian; Gould, Elizabeth

2018-06-21

Ensuring adequate and appropriate training of the workforce is a crucial priority for governmental public health. This is particularly important, given the diverse backgrounds of the public health workforce; the vast majority (approximately 83%) do not have formal training in public health, and those that do have formal training in public health have limited training in management and other essential organizational skills. The purpose of this article is to identify training needs among public health workers in specific job types and settings. This cross section study used 2014 data from the Public Health Workforce Interests and Needs Survey. Qualitative analyses were used to code open-ended responses to questions about training needs. Needs are stratified across job types and jurisdiction. Eight main themes or skill areas were identified with the largest proportion indicating a need for management/leadership skills (28.2%). The second most frequent need was communication skills (21.3%). Across the 9 job types examined, general management skills were either the first or second training need for 7 job types. Among individuals who already have leadership/management positions, budgeting was the most common training need. Findings from this study can inform targeted strategies to address training needs for specific types of employees. Such strategies can influence the efficiency and effectiveness of public health efforts and employee satisfaction. As new public health frameworks-like Public Health 3.0 and the Chief Health Strategist-are advanced nationally, it is necessary to ensure that the workforce has the skills and abilities to implement these frameworks.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

Open-source, community-driven microfluidics with Metafluidics.

PubMed

Kong, David S; Thorsen, Todd A; Babb, Jonathan; Wick, Scott T; Gam, Jeremy J; Weiss, Ron; Carr, Peter A

2017-06-07

Microfluidic devices have the potential to automate and miniaturize biological experiments, but open-source sharing of device designs has lagged behind sharing of other resources such as software. Synthetic biologists have used microfluidics for DNA assembly, cell-free expression, and cell culture, but a combination of expense, device complexity, and reliance on custom set-ups hampers their widespread adoption. We present Metafluidics, an open-source, community-driven repository that hosts digital design files, assembly specifications, and open-source software to enable users to build, configure, and operate a microfluidic device. We use Metafluidics to share designs and fabrication instructions for both a microfluidic ring-mixer device and a 32-channel tabletop microfluidic controller. This device and controller are applied to build genetic circuits using standard DNA assembly methods including ligation, Gateway, Gibson, and Golden Gate. Metafluidics is intended to enable a broad community of engineers, DIY enthusiasts, and other nontraditional participants with limited fabrication skills to contribute to microfluidic research.

Sharing individual patient and parasite-level data through the WorldWide Antimalarial Resistance Network platform: A qualitative case study

PubMed Central

Pisani, Elizabeth; Botchway, Stella

2017-01-01

Background: Increasingly, biomedical researchers are encouraged or required by research funders and journals to share their data, but there's very little guidance on how to do that equitably and usefully, especially in resource-constrained settings. We performed an in-depth case study of one data sharing pioneer: the WorldWide Antimalarial Resistance Network (WWARN). Methods: The case study included a records review, a quantitative analysis of WAARN-related publications, in-depth interviews with 47 people familiar with WWARN, and a witness seminar involving a sub-set of 11 interviewees. Results: WWARN originally aimed to collate clinical, in vitro, pharmacological and molecular data into linked, open-access databases intended to serve as a public resource to guide antimalarial drug treatment policies. Our study describes how WWARN navigated challenging institutional and academic incentive structures, alongside funders' reluctance to invest in capacity building in malaria-endemic countries, which impeded data sharing. The network increased data contributions by focusing on providing free, online tools to improve the quality and efficiency of data collection, and by inviting collaborative authorship on papers addressing policy-relevant questions that could only be answered through pooled analyses. By July 1, 2016, the database included standardised data from 103 molecular studies and 186 clinical trials, representing 135,000 individual patients. Developing the database took longer and cost more than anticipated, and efforts to increase equity for data contributors are on-going. However, analyses of the pooled data have generated new methods and influenced malaria treatment recommendations globally. Despite not achieving the initial goal of real-time surveillance, WWARN has developed strong data governance and curation tools, which are now being adapted relatively quickly for other diseases. Conclusions: To be useful, data sharing requires investment in long-term infrastructure. To be feasible, it requires new incentive structures that favour the generation of reusable knowledge. PMID:29018840

LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays

PubMed Central

2011-01-01

Background Multiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results. Results We present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb) assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings. Conclusions Standardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the LabKey Server NAb tool without installing the software by using the Atlas Science Portal (https://atlas.scharp.org). Atlas is an installation of LabKey Server. PMID:21619655

Sharing individual patient and parasite-level data through the WorldWide Antimalarial Resistance Network platform: A qualitative case study.

PubMed

Pisani, Elizabeth; Botchway, Stella

2017-01-01

Increasingly, biomedical researchers are encouraged or required by research funders and journals to share their data, but there's very little guidance on how to do that equitably and usefully, especially in resource-constrained settings. We performed an in-depth case study of one data sharing pioneer: the WorldWide Antimalarial Resistance Network (WWARN). The case study included a records review, a quantitative analysis of WAARN-related publications, in-depth interviews with 47 people familiar with WWARN, and a witness seminar involving a sub-set of 11 interviewees. WWARN originally aimed to collate clinical, in vitro, pharmacological and molecular data into linked, open-access databases intended to serve as a public resource to guide antimalarial drug treatment policies. Our study describes how WWARN navigated challenging institutional and academic incentive structures, alongside funders' reluctance to invest in capacity building in malaria-endemic countries, which impeded data sharing. The network increased data contributions by focusing on providing free, online tools to improve the quality and efficiency of data collection, and by inviting collaborative authorship on papers addressing policy-relevant questions that could only be answered through pooled analyses. By July 1, 2016, the database included standardised data from 103 molecular studies and 186 clinical trials, representing 135,000 individual patients. Developing the database took longer and cost more than anticipated, and efforts to increase equity for data contributors are on-going. However, analyses of the pooled data have generated new methods and influenced malaria treatment recommendations globally. Despite not achieving the initial goal of real-time surveillance, WWARN has developed strong data governance and curation tools, which are now being adapted relatively quickly for other diseases. To be useful, data sharing requires investment in long-term infrastructure. To be feasible, it requires new incentive structures that favour the generation of reusable knowledge.

An interactive environmental model for economic growth: evidence from a panel of countries.

PubMed

Ramakrishnan, Suresh; Hishan, Sanil S; Nabi, Agha Amad; Arshad, Zeeshan; Kanjanapathy, Malini; Zaman, Khalid; Khan, Faisal

2016-07-01

This study aims to determine an interactive environmental model for economic growth that would be supported by the "sustainability principles" across the globe. The study examines the relationship between environmental pollutants (i.e., carbon dioxide emission, sulfur dioxide emission, mono-nitrogen oxide, and nitrous oxide emission); population growth; energy use; trade openness; per capita food production; and it's resulting impact on the real per capita GDP and sectoral growth (i.e., share of agriculture, industry, and services in GDP) in a panel of 34 high-income OECD, high-income non-OECD, and Europe and Central Asian countries, for the period of 1995-2014. The results of the panel fixed effect regression show that per capita GDP are influenced by sulfur dioxide emission, population growth, and per capita food production variability, while energy and trade openness significantly increases per capita income of the region. The results of the panel Seemingly Unrelated Regression (SUR) show that carbon dioxide emission significantly decreases the share of agriculture and industry in GDP, while it further supports the share of services sector to GDP. Both the sulfur dioxide and mono-nitrogen oxide emission decreases the share of services in GDP; nitrous oxide decreases the share of industry in GDP; while mono-nitrogen oxide supports the industrial activities. The following key growth-specific results has been obtained from the panel SUR estimation, i.e., (i) Both the food production per capita and trade openness significantly associated with the increasing share of agriculture, (ii) food production and energy use significantly increases the service sectors' productivity; (iii) food production decreases the industrial activities; (iv) trade openness decreases the share of services to GDP while it supports the industrial share to GDP; and finally, (v) energy demand decreases along with the increase agricultural share in the region. The results emphasize the need for an interactive environmental model that facilitates the process of sustainable development across the globe.

Initial public perceptions of deep geological and oceanic disposal of carbon dioxide.

PubMed

Palmgren, Claire R; Morgan, M Granger; Bruine de Bruin, Wändi; Keith, David W

2004-12-15

Two studies were conducted to gauge likely public perceptions of proposals to avoid releasing carbon dioxide from power plants to the atmosphere by injecting it into deep geological formations or the deep ocean. Following a modified version of the mental model interview method, Study 1 involved face-to-face interviews with 18 nontechnical respondents. Respondents shared their beliefs after receiving basic information about the technologies and again after getting specific details. Many interviewees wanted to frame the issue in the broader context of alternative strategies for carbon management, but public understanding of mitigation strategies is limited. The second study, administered to a sample of 126 individuals, involved a closed-form survey that measured the prevalence of general beliefs revealed in study 1 and also assessed the respondent's views of these technologies. Study results suggest that the public may develop misgivings about deep injection of carbon dioxide because it can be seen as temporizing and perhaps creating future problems. Ocean injection was seen as more problematic than geological injection. An approach to public communication and regulation that is open and respectful of public concerns is likely to be a prerequisite to the successful adoption of this technology.

Open Management Group Data-Distribution Service (OMG-DDS) as a Data Transport for Vehicular Integration for C4ISR/EW Interoperability Services

DTIC Science & Technology

2012-08-01

15 August 2012 2 UNCLASSIFIED VICTORY Overview • The VICTORY technical approach – Incorporate open-standards – Shared services (VICTORY services...availability) 15 August 2012 3 UNCLASSIFIED VICTORY Shared Services • VICTORY core services (Position, Orientation, Direction- of-Travel, and Time) • Service

17 CFR 230.405 - Definitions of terms.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the estimated public offering price of the shares; or (3) In the case of an issuer whose public float... shares sold. (iii) Once an issuer fails to qualify for smaller reporting company status, it will remain... indebtedness, the number of shares if relating to shares, and the number of units if relating to any other kind...

Attitudes of research participants and the general public towards genomic data sharing: a systematic literature review.

PubMed

Shabani, Mahsa; Bezuidenhout, Louise; Borry, Pascal

2014-11-01

Introducing data sharing practices into the genomic research arena has challenged the current mechanisms established to protect rights of individuals and triggered policy considerations. To inform such policy deliberations, soliciting public and research participants' attitudes with respect to genomic data sharing is a necessity. The main electronic databases were searched in order to retrieve empirical studies, investigating the attitudes of research participants and the public towards genomic data sharing through public databases. In the 15 included studies, participants' attitudes towards genomic data sharing revealed the influence of a constellation of interrelated factors, including the personal perceptions of controllability and sensitivity of data, potential risks and benefits of data sharing at individual and social level and also governance level considerations. This analysis indicates that future policy responses and recruitment practices should be attentive to a wide variety of concerns in order to promote both responsible and progressive research.

Social Media as a New Vital Sign: Commentary.

PubMed

Young, Sean D

2018-04-30

Mobile technologies, such as wireless glucometers and mobile health apps, are increasingly being integrated into health and medical care. Because patients openly share real-time information about their health behaviors and outcomes on social media, social media data may also be used as a tool for monitoring patient care. This commentary describes how recent advances in computer science, psychology, and medicine enable social media data to become a new health "vital sign," as well as actionable steps that public health officials, health systems, and clinics can take to integrate social data into both public and population health as well as into individual patient care. Barriers that first need to be addressed, including privacy concerns, legal and ethical responsibilities, and infrastructure support, are discussed. ©Sean D Young. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 30.04.2018.

Computer Applications in Health Science Education.

PubMed

Juanes, Juan A; Ruisoto, Pablo

2015-09-01

In recent years, computer application development has experienced exponential growth, not only in the number of publications but also in the scope or contexts that have benefited from its use. In health science training, and medicine specifically, the gradual incorporation of technological developments has transformed the teaching and learning process, resulting in true "educational technology". The goal of this paper is to review the main features involved in these applications and highlight the main lines of research for the future. The results of peer reviewed literature published recently indicate the following features shared by the key technological developments in the field of health science education: first, development of simulation and visualization systems for a more complete and realistic representation of learning material over traditional paper format; second, portability and versatility of the applications, adapted for an increasing number of devices and operative systems; third, increasing focus on open source applications such as Massive Open Online Course (MOOC).

Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data.

PubMed

Clark, Alex M; Williams, Antony J; Ekins, Sean

2015-01-01

The current rise in the use of open lab notebook techniques means that there are an increasing number of scientists who make chemical information freely and openly available to the entire community as a series of micropublications that are released shortly after the conclusion of each experiment. We propose that this trend be accompanied by a thorough examination of data sharing priorities. We argue that the most significant immediate benefactor of open data is in fact chemical algorithms, which are capable of absorbing vast quantities of data, and using it to present concise insights to working chemists, on a scale that could not be achieved by traditional publication methods. Making this goal practically achievable will require a paradigm shift in the way individual scientists translate their data into digital form, since most contemporary methods of data entry are designed for presentation to humans rather than consumption by machine learning algorithms. We discuss some of the complex issues involved in fixing current methods, as well as some of the immediate benefits that can be gained when open data is published correctly using unambiguous machine readable formats. Graphical AbstractLab notebook entries must target both visualisation by scientists and use by machine learning algorithms.

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

Health Care Public Sector Share and the U.S. Life Expectancy Lag: A Country-level Longitudinal Study.

PubMed

Reynolds, Megan M

2018-04-01

Growing research on the political economy of health has begun to emphasize sociopolitical influences on cross-national differences in population health above and beyond economic growth. While this research investigates the impact of overall public health spending as a share of GDP ("health care effort"), it has for the most part overlooked the distribution of health care spending across the public and private spheres ("public sector share"). I evaluate the relative contributions of health care effort, public sector share, and GDP to the large and growing disadvantage in U.S. life expectancy at birth relative to peer nations. I do so using fixed effects models with data from 16 wealthy democratic nations between 1960 and 2010. Results indicate that public sector share has a beneficial effect on longevity net of the effect of health care effort and that this effect is nonlinear, decreasing in magnitude as levels rise. Moreover, public sector share is a more powerful predictor of life expectancy at birth than GDP per capita. This study contributes to discussions around the political economy of health, the growth consensus, and the American lag in life expectancy. Policy implications vis-à-vis the U.S. Affordable Care Act are discussed.

Institutional property rights structure, common pool resource (CPR), tragedy of the urban commons: A Review

NASA Astrophysics Data System (ADS)

Ling, G.; Ho, C. S.; Ali, H. M.

2014-02-01

There have been a plethora of researches on the significance of public open space (POS) in contributing to societies' sustainability. However, by virtue of identified maladaptive policy-based-property rights structure, such a shared good becomes vulnerable to tragedy of the urban commons (overexploitation) that subsequently leads to burgeoning number of mismanaged POS e.g., degraded and unkempt urban public spaces. By scrutinising the literatures within property rights domain and commons resources, an objective is highlighted in this paper which is to insightfully discourse institutional property rights structure pertaining to the mechanism, roles and interrelationship between property-rights regimes, bundle of property rights and resource domains; types of goods on how they act upon and tie in the POS with the social quandary. In summary, urban POS tragedy can potentially be triggered by the institutional structure especially if the ownership is left under open-access resource regime and ill-defined property rights which both successively constitute the natures of Common Pool Resource (CPR) within the commons, POS. Therefore, this paper sparks an idea to policy makers that property rights structure is a determinant in sustainably governing the POS in which adaptive assignment of property regimes and property rights are impelled.

PRN: a preprint service for catalyzing R-fMRI and neuroscience related studies

PubMed Central

Yan, Chao-gan; Li, Qingyang; Gao, Lei

2015-01-01

Sharing drafts of scientific manuscripts on preprint hosting services for early exposure and pre-publication feedback is a well-accepted practice in fields such as physics, astronomy, or mathematics. The field of neuroscience, however, has yet to adopt the preprint model. A reason for this reluctance might partly be the lack of central preprint services for the field of neuroscience. To address this issue, we announce the launch of Preprints of the R-fMRI Network (PRN), a community funded preprint hosting service. PRN provides free-submission and free hosting of manuscripts for resting state functional magnetic resonance imaging (R-fMRI) and neuroscience related studies. Submitted articles are openly discussed and receive feedback from readers and a panel of invited consultants from the R-fMRI Network. All manuscripts and feedback are freely accessible online with citable permanent URL for open-access. The goal of PRN is to supplement the peer reviewed journal publication system – by more rapidly communicating the latest research achievements throughout the world. We hope PRN would help the field to embrace the preprint model and thus further accelerate R-fMRI and neuroscience related studies, eventually enhancing human mental health. PMID:25844159

Scientific Software - the role of best practices and recommendations

NASA Astrophysics Data System (ADS)

Fritzsch, Bernadette; Bernstein, Erik; Castell, Wolfgang zu; Diesmann, Markus; Haas, Holger; Hammitzsch, Martin; Konrad, Uwe; Lähnemann, David; McHardy, Alice; Pampel, Heinz; Scheliga, Kaja; Schreiber, Andreas; Steglich, Dirk

2017-04-01

In Geosciences - like in most other communities - scientific work strongly depends on software. For big data analysis, existing (closed or open source) program packages are often mixed with newly developed codes. Different versions of software components and varying configurations can influence the result of data analysis. This often makes reproducibility of results and reuse of codes very difficult. Policies for publication and documentation of used and newly developed software, along with best practices, can help tackle this problem. Within the Helmholtz Association a Task Group "Access to and Re-use of scientific software" was implemented by the Open Science Working Group in 2016. The aim of the Task Group is to foster the discussion about scientific software in the Open Science context and to formulate recommendations for the production and publication of scientific software, ensuring open access to it. As a first step, a workshop gathered interested scientists from institutions across Germany. The workshop brought together various existing initiatives from different scientific communities to analyse current problems, share established best practices and come up with possible solutions. The subjects in the working groups covered a broad range of themes, including technical infrastructures, standards and quality assurance, citation of software and reproducibility. Initial recommendations are presented and discussed in the talk. They are the foundation for further discussions in the Helmholtz Association and the Priority Initiative "Digital Information" of the Alliance of Science Organisations in Germany. The talk aims to inform about the activities and to link with other initiatives on the national or international level.

Making practice transparent through e-portfolio.

PubMed

Stewart, Sarah M

2013-12-01

Midwives are required to maintain a professional portfolio as part of their statutory requirements. Some midwives are using open social networking tools and processes to develop an e-portfolio. However, confidentiality of patient and client data and professional reputation have to be taken into consideration when using online public spaces for reflection. There is little evidence about how midwives use social networking tools for ongoing learning. It is uncertain how reflecting in an e-portfolio with an audience impacts on learning outcomes. This paper investigates ways in which reflective midwifery practice be carried out using e-portfolio in open, social networking platforms using collaborative processes. Using an auto-ethnographic approach I explored my e-portfolio and selected posts that had attracted six or more comments. I used thematic analysis to identify themes within the textual conversations in the posts and responses posted by readers. The analysis identified that my collaborative e-portfolio had four themes: to provide commentary and discuss issues; to reflect and process learning; to seek advice, brainstorm and process ideas for practice, projects and research, and provide evidence of professional development. E-portfolio using open social networking tools and processes is a viable option for midwives because it facilitates collaborative reflection and shared learning. However, my experience shows that concerns about what people think, and client confidentiality does impact on the nature of open reflection and learning outcomes. I conclude this paper with a framework for managing midwifery statutory obligations using online public spaces and social networking tools. Copyright © 2013 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

PubMed Central

Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R.; Rodriguez, Henry

2011-01-01

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the “International Workshop on Proteomic Data Quality Metrics” in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (1) an evolving list of comprehensive quality metrics and (2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals. PMID:22053864

Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)*

PubMed Central

Kinsinger, Christopher R.; Apffel, James; Baker, Mark; Bian, Xiaopeng; Borchers, Christoph H.; Bradshaw, Ralph; Brusniak, Mi-Youn; Chan, Daniel W.; Deutsch, Eric W.; Domon, Bruno; Gorman, Jeff; Grimm, Rudolf; Hancock, William; Hermjakob, Henning; Horn, David; Hunter, Christie; Kolar, Patrik; Kraus, Hans-Joachim; Langen, Hanno; Linding, Rune; Moritz, Robert L.; Omenn, Gilbert S.; Orlando, Ron; Pandey, Akhilesh; Ping, Peipei; Rahbar, Amir; Rivers, Robert; Seymour, Sean L.; Simpson, Richard J.; Slotta, Douglas; Smith, Richard D.; Stein, Stephen E.; Tabb, David L.; Tagle, Danilo; Yates, John R.; Rodriguez, Henry

2011-01-01

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the “International Workshop on Proteomic Data Quality Metrics” in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: 1) an evolving list of comprehensive quality metrics and 2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals. PMID:22052993

Proceedings of the First International Linked Science Workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pouchard, Line Catherine; Kauppinnen, Tomi; Kessler, Carsten

2011-01-01

Scientific efforts are traditionally published only as articles, with an estimate of millions of publications worldwide per year; the growth rate of PubMed alone is now 1 papers per minute. The validation of scientific results requires reproducible methods, which can only be achieved if the same data, processes, and algorithms as those used in the original experiments were available. However, the problem is that although publications, methods and datasets are very related, they are not always openly accessible and interlinked. Even where data is discoverable, accessible and assessable, significant challenges remain in the reuse of the data, in particular facilitatingmore » the necessary correlation, integration and synthesis of data across levels of theory, techniques and disciplines. In the LISC 2011 (1st International Workshop on Linked Science) we will discuss and present results of new ways of publishing, sharing, linking, and analyzing such scientific resources motivated by driving scientific requirements, as well as reasoning over the data to discover interesting new links and scientific insights. Making entities identifiable and referenceable using URIs augmented by semantic, scientifically relevant annotations greatly facilitates access and retrieval for data which used to be hardly accessible. This Linked Science approach, i.e., publishing, sharing and interlinking scientific resources and data, is of particular importance for scientific research, where sharing is crucial for facilitating reproducibility and collaboration within and across disciplines. This integrated process, however, has not been established yet. Bibliographic contents are still regarded as the main scientific product, and associated data, models and software are either not published at all, or published in separate places, often with no reference to the respective paper. In the workshop we will discuss whether and how new emerging technologies (Linked Data, and semantic technologies more generally) can realize the vision of Linked Science. We see that this depends on their enabling capability throughout the research process, leading up to extended publications and data sharing environments. Our workshop aims to address challenges related to enabling the easy creation of data bundles - data, processes, tools, provenance and annotation - supporting both publication and reuse of the data. Secondly, we look for tools and methods for the easy correlation, integration and synthesis of shared data. This problem is often found in many disciplines (including astronomy, biology, geosciences, cultural heritage, earth, climate, environmental and ecological sciences and impacts etc.), as they need to span techniques, levels of theory, scales, and disciplines. With the advent of Linked Science, it is timely and crucial to address these identified research challenges through both practical and formal approaches.« less

Enabling an Open Data Ecosystem for the Neurosciences.

PubMed

Wiener, Martin; Sommer, Friedrich T; Ives, Zachary G; Poldrack, Russell A; Litt, Brian

2016-11-02

As the pace and complexity of neuroscience data grow, an open data ecosystem must develop and grow with it to allow neuroscientists the ability to reach for new heights of discovery. However, the problems and complexities of neuroscience data sharing must first be addressed. Among the challenges facing data sharing in neuroscience, the problem of incentives, discoverability, and sustainability may be the most pressing. We here describe these problems and provide potential future solutions to help cultivate an ecosystem for data sharing. Copyright © 2016 Elsevier Inc. All rights reserved.

Revitalizing communities together: the shared values, goals, and work of education, urban planning, and public health.

PubMed

Cohen, Alison Klebanoff; Schuchter, Joseph W

2013-04-01

Inequities in education, the urban environment, and health co-exist and mutually reinforce each other. Educators, planners, and public health practitioners share commitments to place-based, participatory, youth-focused, and equitable work. They also have shared goals of building community resilience, social capital, and civic engagement. Interdisciplinary programs that embody these shared values and work towards these shared goals are emerging, including school-based health centers, full-service community schools, community health centers, Promise Neighborhoods, and Choice Neighborhoods. The intersection of these three fields represents an opportunity to intervene on social determinants of health. More collaborative research and practice across public health, education, and planning should build from the shared values identified to continue to address these common goals.

Distributed geospatial model sharing based on open interoperability standards

USGS Publications Warehouse

Feng, Min; Liu, Shuguang; Euliss, Ned H.; Fang, Yin

2009-01-01

Numerous geospatial computational models have been developed based on sound principles and published in journals or presented in conferences. However modelers have made few advances in the development of computable modules that facilitate sharing during model development or utilization. Constraints hampering development of model sharing technology includes limitations on computing, storage, and connectivity; traditional stand-alone and closed network systems cannot fully support sharing and integrating geospatial models. To address this need, we have identified methods for sharing geospatial computational models using Service Oriented Architecture (SOA) techniques and open geospatial standards. The service-oriented model sharing service is accessible using any tools or systems compliant with open geospatial standards, making it possible to utilize vast scientific resources available from around the world to solve highly sophisticated application problems. The methods also allow model services to be empowered by diverse computational devices and technologies, such as portable devices and GRID computing infrastructures. Based on the generic and abstract operations and data structures required for Web Processing Service (WPS) standards, we developed an interactive interface for model sharing to help reduce interoperability problems for model use. Geospatial computational models are shared on model services, where the computational processes provided by models can be accessed through tools and systems compliant with WPS. We developed a platform to help modelers publish individual models in a simplified and efficient way. Finally, we illustrate our technique using wetland hydrological models we developed for the prairie pothole region of North America.

The NASA Scientific and Technical Information (STI) Program's Implementation of Open Archives Initiation (OAI) for Data Interoperability and Data Exchange

NASA Technical Reports Server (NTRS)

Rocker, JoAnne; Roncaglia, George J.; Heimerl, Lynn N.; Nelson, Michael L.

2002-01-01

Interoperability and data-exchange are critical for the survival of government information management programs. E-government initiatives are transforming the way the government interacts with the public. More information is to be made available through web-enabled technologies. Programs such as the NASA's Scientific and Technical Information (STI) Program Office are tasked to find more effective ways to disseminate information to the public. The NASA STI Program is an agency-wide program charged with gathering, organizing, storing, and disseminating NASA-produced information for research and public use. The program is investigating the use of a new protocol called the Open Archives Initiative (OAI) as a means to improve data interoperability and data collection. OAI promotes the use of the OAI harvesting protocol as a simple way for data sharing among repositories. In two separate initiatives, the STI Program is implementing OAI In collaboration with the Air Force, Department of Energy, and Old Dominion University, the NASA STI Program has funded research on implementing the OAI to exchange data between the three organizations. The second initiative is the deployment of OAI for the NASA technical report server (TRS) environment. The NASA TRS environment is comprised of distributed technical report servers with a centralized search interface. This paper focuses on the implementation of OAI to promote interoperability among diverse data repositories.

Establishing a reliable framework for harnessing the creative power of the scientific crowd.

PubMed

Carter, Adrian J; Donner, Amy; Lee, Wen Hwa; Bountra, Chas

2017-02-01

Discovering new medicines is difficult and increasingly expensive. The pharmaceutical industry has responded to this challenge by embracing open innovation to access external ideas. Historically, partnerships were usually bilateral, and the drug discovery process was shrouded in secrecy. This model is rapidly changing. With the advent of the Internet, drug discovery has become more decentralised, bottom-up, and scalable than ever before. The term open innovation is now accepted as just one of many terms that capture different but overlapping levels of openness in the drug discovery process. Many pharmaceutical companies recognise the advantages of revealing some proprietary information in the form of results, chemical tools, or unsolved problems in return for valuable insights and ideas. For example, such selective revealing can take the form of openly shared chemical tools to explore new biological mechanisms or by publicly admitting what is not known in the form of an open call. The essential ingredient for addressing these problems is access to the wider scientific crowd. The business of crowdsourcing, a form of outsourcing in which individuals or organisations solicit contributions from Internet users to obtain ideas or desired services, has grown significantly to fill this need and takes many forms today. Here, we posit that open-innovation approaches are more successful when they establish a reliable framework for converting creative ideas of the scientific crowd into practice with actionable plans.

Establishing a reliable framework for harnessing the creative power of the scientific crowd

PubMed Central

Donner, Amy; Lee, Wen Hwa; Bountra, Chas

2017-01-01

Discovering new medicines is difficult and increasingly expensive. The pharmaceutical industry has responded to this challenge by embracing open innovation to access external ideas. Historically, partnerships were usually bilateral, and the drug discovery process was shrouded in secrecy. This model is rapidly changing. With the advent of the Internet, drug discovery has become more decentralised, bottom-up, and scalable than ever before. The term open innovation is now accepted as just one of many terms that capture different but overlapping levels of openness in the drug discovery process. Many pharmaceutical companies recognise the advantages of revealing some proprietary information in the form of results, chemical tools, or unsolved problems in return for valuable insights and ideas. For example, such selective revealing can take the form of openly shared chemical tools to explore new biological mechanisms or by publicly admitting what is not known in the form of an open call. The essential ingredient for addressing these problems is access to the wider scientific crowd. The business of crowdsourcing, a form of outsourcing in which individuals or organisations solicit contributions from Internet users to obtain ideas or desired services, has grown significantly to fill this need and takes many forms today. Here, we posit that open-innovation approaches are more successful when they establish a reliable framework for converting creative ideas of the scientific crowd into practice with actionable plans. PMID:28199324

Patient consent to publication and data sharing in industry and NIH-funded clinical trials.

PubMed

Spence, O'Mareen; Onwuchekwa Uba, Richie; Shin, Seongbin; Doshi, Peter

2018-05-03

Participants are recruited into clinical trials under the assumption that the research will contribute to medical knowledge. Therefore, non-publication trials-and, more recently, lack of data sharing-are widely considered to violate the trust of trial participants. Existing practices regarding patient consent to publication and data sharing have not been evaluated. Analyzing informed consent forms (ICFs), we studied what trial participants were told regarding investigators' intention to contribute to medical knowledge, publish trial results, and share de-identified trial data. We obtained 98 ICFs of industry-funded pre-marketing trials for all (17) antibiotics approved by the European Medicines Agency and 46 ICFs of publicly funded trials from the National Heart, Lung and Blood Institute Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) data repository. Three authors independently reviewed ICFs to identify and extract what was stated or implied regarding: (1) publication of results; (2) sharing de-identified data; (3) data ownership; (4) confidentiality of identifiable data; and (5) whether the trial will produce knowledge that offers public benefit. Consensus was obtained from the two reviewers with the greatest overall agreement on all five measures. Disagreements were resolved through discussion among all authors. Four (3%) trials indicated a commitment to publish trial results; 140 (97%) did not commit to publishing trial results; six (4%) indicated a commitment to share de-identified data with third party researchers. Commitments to share were more common in publicly funded trials than industry-funded trials (7% vs 3%). A total of 103 (72%) ICFs indicated the trials will or may produce knowledge that offers public benefits, while 131 (91%) ICFs left unstated who "owned" trial data; of those with statements, the sponsor always claimed ownership. Patient confidentiality was guaranteed in 137 (95%) trials. Our results suggest that consent forms rarely disclose investigators' intentions regarding the sharing of de-identified data or publication of trial results.

Enabling OpenID Authentication for VO-integrated Portals

NASA Astrophysics Data System (ADS)

Plante, R.; Yekkirala, V.; Baker, W.

2012-09-01

To support interoperating services that share proprietary data and other user-specific information, the VAO Project provides login services for browser-based portals built on the open standard, OpenID. To help portal developers take advantage of this service, we have developed a downloadable toolkit for integrating OpenID single sign-on support into any portal. This toolkit provides APIs in a few languages commonly used on the server-side as well as a command-line version for use in any language. In addition to describing how to use this toolkit, we also discuss the general VAO framework for single sign-on. While a portal may, if it wishes, support any OpenID provider, the VAO service provides a few extra features to support VO interoperability. This includes a portal's ability to retrieve (with the user's permission) an X.509 certificate representing the authenticated user so that the portal can access other restricted services on the user's behalf. Other standard features of OpenID allow portals to request other information about the user; this feature will be used in the future for sharing information about a user's group membership to enable sharing within a group of collaborating scientists.

[History of the public health policy in Chad 1900-1995].

PubMed

Massenet, D

1996-01-01

Public health policy in Chad began after colonization in 1899 and remained under the control of French Army Medical Corps for a long time. Military doctors shared their time between treating service personnel and indigenous people entitled Medical Assistance and making rounds in their sector. Since independence public health in the country has been based on a two-pronged association including fixed facilities (hospitals and dispensaries) and mobile services such as the Endemic Disease Unit whose most notable success was control of sleeping sickness in the southern part of the country. Over the years Chad has built up a national medical staff comprising 150 physicians. A medical school was opened in N'Djamena in 1990 and paramedical personnel are now trained at the National School for Public Health. War and lack of funds interrupted mobile services and there is presently a recrudescence of sleeping sickness. Since 1990 the World Health Organization has imposed its views and primary care is now available for all. However, it is now too early to judge the efficacity of this program in Chad.

Creating Open Education Resources for Teaching and Community Development through Action Research: An Overview of the Makerere AgShare Project

ERIC Educational Resources Information Center

Kaneene, John B.; Ssajjakambwe, Paul; Kisaka, Stevens; Miller, RoseAnn; Kabasa, John D.

2013-01-01

The AgShare Phase I Program, conducted at Makerere University, Kampala, Uganda, was formed to create open education resources for teaching and community development through action research. The study was conducted by an interdisciplinary team of investigators from fields of veterinary medicine and agri-business. Two master of science students…

Collective Designing and Sharing of Open Educational Resources: A Study of the French CARTOUN Platform

ERIC Educational Resources Information Center

Quere, Nolwenn

2017-01-01

Designing and sharing Open Educational Resources (OERs) requires teachers to develop new competences, in particular with digital resources. In this paper, the case of a language resource production group is introduced. Due to the centrality of the OERs in their collective activity, I show that the documents they produce are essential to the…

OpenElectrophy: An Electrophysiological Data- and Analysis-Sharing Framework

PubMed Central

Garcia, Samuel; Fourcaud-Trocmé, Nicolas

2008-01-01

Progress in experimental tools and design is allowing the acquisition of increasingly large datasets. Storage, manipulation and efficient analyses of such large amounts of data is now a primary issue. We present OpenElectrophy, an electrophysiological data- and analysis-sharing framework developed to fill this niche. It stores all experiment data and meta-data in a single central MySQL database, and provides a graphic user interface to visualize and explore the data, and a library of functions for user analysis scripting in Python. It implements multiple spike-sorting methods, and oscillation detection based on the ridge extraction methods due to Roux et al. (2007). OpenElectrophy is open source and is freely available for download at http://neuralensemble.org/trac/OpenElectrophy. PMID:19521545

Report To The Secretary Of Defense-Task Group On A Culture Of Savings: Implementing Behavior Change In DoD

DTIC Science & Technology

2011-01-01

Shared Services in the Public Sector - Accenture Shared Services in Government - AT Kearney – 2009 Global Shared Services Survey Results - Deloitte... Shared Services - a Benchmark Study - The Johnson Group – Economics of Business Process Outsourcing - Technology Association of Georgia – State of... Shared Services and Business Process Outsourcing - Accenture – Public Sector Outsourcing Surge in 2010 - National Outsourcing Association – Naval

Capitalizing on global demands for open data access and interoperability - the USGIN story

NASA Astrophysics Data System (ADS)

Richard, Stephen; Allison, Lee

2016-04-01

U.S. Geoscience Information Network (USGIN - http://usgin.org) data integration framework packages data so that it can be accessible through a broad array of open-source software and applications, including GeoServer, QGIS, GrassGIS, uDig, and gvSIG. USGIN data-sharing networks are designed to interact with other data exchange systems and have the ability to connect information on a granular level without jeopardizing data ownership. The system is compliant with international standards and protocols, scalable, extensible, and can be deployed throughout the world for a myriad of applications. Using GeoSciML as its data transfer standard and a collaborative approach to Content Model development and management, much of the architecture is publically available through GitHub. Initially developed by the USGS and Association of American State Geologists as a distributed, self-maintained platform for sharing geoscience information, USGIN meets all the requirements of the White House Open Data Access Initiative that applies to (almost) all federally-funded research and all federally-maintained data, opening up huge opportunities for further deployment. In December 2015, the USGIN Content Model schema was recommended for adoption by the White House-led US Group on Earth Observations (USGEO) "Draft Common Framework for Earth-Observation Data" for all US earth observation (i.e., satellite) data. The largest USGIN node is the U.S. National Geothermal Data System (NGDS - www.geothermaldata.org). NGDS provides free open access to ~ 10 million data records, maps, and reports, sharing relevant geoscience and land use data to propel geothermal development and production in the U.S. NGDS currently serves information from hundreds of the U.S. Department of Energy's sponsored projects and geologic data feeds from 60+ data providers in all 50 states, using free and open source software, in a federated system where data owners maintain control of their data. This interactive online system is opening new exploration opportunities and shortening project development by making data easily discoverable, accessible, and interoperable at no cost to users. USGIN Foundation, Inc. was established in 2014 as a not-for-profit company to deploy the USGIN data integration framework for other natural resource (energy, water, and minerals), natural hazards, and geoscience investigations applications, nationally and worldwide. The USGIN vision is that as each data node adds to its data repositories, the system-wide USGIN functions become increasingly valuable to it. The long term goal is that the data network reach a 'tipping point' at which it becomes like a data equivalent to the World Wide Web - where everyone will maintain the function because it is expected by its clientele and it fills critical needs.

Towards Social Radiology as an Information Infrastructure: Reconciling the Local With the Global

PubMed Central

2014-01-01

The current widespread use of medical images and imaging procedures in clinical practice and patient diagnosis has brought about an increase in the demand for sharing medical imaging studies among health professionals in an easy and effective manner. This article reveals the existence of a polarization between the local and global demands for radiology practice. While there are no major barriers for sharing such studies, when access is made from a (local) picture archive and communication system (PACS) within the domain of a healthcare organization, there are a number of impediments for sharing studies among health professionals on a global scale. Social radiology as an information infrastructure involves the notion of a shared infrastructure as a public good, affording a social space where people, organizations and technical components may spontaneously form associations in order to share clinical information linked to patient care and radiology practice. This article shows however, that such polarization establishes a tension between local and global demands, which hinders the emergence of social radiology as an information infrastructure. Based on an analysis of the social space for radiology practice, the present article has observed that this tension persists due to the inertia of a locally installed base in radiology departments, for which common teleradiology models are not truly capable of reorganizing as a global social space for radiology practice. Reconciling the local with the global signifies integrating PACS and teleradiology into an evolving, secure, heterogeneous, shared, open information infrastructure where the conceptual boundaries between (local) PACS and (global) teleradiology are transparent, signaling the emergence of social radiology as an information infrastructure. PMID:25600710

The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository.

PubMed

Clark, Kenneth; Vendt, Bruce; Smith, Kirk; Freymann, John; Kirby, Justin; Koppel, Paul; Moore, Stephen; Phillips, Stanley; Maffitt, David; Pringle, Michael; Tarbox, Lawrence; Prior, Fred

2013-12-01

The National Institutes of Health have placed significant emphasis on sharing of research data to support secondary research. Investigators have been encouraged to publish their clinical and imaging data as part of fulfilling their grant obligations. Realizing it was not sufficient to merely ask investigators to publish their collection of imaging and clinical data, the National Cancer Institute (NCI) created the open source National Biomedical Image Archive software package as a mechanism for centralized hosting of cancer related imaging. NCI has contracted with Washington University in Saint Louis to create The Cancer Imaging Archive (TCIA)-an open-source, open-access information resource to support research, development, and educational initiatives utilizing advanced medical imaging of cancer. In its first year of operation, TCIA accumulated 23 collections (3.3 million images). Operating and maintaining a high-availability image archive is a complex challenge involving varied archive-specific resources and driven by the needs of both image submitters and image consumers. Quality archives of any type (traditional library, PubMed, refereed journals) require management and customer service. This paper describes the management tasks and user support model for TCIA.

Clinical records anonymisation and text extraction (CRATE): an open-source software system.

PubMed

Cardinal, Rudolf N

2017-04-26

Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.

The development of a new methodology for knowledge sharing in the interface between university and society--an example from the meat sector.

PubMed

Algers, Anne; Silva-Fletcher, Ayona; Gregory, Neville; Hunt, Melvin

2013-11-01

Design science research was used for the generation, use and evaluation of a model for knowledge sharing in the user community through open educational resources (OER). The focus of interest was on the development process of a model for knowledge sharing that emphasizes the characteristics and the needs of the user community; the empowerment and democratic issues of openness; the collaboration between institutions and dialog with society; and the consideration of quality and sustainability issues. Initially, the community needs were analyzed through surveys and workshops, and the findings used, through negotiations, to formulate the development process. An open-training platform served as an infrastructure and included a repository with OER, a wiki and a discussion forum. The purpose of this article is an attempt to provide universities with a plan and template for integrated knowledge sharing that responds to societal needs. Usability and usefulness has not been evaluated. Copyright © 2013 Elsevier Ltd. All rights reserved.

Legal and policy barriers to sharing data between public health programs in New York City: a case study.

PubMed

Gasner, M Rose; Fuld, Jennifer; Drobnik, Ann; Varma, Jay K

2014-06-01

Integration of public health surveillance data within health departments is important for public health activities and cost-efficient coordination of care. Access to and use of surveillance data are governed by public health law and by agency confidentiality and security policies. In New York City, we examined public health laws and agency policies for data sharing across HIV, sexually transmitted disease, tuberculosis, and viral hepatitis surveillance programs. We found that recent changes to state laws provide greater opportunities for data sharing but that agency policies must be updated because they limit increased data integration. Our case study can help other health departments conduct similar reviews of laws and policies to increase data sharing and integration of surveillance data.

The science commons in health research: structure, function, and value.

PubMed

Cook-Deegan, Robert

The "science commons," knowledge that is widely accessible at low or no cost, is a uniquely important input to scientific advance and cumulative technological innovation. It is primarily, although not exclusively, funded by government and nonprofit sources. Much of it is produced at academic research centers, although some academic science is proprietary and some privately funded R&D enters the science commons. Science in general aspires to Mertonian norms of openness, universality, objectivity, and critical inquiry. The science commons diverges from proprietary science primarily in being open and being very broadly available. These features make the science commons particularly valuable for advancing knowledge, for training innovators who will ultimately work in both public and private sectors, and in providing a common stock of knowledge upon which all players-both public and private-can draw readily. Open science plays two important roles that proprietary R&D cannot: it enables practical benefits even in the absence of profitable markets for goods and services, and its lays a shared foundation for subsequent private R&D. The history of genomics in the period 1992-2004, covering two periods when genomic startup firms attracted significant private R&D investment, illustrates these features of how a science commons contributes value. Commercial interest in genomics was intense during this period. Fierce competition between private sector and public sector genomics programs was highly visible. Seemingly anomalous behavior, such as private firms funding "open science," can be explained by unusual business dynamics between established firms wanting to preserve a robust science commons to prevent startup firms from limiting established firms' freedom to operate. Deliberate policies to create and protect a large science commons were pursued by nonprofit and government funders of genomics research, such as the Wellcome Trust and National Institutes of Health. These policies were crucial to keeping genomic data and research tools widely available at low cost.

A Case for Open Network Health Systems: Systems as Networks in Public Mental Health.

PubMed

Rhodes, Michael Grant; de Vries, Marten W

2017-01-08

Increases in incidents involving so-called confused persons have brought attention to the potential costs of recent changes to public mental health (PMH) services in the Netherlands. Decentralized under the (Community) Participation Act (2014), local governments must find resources to compensate for reduced central funding to such services or "innovate." But innovation, even when pressure for change is intense, is difficult. This perspective paper describes experience during and after an investigation into a particularly violent incident and murder. The aim was to provide recommendations to improve the functioning of local PMH services. The investigation concluded that no specific failure by an individual professional or service provider facility led to the murder. Instead, also as a result of the Participation Act that severed communication lines between individuals and organizations, information sharing failures were likely to have reduced system level capacity to identify risks. The methods and analytical frameworks employed to reach this conclusion, also lead to discussion as to the plausibility of an unconventional solution. If improving communication is the primary problem, non-hierarchical information, and organizational networks arise as possible and innovative system solutions. The proposal for debate is that traditional "health system" definitions, literature and narratives, and operating assumptions in public (mental) health are 'locked in' constraining technical and organization innovations. If we view a "health system" as an adaptive system of economic and social "networks," it becomes clear that the current orthodox solution, the so-called integrated health system, typically results in a "centralized hierarchical" or "tree" network. An overlooked alternative that breaks out of the established policy narratives is the view of a 'health systems' as a non-hierarchical organizational structure or 'Open Network.' In turn, this opens new technological and organizational possibilities in seeking policy solutions, and suggests an alternative governance model of huge potential value in public health both locally and globally. © 2017 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Spleen removal - open - adults - discharge

MedlinePlus

... medlineplus.gov/ency/patientinstructions/000287.htm Spleen removal - open - adults - discharge To use the sharing features on ... The type of surgery you had is called open surgery. The surgeon made a cut (incision) in ...

Open heart surgery

MedlinePlus

... this page: //medlineplus.gov/ency/article/002950.htm Open heart surgery To use the sharing features on this ... large arteries connected to the heart. The term "open heart surgery" means that you are connected to a ...

Willingness to share personal health record data for care improvement and public health: a survey of experienced personal health record users.

PubMed

Weitzman, Elissa R; Kelemen, Skyler; Kaci, Liljana; Mandl, Kenneth D

2012-05-22

Data stored in personally controlled health records (PCHRs) may hold value for clinicians and public health entities, if patients and their families will share them. We sought to characterize consumer willingness and unwillingness (reticence) to share PCHR data across health topics, and with different stakeholders, to advance understanding of this issue. Cross-sectional 2009 Web survey of repeat PCHR users who were patients over 18 years old or parents of patients, to assess willingness to share their PCHR data with an-out-of-hospital provider to support care, and the state/local public health authority to support monitoring; the odds of reticence to share PCHR information about ten exemplary health topics were estimated using a repeated measures approach. Of 261 respondents (56% response rate), more reported they would share all information with the state/local public health authority (63.3%) than with an out-of-hospital provider (54.1%) (OR 1.5, 95% CI 1.1, 1.9; p = .005); few would not share any information with these parties (respectively, 7.9% and 5.2%). For public health sharing, reticence was higher for most topics compared to contagious illness (ORs 4.9 to 1.4, all p-values < .05), and reflected concern about anonymity (47.2%), government insensitivity (41.5%), discrimination (24%). For provider sharing, reticence was higher for all topics compared to contagious illness (ORs 6.3 to 1.5, all p-values < .05), and reflected concern for relevance (52%), disclosure to insurance (47.6%) and/or family (20.5%). Pediatric patients and their families are often willing to share electronic health information to support health improvement, but remain cautious. Robust trust models for PCHR sharing are needed.

Shared Services for Rural and Small Schools.

ERIC Educational Resources Information Center

Hanuske, Sarah

As school populations decline and costs rise due to inflation, rural and small schools are turning to shared services in order to keep community schools open, meet federal mandates, and improve educational opportunities. Sharing ventures may be for limited purposes, such as sharing a physics teacher or having a joint drama production, or for more…

MIRA: An R package for DNA methylation-based inference of regulatory activity.

PubMed

Lawson, John T; Tomazou, Eleni M; Bock, Christoph; Sheffield, Nathan C

2018-03-01

DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for independent region sets with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for each region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of open chromatin and protein binding regions to be leveraged for novel insight into the regulatory state of DNA methylation datasets. R package available on Bioconductor: http://bioconductor.org/packages/release/bioc/html/MIRA.html. nsheffield@virginia.edu.

Participating in the Geospatial Web: Collaborative Mapping, Social Networks and Participatory GIS

NASA Astrophysics Data System (ADS)

Rouse, L. Jesse; Bergeron, Susan J.; Harris, Trevor M.

In 2005, Google, Microsoft and Yahoo! released free Web mapping applications that opened up digital mapping to mainstream Internet users. Importantly, these companies also released free APIs for their platforms, allowing users to geo-locate and map their own data. These initiatives have spurred the growth of the Geospatial Web and represent spatially aware online communities and new ways of enabling communities to share information from the bottom up. This chapter explores how the emerging Geospatial Web can meet some of the fundamental needs of Participatory GIS projects to incorporate local knowledge into GIS, as well as promote public access and collaborative mapping.

Health Data Sharing Preferences of Consumers: Public Policy and Legal Implications of Consumer-Mediated Data Management

ERIC Educational Resources Information Center

Moon, Lisa A.

2017-01-01

An individual's choice to share or have control of the sharing or withholding of their personal health information is one of the most significant public policy challenges associated with electronic information exchange. There were four aims of this study. First, to describe predictors of health data sharing preferences of consumers. Second, to…

Public availability of research data in dentistry journals indexed in Journal Citation Reports.

PubMed

Vidal-Infer, Antonio; Tarazona, Beatriz; Alonso-Arroyo, Adolfo; Aleixandre-Benavent, Rafael

2018-01-01

Dentistry is a medical discipline with an increasing scientific production in the last years. Due to the importance of data sharing in science, this study aims at analyzing the availability of raw data in articles from scientific journals indexed in the Dentistry category of the 2014 edition of the Journal Citation Reports. A review of the 88 websites of journals from the Dentistry category was conducted to determine the data-sharing editorial policies. Furthermore, a search in the PubMed Central repository to collect information about the characteristics of the supplementary material of articles from those journals was carried out. The possibility of publishing a supplementary material was higher in the first quartile journals. A percentage of 7.6% of the articles registered in PubMed Central contained a supplementary material, especially text documents, but the presence of spreadsheets was scarce. There is a relationship between openness policies and the impact of the journals according to their quartile or position ranking by the impact factor in the JCR, but the willingness of sharing raw data in spreadsheets format is still limited. This study will reveal the resources of raw data which will improve quality of research and clinical practice.

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

The open-source software movement is gaining increasing momentum in China. Of the limited numbers of open-source software in China, "Red Flag Linux" stands out most strikingly, commanding 30 percent share of Chinese software market. Unlike the spontaneity of open-source movement in North America, open-source software development in…

Teaching, Learning, and Sharing Openly Online

ERIC Educational Resources Information Center

O'Byrne, W. Ian; Roberts, Verena; LaBonte, Randy; Graham, Lee

2015-01-01

Open learning is becoming a critical focus for K-12 technology-supported programs as the importance of digital literacy and digital freedoms for all learners grows. This article describes current open learning policy, open educational resources and potential implications for open practice and ends with suggestions for future research in open…

ITK: enabling reproducible research and open science

PubMed Central

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46. PMID:24600387

ITK: enabling reproducible research and open science.

PubMed

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

Open Access to Research Articles and Data: Library Roles

NASA Astrophysics Data System (ADS)

Joseph, Heather

2015-08-01

Over the past decade, a handful of key developments have caused scholars and researchers to rethink not only the way they conduct their work, but also the way in which they communicate it to others. The advent of the Internet has provided unprecedented opportunities for immediate, cost effective global connectivity, opening up new possibilities for collaboration and communication. This has resulted in scholarship increasingly being conducted in the online environment, and a vast amount of new digital information being generated and made widely available to those interested in using it. Additionally, the Internet is a dynamic environment, with new channels for producing and sharing information in a myriad of formats emerging frequently.In higher education, the momentum of the burgeoning movement towards "open" sharing of information of all kinds continues to gain traction. In particular, advancements in the areas of opening up access to articles and reserch data are increasingly visible. In both of these areas, academic and research libraries are playing important, central roles in promoting the awareness of the potential costs and benefits of a more open research environment, as well as defining new roles for libraries in this digital environment.As this push for grater openness continues, these fronts are intersecting in interesting and potentially transformative ways. The Open Access and Open Data movements share fundamental philosophical commonalities that make collaboration a natural outcome. Both movements place a premium on reducing barriers to discovering and accessing pertinent digital information. Perhaps even more significantly, both explicitly recognize that enabling productive use of digital information is key to unlocking its full value. As a result of these shared priorities, there are a wide variety of common strategies that libraries can take to help advance research, presenting new opportunities for deeper collaboration to take place.This talk will explore what is happening in these "open" movements from both a practical and policy standpoint; how this might directly impact academia, the research community, and especially, libraries.

Mapping of Indian neuroscience research: a scientometric analysis of research output during 1999-2008.

PubMed

Bala, Adarsh; Gupta, B M

2010-01-01

This study analyses the research output in India in neurosciences during the period 1999-2008 and the analyses included research growth, rank, global publications' share, citation impact, share of international collaborative papers and major collaborative partner countries and patterns of research communication in most productive journals. It also analyses the characteristics of most productive institutions, authors and high-cited papers. The publication output and impact of India is also compared with China, Brazil and South Korea. Scopus Citation database was used for retrieving the publications' output of India and other countries in neurosciences during 1999-2008. India's global publications' share in neurosciences during the study period was 0.99% (with 4503 papers) and it ranked 21 st among the top 26 countries in neurosciences. The average annual publication growth rate was 11.37%, shared 17.34% of international collaborative papers and the average citation per paper was 4.21. India was far behind China, Brazil and South Korea in terms of publication output, citation quality and share of international collaborative papers in neurosciences. India is far behind in terms of publication output, citation quality and share of international collaborative papers in neurosciences when compared to other countries with an emerging economy. There is an urgent need to substantially increase the research activities in the field of neurosciences in India.

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals.

PubMed

Stodden, Victoria; Guo, Peixuan; Ma, Zhaokun

2013-01-01

Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38% had a data policy, 22% had a code policy, and 66% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

PubMed Central

Stodden, Victoria; Guo, Peixuan; Ma, Zhaokun

2013-01-01

Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38% had a data policy, 22% had a code policy, and 66% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals. PMID:23805293

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feibel, C.E.

This study uses multiple data collection and research methods including in depth interviews, 271 surveys of shared taxi and minibus operators, participant observation, secondary sources, and the literature on public transport from low, medium, and high-income countries. Extensive use is also made of a survey administered in Istanbul in 1976 to 1935 paratransit operators. Primary findings are that private buses are more efficient than public buses on a cost per passenger-km basis, and that private minibuses are as efficient as public buses. In terms of energy efficiency, minibuses are almost as efficient as public and private buses using actual-occupancy levels.more » Large shared taxis are twice as cost and energy efficient as cars, and small shared taxis 50% more efficient. In terms of investment cost per seat, large shared taxis have the lowest cost followed by smaller shared taxis, minibuses, and buses. Considering actual occupancy levels, minibuses are only slightly less effective in terms of congestion than buses, and large and small shared taxis are twice as effective as cars. It is also shown that minibuses and shared taxis have better service quality than buses because of higher frequencies and speeds, and because they provide a much higher probability of getting a seat than buses. Analysis of regulation and policy suggests that there are many unintended cost of public-transport regulations.« less

Community response to noise: research in Central, Eastern and South-Eastern Europe and Newly Independent States.

PubMed

Jeram, Sonja; Lekaviciute, Jurgita; Krukle, Zanda; Argalasova-Sobotova, Lubica; Ristovska, Gordana; Paunovic, Katarina; Pawlaczyk-Luszczynska, Malgorzata

2013-01-01

The systems of public complaints on environmental noise were reviewed in seven countries of Central and Eastern Europe (CEE), South-East Europe (SEE), and Newly Independent States (NIS). Public complaints remain an important issue due to differences in public sensitivity to noise and due to several cases where a measurement of noise intensity does not give a satisfying solution to the problem. The unresolved problem remaining in the residential neighborhoods is the noise from pubs and restaurants that are open until late in the night. In our review, we compiled information on the institutions responsible for the implementation of environmental noise legislation and organizations that are responsible for dealing with public complaints. Information on activities for increasing public awareness on hazards rising from environmental noise and the role of civil initiative was explored. In seven countries, and among them, Slovenia, Lithuania, Latvia, Slovakia, The Former Yugoslav Republic of Macedonia, Serbia, and Poland, the responsibilities and duties are shared among different institutions at national and regional levels, depending on the noise source. The problem of gathering information on complaints and using it for improving the wellbeing and health of citizens remains often difficult and unsolved.

Open Availability of Patient Medical Photographs in Google Images Search Results: Cross-Sectional Study of Transgender Research.

PubMed

Marshall, Zack; Brunger, Fern; Welch, Vivian; Asghari, Shabnam; Kaposy, Chris

2018-02-26

This paper focuses on the collision of three factors: a growing emphasis on sharing research through open access publication, an increasing awareness of big data and its potential uses, and an engaged public interested in the privacy and confidentiality of their personal health information. One conceptual space where this collision is brought into sharp relief is with the open availability of patient medical photographs from peer-reviewed journal articles in the search results of online image databases such as Google Images. The aim of this study was to assess the availability of patient medical photographs from published journal articles in Google Images search results and the factors impacting this availability. We conducted a cross-sectional study using data from an evidence map of research with transgender, gender non-binary, and other gender diverse (trans) participants. For the original evidence map, a comprehensive search of 15 academic databases was developed in collaboration with a health sciences librarian. Initial search results produced 25,230 references after duplicates were removed. Eligibility criteria were established to include empirical research of any design that included trans participants or their personal information and that was published in English in peer-reviewed journals. We identified all articles published between 2008 and 2015 with medical photographs of trans participants. For each reference, images were individually numbered in order to track the total number of medical photographs. We used odds ratios (OR) to assess the association between availability of the clinical photograph on Google Images and the following factors: whether the article was openly available online (open access, Researchgate.net, or Academia.edu), whether the article included genital images, if the photographs were published in color, and whether the photographs were located on the journal article landing page. We identified 94 articles with medical photographs of trans participants, including a total of 605 photographs. Of the 94 publications, 35 (37%) included at least one medical photograph that was found on Google Images. The ability to locate the article freely online contributes to the availability of at least one image from the article on Google Images (OR 2.99, 95% CI 1.20-7.45). This is the first study to document the existence of medical photographs from peer-reviewed journals appearing in Google Images search results. Almost all of the images we searched for included sensitive photographs of patient genitals, chests, or breasts. Given that it is unlikely that patients consented to sharing their personal health information in these ways, this constitutes a risk to patient privacy. Based on the impact of current practices, revisions to informed consent policies and guidelines are required. ©Zack Marshall, Fern Brunger, Vivian Welch, Shabnam Asghari, Chris Kaposy. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 26.02.2018.

Analysing researchers’ outreach efforts and the association with publication metrics: A case study of Kudos

PubMed Central

Aung, Htet Htet; Aw, Ashley Sara; Rapple, Charlie; Theng, Yin-Leng

2017-01-01

With the growth of scholarly collaboration networks and social communication platforms, members of the scholarly community are experimenting with their approach to disseminating research outputs, in an effort to increase their audience and outreach. However, from a researcher’s point of view, it is difficult to determine whether efforts to make work more visible are worthwhile (in terms of the association with publication metrics) and within that, difficult to assess which platform or network is most effective for sharing work and connecting to a wider audience. We undertook a case study of Kudos (https://www.growkudos.com), a web-based service that claims to help researchers increase the outreach of their publications, to examine the most effective tools for sharing publications online, and to investigate which actions are associated with improved metrics. We extracted a dataset from Kudos of 830,565 unique publications claimed by authors, for which 20,775 had actions taken to explain or share via Kudos, and for 4,867 of these full text download data from publishers was available. Findings show that researchers are most likely to share their work on Facebook, but links shared on Twitter are more likely to be clicked on. A Mann-Whitney U test revealed that a treatment group (publications having actions in Kudos) had a significantly higher median average of 149 full text downloads (23.1% more) per publication as compared to a control group (having no actions in Kudos) with a median average of 121 full text downloads per publication. These findings suggest that performing actions on publications, such as sharing, explaining, or enriching, could help to increase the number of full text downloads of a publication. PMID:28817627

47 CFR 27.1305 - Shared wireless broadband network.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Shared wireless broadband network. 27.1305... broadband network. The Shared Wireless Broadband Network developed by the 700 MHz Public/Private Partnership must be designed to meet requirements associated with a nationwide, public safety broadband network. At...

47 CFR 90.1405 - Shared wireless broadband network.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 5 2011-10-01 2011-10-01 false Shared wireless broadband network. 90.1405... broadband network. The Shared Wireless Broadband Network developed by the 700 MHz Public/Private Partnership must be designed to meet requirements associated with a nationwide, public safety broadband network. At...

47 CFR 27.1305 - Shared wireless broadband network.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 2 2011-10-01 2011-10-01 false Shared wireless broadband network. 27.1305... broadband network. The Shared Wireless Broadband Network developed by the 700 MHz Public/Private Partnership must be designed to meet requirements associated with a nationwide, public safety broadband network. At...

47 CFR 90.1405 - Shared wireless broadband network.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 5 2010-10-01 2010-10-01 false Shared wireless broadband network. 90.1405... broadband network. The Shared Wireless Broadband Network developed by the 700 MHz Public/Private Partnership must be designed to meet requirements associated with a nationwide, public safety broadband network. At...

42 CFR 438.108 - Cost sharing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 4 2010-10-01 2010-10-01 false Cost sharing. 438.108 Section 438.108 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS MANAGED CARE Enrollee Rights and Protections § 438.108 Cost sharing. The contract must...

47 CFR 27.1305 - Shared wireless broadband network.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 2 2012-10-01 2012-10-01 false Shared wireless broadband network. 27.1305... broadband network. The Shared Wireless Broadband Network developed by the 700 MHz Public/Private Partnership must be designed to meet requirements associated with a nationwide, public safety broadband network. At...

47 CFR 90.1405 - Shared wireless broadband network.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 5 2012-10-01 2012-10-01 false Shared wireless broadband network. 90.1405... broadband network. The Shared Wireless Broadband Network developed by the 700 MHz Public/Private Partnership must be designed to meet requirements associated with a nationwide, public safety broadband network. At...

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

PubMed Central

Argimón, Silvia; Abudahab, Khalil; Goater, Richard J. E.; Fedosejev, Artemij; Bhai, Jyothish; Glasner, Corinna; Feil, Edward J.; Holden, Matthew T. G.; Yeats, Corin A.; Grundmann, Hajo; Spratt, Brian G.

2016-01-01

Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets. PMID:28348833

[Social media and medical apps: how they can change health communication, education and care].

PubMed

Santoro, Eugenio

2013-05-01

Social media and medical apps for smartphones and tablets are changing health communication, education and care. This change involves physicians and other health care professionals which for their education, training and updating have started to follow public pages and profiles opened by medical journals and professional societies on the online social networking sites (such as Facebook, Twitter and Google+), to access scientific content (videos, images, slides) available on user-generated contents sites (such as SlideShare, Pinterest and YouTube) or on health professional online communities such as Sermo, and to use medical and health apps on their smartphones and tablets. As shown by a number of experiences conducted in US by health institutions such as the Centers for Disease Control and Prevention of Atlanta and hospitals such a the Mayo Clinic, these tools are also transforming the way to make health promotion activities and communication, promote healthy habits and lifestyles, and prevent chronic diseases. Finally this change involves patients which are starting to use medical and health apps on their smartphones and tablets to monitor their diseases, and tools such as Patients Like Me (an online patients' community), Facebook and Twitter to share with others the same disease experience, to learn about the disease and treatments, and to find opinions on physicians, hospitals and medical centers. These new communication tools allow users to move to a kind of collaborative education and updating where news and contents (such as public health recommendations, results of the most recent clinical researches or medical guidelines) may be shared and discussed.

A Case for Open Network Health Systems: Systems as Networks in Public Mental Health

PubMed Central

Rhodes, Michael Grant; de Vries, Marten W.

2017-01-01

Increases in incidents involving so-called confused persons have brought attention to the potential costs of recent changes to public mental health (PMH) services in the Netherlands. Decentralized under the (Community) Participation Act (2014), local governments must find resources to compensate for reduced central funding to such services or "innovate." But innovation, even when pressure for change is intense, is difficult. This perspective paper describes experience during and after an investigation into a particularly violent incident and murder. The aim was to provide recommendations to improve the functioning of local PMH services. The investigation concluded that no specific failure by an individual professional or service provider facility led to the murder. Instead, also as a result of the Participation Act that severed communication lines between individuals and organizations, information sharing failures were likely to have reduced system level capacity to identify risks. The methods and analytical frameworks employed to reach this conclusion, also lead to discussion as to the plausibility of an unconventional solution. If improving communication is the primary problem, non-hierarchical information, and organizational networks arise as possible and innovative system solutions. The proposal for debate is that traditional "health system" definitions, literature and narratives, and operating assumptions in public (mental) health are ‘locked in’ constraining technical and organization innovations. If we view a "health system" as an adaptive system of economic and social "networks," it becomes clear that the current orthodox solution, the so-called integrated health system, typically results in a "centralized hierarchical" or "tree" network. An overlooked alternative that breaks out of the established policy narratives is the view of a ‘health systems’ as a non-hierarchical organizational structure or ‘Open Network.’ In turn, this opens new technological and organizational possibilities in seeking policy solutions, and suggests an alternative governance model of huge potential value in public health both locally and globally. PMID:28812792

On NAAMP and the use of the Internet as a forum for evolving science

USGS Publications Warehouse

Schmieder, R.

1996-01-01

Traditionally, science has been communicated through peerreviewed hardcopy. With the rapid growth of internet technology, many new potentials for sharing and evolution of ideas are possible: open, low cost communication between researchers, both accredited and amateur, may allow not joint problem solving at scales previously not possible. Conservation especially, is a dynamic field which may benefit from such rapid dissemination of information. However, among many concerns for the use of this media include 1) lack of peer review, 2) potential for , 3) dissemination of misinformation, especially when dealing with charismatic taxa 4) the possibility of creating an apparent need for an exciting technology, 5) implications of sharing data, 6) potential for distraction and additional concerns added by exposure to media and public attention, and 7) overall gain to effort ratio. With the increased facility of commmunication, feedback from the implementation of NAAMP III Online will help guide the direction and media choice of future conferences.

Science as a Web of Trails: Redesigning Science Education with the Tools of the Present to Meet the Needs of the Future

NASA Astrophysics Data System (ADS)

Karno, Donna; Glassman, Michael

2013-12-01

Science education has experienced significant changes since the mid-20th century, most recently with the creation of STEM curricula (DeBoer 1991; Yager 2000). The emergence of the World Wide Web as a tool in research and discovery offers Pre-K-12 science education an opportunity to share information and perspectives which engage students with the scientific community (Zoller 2011). Students are able to access open, transparent sites creating common resources pools and autonomous working groups which can be used for shared problem solving. Science teachers should carefully build web 2.0 technology into their practice based on a changing pedagogy. Instead of focusing on teaching rule-based concepts and processes in which the teacher's role is that of expert, education should be focusing on possibilities of the web both in scientific research and understanding. In addition, web-focused education can also help remake scientific product as a public good in the lives of both science researchers and science consumers.

ARX - A Comprehensive Tool for Anonymizing Biomedical Data

PubMed Central

Prasser, Fabian; Kohlmayer, Florian; Lautenschläger, Ronald; Kuhn, Klaus A.

2014-01-01

Collaboration and data sharing have become core elements of biomedical research. Especially when sensitive data from distributed sources are linked, privacy threats have to be considered. Statistical disclosure control allows the protection of sensitive data by introducing fuzziness. Reduction of data quality, however, needs to be balanced against gains in protection. Therefore, tools are needed which provide a good overview of the anonymization process to those responsible for data sharing. These tools require graphical interfaces and the use of intuitive and replicable methods. In addition, extensive testing, documentation and openness to reviews by the community are important. Existing publicly available software is limited in functionality, and often active support is lacking. We present ARX, an anonymization tool that i) implements a wide variety of privacy methods in a highly efficient manner, ii) provides an intuitive cross-platform graphical interface, iii) offers a programming interface for integration into other software systems, and iv) is well documented and actively supported. PMID:25954407

On Proportionate and Truthful International Alliance Contributions: An Analysis of IncentiveCompatible Cost Sharing Mechanisms to Burden Sharing

DTIC Science & Technology

2017-03-23

Therefore, the mecha- nism induces a stable cost sharing scheme wherein a subset of colluding players will not all benefit . In a subset of colluding...goods are not divisible and are not excludable. Cost sharing mechanisms specific to public goods have been researched extensively in the literature...Jackson & Moulin [1992] consider the sharing of cost for an indivisible public project among many players, and their work was extended by Bag [1997] to

Building the Synergy between Public Sector and Research Data Infrastructures

NASA Astrophysics Data System (ADS)

Craglia, Massimo; Friis-Christensen, Anders; Ostländer, Nicole; Perego, Andrea

2014-05-01

INSPIRE is a European Directive aiming to establish a EU-wide spatial data infrastructure to give cross-border access to information that can be used to support EU environmental policies, as well as other policies and activities having an impact on the environment. In order to ensure cross-border interoperability of data infrastructures operated by EU Member States, INSPIRE sets out a framework based on common specifications for metadata, data, network services, data and service sharing, monitoring and reporting. The implementation of INSPIRE has reached important milestones: the INSPIRE Geoportal was launched in 2011 providing a single access point for the discovery of INSPIRE data and services across EU Member States (currently, about 300K), while all the technical specifications for the interoperability of data across the 34 INSPIRE themes were adopted at the end of 2013. During this period a number of EU and international initiatives has been launched, concerning cross-domain interoperability and (Linked) Open Data. In particular, the EU Open Data Portal, launched in December 2012, made provisions to access government and scientific data from EU institutions and bodies, and the EU ISA Programme (Interoperability Solutions for European Public Administrations) promotes cross-sector interoperability by sharing and re-using EU-wide and national standards and components. Moreover, the Research Data Alliance (RDA), an initiative jointly funded by the European Commission, the US National Science Foundation and the Australian Research Council, was launched in March 2013 to promote scientific data sharing and interoperability. The Joint Research Centre of the European Commission (JRC), besides being the technical coordinator of the implementation of INSPIRE, is also actively involved in the initiatives promoting cross-sector re-use in INSPIRE, and sustainable approaches to address the evolution of technologies - in particular, how to support Linked Data in INSPIRE and the use of global persistent identifiers. It is evident that government and scientific data infrastructures are currently facing a number of issues that have already been addressed in INSPIRE. Sharing experiences and competencies will avoid re-inventing the wheel, and help promoting the cross-domain adoption of consistent solutions. Actually, one of the lessons learnt from INSPIRE and the initiatives in which JRC is involved, is that government and research data are not two separate worlds. Government data are commonly used as a basis to create scientific data, and vice-versa. Consequently, it is fundamental to adopt a consistent approach to address interoperability and data management issues shared by both government and scientific data. The presentation illustrates some of the lessons learnt during the implementation of INSPIRE and in work on data and service interoperability coordinated with European and international initiatives. We describe a number of critical interoperability issues and barriers affecting both scientific and government data, concerning, e.g., data terminologies, quality and licensing, and propose how these problems could be effectively addressed by a closer collaboration of the government and scientific communities, and the sharing of experiences and practices.

Privacy preserving RBF kernel support vector machine.

PubMed

Li, Haoran; Xiong, Li; Ohno-Machado, Lucila; Jiang, Xiaoqian

2014-01-01

Data sharing is challenging but important for healthcare research. Methods for privacy-preserving data dissemination based on the rigorous differential privacy standard have been developed but they did not consider the characteristics of biomedical data and make full use of the available information. This often results in too much noise in the final outputs. We hypothesized that this situation can be alleviated by leveraging a small portion of open-consented data to improve utility without sacrificing privacy. We developed a hybrid privacy-preserving differentially private support vector machine (SVM) model that uses public data and private data together. Our model leverages the RBF kernel and can handle nonlinearly separable cases. Experiments showed that this approach outperforms two baselines: (1) SVMs that only use public data, and (2) differentially private SVMs that are built from private data. Our method demonstrated very close performance metrics compared to nonprivate SVMs trained on the private data.

Improving the dependability of research in personality and social psychology: recommendations for research and educational practice.

PubMed

Funder, David C; Levine, John M; Mackie, Diane M; Morf, Carolyn C; Sansone, Carol; Vazire, Simine; West, Stephen G

2014-02-01

In this article, the Society for Personality and Social Psychology (SPSP) Task Force on Publication and Research Practices offers a brief statistical primer and recommendations for improving the dependability of research. Recommendations for research practice include (a) describing and addressing the choice of N (sample size) and consequent issues of statistical power, (b) reporting effect sizes and 95% confidence intervals (CIs), (c) avoiding "questionable research practices" that can inflate the probability of Type I error, (d) making available research materials necessary to replicate reported results, (e) adhering to SPSP's data sharing policy, (f) encouraging publication of high-quality replication studies, and (g) maintaining flexibility and openness to alternative standards and methods. Recommendations for educational practice include (a) encouraging a culture of "getting it right," (b) teaching and encouraging transparency of data reporting, (c) improving methodological instruction, and (d) modeling sound science and supporting junior researchers who seek to "get it right."

Are you afraid of the dark? Notes on the psychology of belief in histories of science and the occult.

PubMed

Sommer, Andreas

2016-04-02

The popular view of the inherent conflict between science and the occult has been rendered obsolete by recent advances in the history of science. Yet, these historiographical revisions have gone unnoticed in the public understanding of science and public education at large. Particularly, reconstructions of the formation of modern psychology and its links to psychical research can show that the standard view of the latter as motivated by metaphysical bias fails to stand up to scrutiny. After highlighting certain basic methodological maxims shared by psychotherapists and historians, I will try to counterbalance simplistic claims of a 'need to believe' as a precondition of scientific open-mindedness regarding the occurrence of parapsychological phenomena by discussing instances revealing a presumably widespread 'will to disbelieve' in the occult. I shall argue that generalized psychological explanations are only helpful in our understanding of history if we apply them in a symmetrical manner.

Autonomy and Authority in Public Research Organisations: Structure and Funding Factors.

PubMed

Cruz-Castro, Laura; Sanz-Menéndez, Luis

2018-01-01

This paper establishes a structural typology of the organisational configurations of public research organisations which vary in their relative internal sharing of authority between researchers and managers; we distinguish between autonomous, heteronomous and managed research organisations. We assume that there are at least two sources of legitimate authority within research organisations, one derived from formal hierarchy (organisational leadership) and another derived from the research community (professional); the balance of authority between researchers and managers is essentially structural but is empirically mediated by the funding portfolio of organisations and the corresponding endowment of resources at the disposal of leaders or researchers. Changes in the level, sources and strings of organisational and individual research funding are expected to affect the balance of internal authority in different ways depending on the organisational configuration, and to open the door to the influence of external actors in the development of research agendas.

Privacy Preserving RBF Kernel Support Vector Machine

PubMed Central

Xiong, Li; Ohno-Machado, Lucila

2014-01-01

Data sharing is challenging but important for healthcare research. Methods for privacy-preserving data dissemination based on the rigorous differential privacy standard have been developed but they did not consider the characteristics of biomedical data and make full use of the available information. This often results in too much noise in the final outputs. We hypothesized that this situation can be alleviated by leveraging a small portion of open-consented data to improve utility without sacrificing privacy. We developed a hybrid privacy-preserving differentially private support vector machine (SVM) model that uses public data and private data together. Our model leverages the RBF kernel and can handle nonlinearly separable cases. Experiments showed that this approach outperforms two baselines: (1) SVMs that only use public data, and (2) differentially private SVMs that are built from private data. Our method demonstrated very close performance metrics compared to nonprivate SVMs trained on the private data. PMID:25013805

When data sharing gets close to 100%: what human paleogenetics can teach the open science movement.

PubMed

Anagnostou, Paolo; Capocasa, Marco; Milia, Nicola; Sanna, Emanuele; Battaggia, Cinzia; Luzi, Daniela; Destro Bisol, Giovanni

2015-01-01

This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals' editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers' awareness of the importance of openness and transparency for scientific progress may complement stakeholders' policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges.

5 CFR 1632.4 - Meetings open to public observation.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 5 Administrative Personnel 3 2012-01-01 2012-01-01 false Meetings open to public observation. 1632... PUBLIC OBSERVATION OF MEETINGS § 1632.4 Meetings open to public observation. (a) Except as provided in § 1632.5 of this part, every portion of every meeting of the agency shall be open to public observation...

5 CFR 1632.4 - Meetings open to public observation.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Meetings open to public observation. 1632... PUBLIC OBSERVATION OF MEETINGS § 1632.4 Meetings open to public observation. (a) Except as provided in § 1632.5 of this part, every portion of every meeting of the agency shall be open to public observation...

5 CFR 1632.4 - Meetings open to public observation.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 5 Administrative Personnel 3 2014-01-01 2014-01-01 false Meetings open to public observation. 1632... PUBLIC OBSERVATION OF MEETINGS § 1632.4 Meetings open to public observation. (a) Except as provided in § 1632.5 of this part, every portion of every meeting of the agency shall be open to public observation...

5 CFR 1632.4 - Meetings open to public observation.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 5 Administrative Personnel 3 2013-01-01 2013-01-01 false Meetings open to public observation. 1632... PUBLIC OBSERVATION OF MEETINGS § 1632.4 Meetings open to public observation. (a) Except as provided in § 1632.5 of this part, every portion of every meeting of the agency shall be open to public observation...

5 CFR 1632.4 - Meetings open to public observation.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 5 Administrative Personnel 3 2011-01-01 2011-01-01 false Meetings open to public observation. 1632... PUBLIC OBSERVATION OF MEETINGS § 1632.4 Meetings open to public observation. (a) Except as provided in § 1632.5 of this part, every portion of every meeting of the agency shall be open to public observation...

Where Did They Go? Market Share Trends of Business Student Enrollment at Public, Not-for-Profit, and For-Profit Institutions from 1996 to 2008

ERIC Educational Resources Information Center

Fox Garrity, Bonnie Kathleen

2012-01-01

The author presents the trends in market share of business student enrollment at public, not-for-profit, and for-profit 4-year-and-above institutions from 1996 to 2008. Although each sector of the institutions has experienced growth in overall enrollments, the relative market share of public and not-for-profit institutions has dropped, whereas the…

36 CFR 230.43 - Cost-share assistance-prohibited practices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 2 2012-07-01 2012-07-01 false Cost-share assistance-prohibited practices. 230.43 Section 230.43 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE STATE AND PRIVATE FORESTRY ASSISTANCE Forest Land Enhancement Program § 230.43 Cost-share...

36 CFR 230.43 - Cost-share assistance-prohibited practices.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 2 2014-07-01 2014-07-01 false Cost-share assistance-prohibited practices. 230.43 Section 230.43 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE STATE AND PRIVATE FORESTRY ASSISTANCE Forest Land Enhancement Program § 230.43 Cost-share...

36 CFR 230.43 - Cost-share assistance-prohibited practices.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Cost-share assistance-prohibited practices. 230.43 Section 230.43 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE STATE AND PRIVATE FORESTRY ASSISTANCE Forest Land Enhancement Program § 230.43 Cost-share...

36 CFR 230.43 - Cost-share assistance-prohibited practices.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 2 2013-07-01 2013-07-01 false Cost-share assistance-prohibited practices. 230.43 Section 230.43 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE STATE AND PRIVATE FORESTRY ASSISTANCE Forest Land Enhancement Program § 230.43 Cost-share...

42 CFR 447.70 - General alternative cost sharing protections.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 4 2011-10-01 2011-10-01 false General alternative cost sharing protections. 447.70 Section 447.70 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS PAYMENTS FOR SERVICES Payments: General Provisions Alternative Premiums and Cost Sharing Under...

42 CFR 447.70 - General alternative cost sharing protections.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 4 2010-10-01 2010-10-01 false General alternative cost sharing protections. 447.70 Section 447.70 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS PAYMENTS FOR SERVICES Payments: General Provisions Alternative Premiums and Cost Sharing Under...

42 CFR 447.70 - General alternative cost sharing protections.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 4 2013-10-01 2013-10-01 false General alternative cost sharing protections. 447.70 Section 447.70 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS PAYMENTS FOR SERVICES Payments: General Provisions Alternative Premiums and Cost Sharing Under...

42 CFR 447.70 - General alternative cost sharing protections.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 4 2012-10-01 2012-10-01 false General alternative cost sharing protections. 447.70 Section 447.70 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS PAYMENTS FOR SERVICES Payments: General Provisions Alternative Premiums and Cost Sharing Under...

45 CFR 63.22 - Cost sharing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 1 2010-10-01 2010-10-01 false Cost sharing. 63.22 Section 63.22 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION GRANT PROGRAMS ADMINISTERED BY THE OFFICE OF THE ASSISTANT SECRETARY FOR PLANNING AND EVALUATION Financial Provisions § 63.22 Cost sharing. Policy...

Automatic Generation of OpenMP Directives and Its Application to Computational Fluid Dynamics Codes

NASA Technical Reports Server (NTRS)

Yan, Jerry; Jin, Haoqiang; Frumkin, Michael; Yan, Jerry (Technical Monitor)

2000-01-01

The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. As great progress was made in hardware and software technologies, performance of parallel programs with compiler directives has demonstrated large improvement. The introduction of OpenMP directives, the industrial standard for shared-memory programming, has minimized the issue of portability. In this study, we have extended CAPTools, a computer-aided parallelization toolkit, to automatically generate OpenMP-based parallel programs with nominal user assistance. We outline techniques used in the implementation of the tool and discuss the application of this tool on the NAS Parallel Benchmarks and several computational fluid dynamics codes. This work demonstrates the great potential of using the tool to quickly port parallel programs and also achieve good performance that exceeds some of the commercial tools.

Data Communities are Stronger Together: RDA and the broader landscape

NASA Astrophysics Data System (ADS)

Yarmey, L.

2016-12-01

The Research Data Alliance (RDA) is a community-driven, action-oriented, virtual organization committed to enabling open sharing of data by building social and technical bridges. The international RDA community includes over 4000 members, each bringing diverse perspectives, domains, and expertise. RDA members work together to identify common interests and form exploratory Interest Groups and outcome-oriented Working Groups. Participants exchange knowledge, share discoveries, discuss barriers and potential solutions, articulate policies, and align standards to enhance and facilitate global data sharing within and across domains and communities. RDA is an organization of action. 18 months after the 2013 RDA launch, the first Working Groups had already produced a series of well-defined, endorsed, and adopted Recommendations publically available for wider integration. The adopted and endorsed RDA Recommendations at time of writing include Persistent Identifier Information Types, Foundational Terminology query tool, Machine Actionable Policy Templates, and Data Type Model and Registry. Other Recommendations, including bibliometrics, metadata standards, and repository audit and certification are currently under community review on their way to endorsement. The number of RDA Working Groups and resulting Recommendations is expected to increase over time. RDA members are individuals and organizations who subscribe to RDA's Guiding Principles including Openness, Consensus, and Balance. In most (if not all) cases, RDA members also participate in other communities and/or partnerships. This raises important considerations for RDA in terms of scope, sustainability, realistic volunteer engagement, facilitation, and coordinated partnerships across the data landscape. By identifying common interests and maintaining ongoing partnerships and collaboration, individuals and data communities alike can increase our collective ability to create and maintain critical, integrated, and usable data infrastructure.

Making Transporter Models for Drug-Drug Interaction Prediction Mobile.

PubMed

Ekins, Sean; Clark, Alex M; Wright, Stephen H

2015-10-01

The past decade has seen increased numbers of studies publishing ligand-based computational models for drug transporters. Although they generally use small experimental data sets, these models can provide insights into structure-activity relationships for the transporter. In addition, such models have helped to identify new compounds as substrates or inhibitors of transporters of interest. We recently proposed that many transporters are promiscuous and may require profiling of new chemical entities against multiple substrates for a specific transporter. Furthermore, it should be noted that virtually all of the published ligand-based transporter models are only accessible to those involved in creating them and, consequently, are rarely shared effectively. One way to surmount this is to make models shareable or more accessible. The development of mobile apps that can access such models is highlighted here. These apps can be used to predict ligand interactions with transporters using Bayesian algorithms. We used recently published transporter data sets (MATE1, MATE2K, OCT2, OCTN2, ASBT, and NTCP) to build preliminary models in a commercial tool and in open software that can deliver the model in a mobile app. In addition, several transporter data sets extracted from the ChEMBL database were used to illustrate how such public data and models can be shared. Predicting drug-drug interactions for various transporters using computational models is potentially within reach of anyone with an iPhone or iPad. Such tools could help prioritize which substrates should be used for in vivo drug-drug interaction testing and enable open sharing of models. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

Open Access Could Transform Drug Discovery: A Case Study of JQ1.

PubMed

Arshad, Zeeshaan; Smith, James; Roberts, Mackenna; Lee, Wen Hwa; Davies, Ben; Bure, Kim; Hollander, Georg A; Dopson, Sue; Bountra, Chas; Brindley, David

2016-01-01

The cost to develop a new drug from target discovery to market is a staggering $1.8 billion, largely due to the very high attrition rate of drug candidates and the lengthy transition times during development. Open access is an emerging model of open innovation that places no restriction on the use of information and has the potential to accelerate the development of new drugs. To date, no quantitative assessment has yet taken place to determine the effects and viability of open access on the process of drug translation. This need is addressed within this study. The literature and intellectual property landscapes of the drug candidate JQ1, which was made available on an open access basis when discovered, and conventionally developed equivalents that were not are compared using the Web of Science and Thomson Innovation software, respectively. Results demonstrate that openly sharing the JQ1 molecule led to a greater uptake by a wider and more multi-disciplinary research community. A comparative analysis of the patent landscapes for each candidate also found that the broader scientific diaspora of the publically released JQ1 data enhanced innovation, evidenced by a greater number of downstream patents filed in relation to JQ1. The authors' findings counter the notion that open access drug discovery would leak commercial intellectual property. On the contrary, JQ1 serves as a test case to evidence that open access drug discovery can be an economic model that potentially improves efficiency and cost of drug discovery and its subsequent commercialization.

Kilohoku - Ho‘okele Wa‘a: Hawaiian Navigational Astronomy

NASA Astrophysics Data System (ADS)

Dye, Ahia; Ha'o, Celeste; Slater, Timothy F.; Slater, Stephanie

2015-01-01

Over thousands of years of Pacific Basin settlement, Polynesians developed a complex, scientific understanding of the cosmos, including a generative view of the celestial sphere. Memorizing the location and spatial relationships of hundreds of stars, across changing latitudes, this astronomy was one of the four scientific knowledge bases Polynesians used to navigate thousands of miles, across open water, without instrumentation. After Western colonization, this large body of knowledge was nearly lost to Hawaiians. Since the Hawaiian Renaissance, much of this knowledge has been reconstructed, and is again in use in open oceanic navigation. While some of this knowledge has been shared with the broader public, much of what we know has been unavailable to those beyond the family of navigators. This paper represents an attempt to begin sharing this catalog of knowledge with the outside world, with the hopes that the larger community will appreciate the complexity of astronomical knowledge possessed by navigators, and that the international body of astronomy historians will help insure that this knowledge will not be lost again. This paper will present, Na ´Ohanahōkū, the Hawaiian star families that divide the celestial sphere into four wedges, running from the circumpolar north, beyond the horizon to the south. Na Hoku Huihui, or Hawaiian constellations will be discussed, in addition to a brief introduction to the setting and rising pairs that are used to determine direction and latitude.

Unclassified Information Sharing and Coordination in Security, Stabilization, Transition and Reconstruction Efforts

DTIC Science & Technology

2008-03-01

is implemented using the Drupal (2007) content management system (CMS) and many of the baseline information sharing and collaboration tools have...been contributed through the Dru- pal open source community. Drupal is a very modular open source software written in PHP hypertext processor...needed to suit the particular problem domain. While other frameworks have the potential to provide similar advantages (“Ruby,” 2007), Drupal was

Paleomagnetism.org - An online multi-platform and open source environment for paleomagnetic analysis.

NASA Astrophysics Data System (ADS)

Koymans, Mathijs; Langereis, Cor; Pastor-Galán, Daniel; van Hinsbergen, Douwe

2017-04-01

This contribution gives an overview of Paleomagnetism.org (Koymans et al., 2016), an online environment for paleomagnetic analysis. The application is developed in JavaScript and is fully open-sourced. It presents an interactive website in which paleomagnetic data can be interpreted, evaluated, visualized, and shared with others. The application has been available from late 2015 and since then has evolved with the addition of a magnetostratigraphic tool, additional input formats, and features that emphasize on the link between geomagnetism and tectonics. In the interpretation portal, principle component analysis (Kirschvink et al., 1981) can be applied on visualized demagnetization data (Zijderveld, 1967). Interpreted directions and great circles are combined using the iterative procedure described by (McFadden and McElhinny, 1988). The resulting directions can be further used in the statistics portal or exported as raw tabulated data and high-quality figures. The available tools in the statistics portal cover standard Fisher statistics for directional data and virtual geomagnetic poles (Fisher, 1953; Butler, 1992; Deenen et al., 2011). Other tools include the eigenvector approach foldtest (Tauxe and Watson, 1994), a bootstrapped reversal test (Tauxe et al., 2009), and the classical reversal test (McFadden and McElhinny, 1990). An implementation exists for the detection and correction of inclination shallowing in sediments (Tauxe and Kent, 2004; Tauxe et al., 2008), and a module to visualize apparent polar wander paths (Torsvik et al., 2012; Kent and Irving, 2010; Besse and Courtillot, 2002) for large continent-bearing plates. A miscellaneous portal exists for a set of tools that include a boostrapped oroclinal test (Pastor-Galán et al., 2016) for assessing possible linear relationships between strike and declination. Another tool that is available completes a net tectonic rotation analysis (after Morris et al., 1999) that restores a dyke to its paleo-vertical and can be used in determining paleo-spreading directions fundamental to plate reconstructions. Paleomagnetism.org provides an integrated approach for researchers to export and share paleomagnetic data through a common interface. The portals create a custom exportable file that can be distributed and included in public databases. With a publication, this file can be appended and would contain all paleomagnetic data discussed in the publication. The appended file can then be imported to the application by other researchers for reviewing. The accessibility and simplicity through which paleomagnetic data can be interpreted, analyzed, visualized, and shared should make Paleomagnetism.org of interest to the paleomagnetic and tectonic communities.

An Open and Holistic Approach for Geo and Space Sciences

NASA Astrophysics Data System (ADS)

Ritschel, Bernd; Seelus, Christoph; Neher, Günther; Toshihiko, Iyemori; Yatagai, Akiyo; Koyama, Yukinobu; Murayama, Yasuhiro; King, Todd; Hughes, Steve; Fung, Shing; Galkin, Ivan; Hapgood, Mike; Belehaki, Anna

2016-04-01

Geo and space sciences thus far have been very successful, even often an open, cross-domain and holistic approach did not play an essential role. But this situation is changing rapidly. The research focus is shifting into more complex, non-linear and multi-domain specified phenomena, such as e.g. climate change or space environment. This kind of phenomena only can be understood step by step using the holistic idea. So, what is necessary for a successful cross-domain and holistic approach in geo and space sciences? Research and science in general become more and more dependent from a rich fundus of multi-domain data sources, related context information and the use of highly advanced technologies in data processing. Such buzzword phrases as Big Data and Deep Learning are reflecting this development. Big Data also addresses the real exponential growing of data and information produced by measurements or simulations. Deep Learning technology may help to detect new patterns and relationships in data describing high sophisticated natural phenomena. And further on, we should not forget science and humanities are only two sides of the same medal in the continuing human process of knowledge discovery. The concept of Open Data or in particular the open access to scientific data is addressing the free and open availability of -at least publicly founded and generated- data. The open availability of data covers the free use, reuse and redistribution of data which have been established with the formation of World Data Centers already more than 50 years ago. So, we should not forget, the foundation for open data is the responsibility of the individual scientist up until the big science institutions and organizations for a sustainable management of data. Other challenges are discovering and collecting the appropriate data, and preferably all of them or at least the majority of the right data. Therefore a network of individual or even better institutional catalog-based and at least domain-specific data servers is necessary. In times of the WWW or nowadays Semantic Web, context enriched and mashed-up open data catalogs pointing to the appropriate data sources, step-by-step will help to overcome the burden of the users to find the right data. Further on, the Semantic Web provides an interoperable and universal format for data and metadata. The Resource Description Formation (RDF) inherently enables a domain and cross-domain mashup of data, e.g. realized in the Linked Open Data project. Scientific work and appropriate papers in the geo and space domain often are based on data, physical models and previous publications, which again have been dependent on data, models and publications. So, in order to guarantee a high quality of scientific work, the complete verification process of the results is necessary. This is nothing new, but in times of Big Data a real challenge. So, what do we need for a complete verification of presented results? Yes, especially we need all the original data which has been used. But it is also necessary to get complete information about the context of the research objectives and the resulting constraints in the preparation of the raw data. Further on we need knowledge about the methods and the appropriate processing software, which has been used to generate the results. The Open Data approach enriched by the Open Archive idea is providing the concept for sustainable and verifiable scientific work. Open Archive of course stands for the free availability of scientific papers. But furthermore it focuses on mechanisms and methods within the realm of scientific publications for referencing and providing the underlying data, methods and software. Such reference mechanism are the use of Digital Object Identifier (DOI) or Uniform Resource Identifier (URI) within the Semantic Web -in our case for geo and space science data- but also methods and software code. Nowadays, more and more open and private publishers are demanding such kind of references in preparation of the publishing process. In addition, references to well documented earth and space science data are available via an increasing amount of data publications. This approach serves both, the institutional geo and space data centers which increase their awareness and importance, but also the scientists, which will find the right and already DOI-referenced data in the appropriate data journals. The Open Data and Open Archive approach finally merges in the concept of Open Science. Open Science emphasizes an open sharing of knowledge of all kind, based on a transparent multi-disciplinary and cross-domain scientific work. But Open Science is not just an idea, it also stands for a variety of projects which following the rules of Open Science, such as open methodology, open source, open data, open access, open peer review and open educational resources. Open Science also demands a new culture of scientific collaboration based on social media, and the use of shared cloud technology for data storage and computing. But, we should not forget, the WWW is not a one way road. As more data, methods and software for science research become freely available at the Internet, as more chances for a commercial or even destructive use of scientific data are opened. Already now, the giant search engine provider, such as Google or Microsoft and others are collecting, storing and analyzing all data which is available at the net. The usage of Deep Learning for the detection of semantical coherence of data for e.g. the creation of personalized on time and on location predictions using neuronal networks and artificial intelligence methods should not be reserved for them but also used within Open Science for the creation of new scientific knowledge. Open Science does not mean just to dump our scientific data, information and knowledge into the Web. Far from it, we are still responsible for a sustainable handling of our data for the benefit of humankind. The usage of the principles of Open Science is demonstrated on the scientific and software engineering activities for the mashup of the Japanese IUGONET, European Union ESPAS and GFZ ISDC related data server covering different geo and space science domains.

Openness and Praxis: Exploring the Use of Open Educational Practices in Higher Education

ERIC Educational Resources Information Center

Cronin, Catherine

2017-01-01

Open educational practices (OEP) is a broad descriptor of practices that include the creation, use, and reuse of open educational resources (OER) as well as open pedagogies and open sharing of teaching practices. As compared with OER, there has been little empirical research on individual educators' use of OEP for teaching in higher education.…

Opportunities for Scientists to Engage the Public & Inspire Students in Science

NASA Astrophysics Data System (ADS)

Vaughan, R. G.; Worssam, J.; Vaughan, A. F.

2014-12-01

Increasingly, research scientists are learning that communicating science to broad, non-specialist audiences, particularly students, is just as important as communicating science to their peers via peer-reviewed scientific publications. This presentation highlights opportunities that scientists in Flagstaff, AZ have to foster public support of science & inspire students to study STEM disciplines. The goal here is to share ideas, personal experiences, & the rewards, for both students & research professionals, of engaging in science education & public outreach. Flagstaff, AZ, "America's First STEM Community," has a uniquely rich community of organizations engaged in science & engineering research & innovation, including the Flagstaff Arboretum, Coconino Community College, Gore Industries, Lowell Observatory, Museum of Northern Arizona, National Weather Service, National Park Service, National Forest Service, Northern Arizona University, Northern Arizona Center for Entrepreneurship & Technology, US Geological Survey, US Naval Observatory, & Willow Bend Environmental Education Center. These organizations connect with the Northern Arizona community during the yearly Flagstaff Festival of Science - the third oldest science festival in the world - a 10 day long, free, science festival featuring daily public lectures, open houses, interactive science & technology exhibits, field trips, & in-school speaker programs. Many research scientists from these organizations participate in these activities, e.g., public lectures, open houses, & in-school speaker programs, & also volunteer as mentors for science & engineering themed clubs in local schools. An example of a novel, innovative program, developed by a local K-12 science teacher, is the "Scientists-in-the-Classroom" mentor program, which pairs all 7th & 8th grade students with a working research scientist for the entire school year. Led by the student & guided by the mentor, they develop a variety of science / technology projects, which the students then present at year's end. From the perspective of an active research scientist, such outreach activities take little time & effort (~ 0.05 FTE), but pay large dividends in the long run, in inciting public support for science & inspiring the next generation of scientists & engineers.

Total energy expenditure in adults aged 65 years and over measured using doubly-labelled water: international data availability and opportunities for data sharing.

PubMed

Porter, Judi; Nguo, Kay; Gibson, Simone; Huggins, Catherine E; Collins, Jorja; Kellow, Nicole J; Truby, Helen

2018-03-26

Increasing population lifespan necessitates a greater understanding of nutritional needs in older adults (65 year and over). A synthesis of total energy expenditure in the older population has not been undertaken and is needed to inform nutritional requirements. We aimed to establish the extent of the international evidence for total energy expenditure (TEE) using doubly-labelled water (DLW) in older adults (65 years and over), report challenges in obtaining primary data, and make recommendations for future data sharing. Four databases were searched to identify eligible studies; original research of any study design where participant level TEE was measured using DLW in participants aged ≥65 years. Once studies were identified for inclusion, authors were contacted where data were not publicly available. Screening was undertaken of 1223 records; the review of 317 full text papers excluded 170 records. Corresponding or first authors of 147 eligible studies were contacted electronically. Participant level data were publicly available or provided by authors for 45 publications (890 participants aged ≥65 years, with 248 aged ≥80 years). Sixty-seven percent of the DLW data in this population were unavailable due to authors unable to be contacted or declining to participate, or data being irretrievable. The lack of data access limits the value of the original research and its contribution to nutrition science. Openly accessible DLW data available through publications or a new international data repository would facilitate greater integration of current research with previous findings and ensure evidence is available to support the needs of the ageing population. The protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO), registration number CRD42016047549 .

Time to consider sharing data extracted from trials included in systematic reviews.

PubMed

Wolfenden, Luke; Grimshaw, Jeremy; Williams, Christopher M; Yoong, Sze Lin

2016-11-03

While the debate regarding shared clinical trial data has shifted from whether such data should be shared to how this is best achieved, the sharing of data collected as part of systematic reviews has received little attention. In this commentary, we discuss the potential benefits of coordinated efforts to share data collected as part of systematic reviews. There are a number of potential benefits of systematic review data sharing. Shared information and data obtained as part of the systematic review process may reduce unnecessary duplication, reduce demand on trialist to service repeated requests from reviewers for data, and improve the quality and efficiency of future reviews. Sharing also facilitates research to improve clinical trial and systematic review methods and supports additional analyses to address secondary research questions. While concerns regarding appropriate use of data, costs, or the academic return for original review authors may impede more open access to information extracted as part of systematic reviews, many of these issues are being addressed, and infrastructure to enable greater access to such information is being developed. Embracing systems to enable more open access to systematic review data has considerable potential to maximise the benefits of research investment in undertaking systematic reviews.

42 CFR 423.6 - Cost-sharing in beneficiary education and enrollment-related costs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 3 2010-10-01 2010-10-01 false Cost-sharing in beneficiary education and enrollment-related costs. 423.6 Section 423.6 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES... BENEFIT General Provisions § 423.6 Cost-sharing in beneficiary education and enrollment-related costs. The...

Open Data in Biomedical Science: Policy Drivers and Recent ...

EPA Pesticide Factsheets

EPA's progress in implementing the open data initiatives first outlined in the 2009 Presidential memorandum on open government and more specifically regarding publications and data from publications in the 2013 Holdren memorandum. The presentation outlines the major points in both memorandums regarding open data, presents several (but not exhaustive) EPA initiatives on open data, some of which occurred will before both policy memorandums. The presentation concludes by outlining the initiatives to ensure public access to all EPA publications through PubMed Central and all publication-associated data through the Environmental Data Gateway and Data.gov. The purpose of this presentation is to present EPA's progress in implementing the open data initiatives first outlined in the 2009 Presidential memorandum on open government and more specifically regarding publications and data from publications in the 2013 Holdren memorandum.

A Case Study of Scholars' Open and Sharing Practices

ERIC Educational Resources Information Center

Veletsianos, George

2015-01-01

Although the open scholarship movement has successfully captured the attention and interest of higher education stakeholders, researchers currently lack an understanding of the degree to which open scholarship is enacted in institutions that lack institutional support for openness. I help fill this gap in the literature by presenting a descriptive…

Data publication and sharing using the SciDrive service

NASA Astrophysics Data System (ADS)

Mishin, Dmitry; Medvedev, D.; Szalay, A. S.; Plante, R. L.

2014-01-01

Despite the last years progress in scientific data storage, still remains the problem of public data storage and sharing system for relatively small scientific datasets. These are collections forming the “long tail” of power log datasets distribution. The aggregated size of the long tail data is comparable to the size of all data collections from large archives, and the value of data is significant. The SciDrive project's main goal is providing the scientific community with a place to reliably and freely store such data and provide access to it to broad scientific community. The primary target audience of the project is astoromy community, and it will be extended to other fields. We're aiming to create a simple way of publishing a dataset, which can be then shared with other people. Data owner controls the permissions to modify and access the data and can assign a group of users or open the access to everyone. The data contained in the dataset will be automaticaly recognized by a background process. Known data formats will be extracted according to the user's settings. Currently tabular data can be automatically extracted to the user's MyDB table where user can make SQL queries to the dataset and merge it with other public CasJobs resources. Other data formats can be processed using a set of plugins that upload the data or metadata to user-defined side services. The current implementation targets some of the data formats commonly used by the astronomy communities, including FITS, ASCII and Excel tables, TIFF images, and YT simulations data archives. Along with generic metadata, format-specific metadata is also processed. For example, basic information about celestial objects is extracted from FITS files and TIFF images, if present. A 100TB implementation has just been put into production at Johns Hopkins University. The system features public data storage REST service supporting VOSpace 2.0 and Dropbox protocols, HTML5 web portal, command-line client and Java standalone client to synchronize a local folder with the remote storage. We use VAO SSO (Single Sign On) service from NCSA for users authentication that provides free registration for everyone.

Interoperable Data Access Services for NOAA IOOS

NASA Astrophysics Data System (ADS)

de La Beaujardiere, J.

2008-12-01

The Integrated Ocean Observing System (IOOS) is intended to enhance our ability to collect, deliver, and use ocean information. The goal is to support research and decision-making by providing data on our open oceans, coastal waters, and Great Lakes in the formats, rates, and scales required by scientists, managers, businesses, governments, and the public. The US National Oceanic and Atmospheric Administration (NOAA) is the lead agency for IOOS. NOAA's IOOS office supports the development of regional coastal observing capability and promotes data management efforts to increase data accessibility. Geospatial web services have been established at NOAA data providers including the National Data Buoy Center (NDBC), the Center for Operational Oceanographic Products and Services (CO-OPS), and CoastWatch, and at regional data provider sites. Services established include Open-source Project for a Network Data Access Protocol (OpenDAP), Open Geospatial Consortium (OGC) Sensor Observation Service (SOS), and OGC Web Coverage Service (WCS). These services provide integrated access to data holdings that have been aggregated at each center from multiple sources. We wish to collaborate with other groups to improve our service offerings to maximize interoperability and enhance cross-provider data integration, and to share common service components such as registries, catalogs, data conversion, and gateways. This paper will discuss the current status of NOAA's IOOS efforts and possible next steps.

75 FR 15753 - Sunshine Act Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-30

.... STATUS: Parts of this meeting will be open to the public. The rest of the meeting will be closed to the public. The public session will be podcast. MATTERS TO BE CONSIDERED: PORTIONS OPEN TO THE PUBLIC: 1. Review of Postal-related congressional activity (open). 2. Report on international activities (open). 3...

Involving Research Stakeholders in Developing Policy on Sharing Public Health Research Data in Kenya

PubMed Central

Jao, Irene; Kombe, Francis; Mwalukore, Salim; Bull, Susan; Parker, Michael; Kamuya, Dorcas; Molyneux, Sassy

2015-01-01

Increased global sharing of public health research data has potential to advance scientific progress but may present challenges to the interests of research stakeholders, particularly in low-to-middle income countries. Policies for data sharing should be responsive to public views, but there is little evidence of the systematic study of these from low-income countries. This qualitative study explored views on fair data-sharing processes among 60 stakeholders in Kenya with varying research experience, using a deliberative approach. Stakeholders’ attitudes were informed by perceptions of benefit and concerns for research data sharing, including risks of stigmatization, loss of privacy, and undermining scientific careers and validity, reported in detail elsewhere. In this article, we discuss institutional trust-building processes seen as central to perceptions of fairness in sharing research data in this setting, including forms of community involvement, individual prior awareness and agreement to data sharing, independence and accountability of governance mechanisms, and operating under a national framework. PMID:26297748

Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.

PubMed

Kapur, Tina; Pieper, Steve; Fedorov, Andriy; Fillion-Robin, J-C; Halle, Michael; O'Donnell, Lauren; Lasso, Andras; Ungi, Tamas; Pinter, Csaba; Finet, Julien; Pujol, Sonia; Jagadeesan, Jayender; Tokuda, Junichi; Norton, Isaiah; Estepar, Raul San Jose; Gering, David; Aerts, Hugo J W L; Jakab, Marianna; Hata, Nobuhiko; Ibanez, Luiz; Blezek, Daniel; Miller, Jim; Aylward, Stephen; Grimson, W Eric L; Fichtinger, Gabor; Wells, William M; Lorensen, William E; Schroeder, Will; Kikinis, Ron

2016-10-01

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision. Copyright © 2016 Elsevier B.V. All rights reserved.

Data sharing for public health research: A qualitative study of industry and academia.

PubMed

Saunders, Pamela A; Wilhelm, Erin E; Lee, Sinae; Merkhofer, Elizabeth; Shoulson, Ira

2014-01-01

Data sharing is a key biomedical research theme for the 21st century. Biomedical data sharing is the exchange of data among (non)affiliated parties under mutually agreeable terms to promote scientific advancement and the development of safe and effective medical products. Wide sharing of research data is important for scientific discovery, medical product development, and public health. Data sharing enables improvements in development of medical products, more attention to rare diseases, and cost-efficiencies in biomedical research. We interviewed 11 participants about their attitudes and beliefs about data sharing. Using a qualitative, thematic analysis approach, our analysis revealed a number of themes including: experiences, approaches, perceived challenges, and opportunities for sharing data.

45 CFR 400.27 - Safeguarding and sharing of information.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 2 2010-10-01 2010-10-01 false Safeguarding and sharing of information. 400.27 Section 400.27 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM...

45 CFR 1321.47 - Statewide non-Federal share requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 4 2011-10-01 2011-10-01 false Statewide non-Federal share requirements. 1321.47 Section 1321.47 Public Welfare Regulations Relating to Public Welfare (Continued) OFFICE OF HUMAN DEVELOPMENT SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES THE ADMINISTRATION ON AGING, OLDER AMERICANS...

Information Sharing for IT Security Professionals

ERIC Educational Resources Information Center

Petersen, Rodney J.

2008-01-01

Information sharing is a core value for information technology (IT) security professionals. It is also a familiar concept for those who work at institutions of higher education because of their long history of collaboration and openness. Information sharing has become part of the national fabric as IT security professionals attempt to secure cyber…

Weaving a knowledge network for Deep Carbon Science

NASA Astrophysics Data System (ADS)

Ma, Xiaogang; West, Patrick; Zednik, Stephan; Erickson, John; Eleish, Ahmed; Chen, Yu; Wang, Han; Zhong, Hao; Fox, Peter

2017-05-01

Geoscience researchers are increasingly dependent on informatics and the Web to conduct their research. Geoscience is one of the first domains that take lead in initiatives such as open data, open code, open access, and open collections, which comprise key topics of Open Science in academia. The meaning of being open can be understood at two levels. The lower level is to make data, code, sample collections and publications, etc. freely accessible online and allow reuse, modification and sharing. The higher level is the annotation and connection between those resources to establish a network for collaborative scientific research. In the data science component of the Deep Carbon Observatory (DCO), we have leveraged state-of-the-art information technologies and existing online resources to deploy a web portal for the over 1000 researchers in the DCO community. An initial aim of the portal is to keep track of all research and outputs related to the DCO community. Further, we intend for the portal to establish a knowledge network, which supports various stages of an open scientific process within and beyond the DCO community. Annotation and linking are the key characteristics of the knowledge network. Not only are key assets, including DCO data and methods, published in an open and inter-linked fashion, but the people, organizations, groups, grants, projects, samples, field sites, instruments, software programs, activities, meetings, etc. are recorded and connected to each other through relationships based on well-defined, formal conceptual models. The network promotes collaboration among DCO participants, improves the openness and reproducibility of carbon-related research, facilitates accreditation to resource contributors, and eventually stimulates new ideas and findings in deep carbon-related studies.

Hybrid MPI+OpenMP Programming of an Overset CFD Solver and Performance Investigations

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Jin, Haoqiang H.; Biegel, Bryan (Technical Monitor)

2002-01-01

This report describes a two level parallelization of a Computational Fluid Dynamic (CFD) solver with multi-zone overset structured grids. The approach is based on a hybrid MPI+OpenMP programming model suitable for shared memory and clusters of shared memory machines. The performance investigations of the hybrid application on an SGI Origin2000 (O2K) machine is reported using medium and large scale test problems.

Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2017-01-01

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon-HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon-HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon-HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5. PMID:28649160

Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-02-13

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon-HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon-HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon-HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments

NASA Astrophysics Data System (ADS)

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-02-01

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon- HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon- HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon- HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

[Globalization and its impact on pharmacy services in the Slovak Republic].

PubMed

Malovecká, Ivona; Minarovič, Igor; Mináriková, Daniela; Lehocká, Lubica; Snopková, Miroslava; Foltán, Viliam

2014-02-01

Public pharmacies are excellent medical facilities having the largest number of contacts with patients. They are the facilities of the first and last contact with the health care system for the patient. Public pharmacies are unique and easily accessible places in the health care system with a high proficiency in the provision of pharmaceutical care and highly qualified medical staff. The aim of this paper was to determine geographical-demographic situation, the legal form of the ownership of public pharmacies, and the owner share of pharmacists on the capital of public pharmacies in Slovakia. The number on of providers of pharmaceutical care depends on the population at the level of regions, districts, towns and villages with differing tightness of binding. The most common legal form of the provider of pharmaceutical care in Slovakia in public pharmacies were limited companies with 73.6% share, a sole proprietor - pharmacist had 23.9%, and public limited companies had 1.3%. In the branches of public pharmacies the limited companies had 73.4% share, a sole proprietor - pharmacist had 26%, public limited companies had 1%. The owner share of the pharmacist on the capital in public pharmacies was 50.4%, and in the branches of public pharmacies it was 66%, owned by a sole proprietor or limited company.

The gates open wide. [The Energy Policy Act of 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burton, S.D.

1993-01-01

For independent electric producers, the new energy law opens wide the gate to the future. It does not give an entitlement or a subsidy; merely the freedom to expand - along with utilities - electricity's share of the next century's energy market. If anything, the new law, by removing investment barriers and creating the right to transmission access, affirms the potential of electrical generation and urges us all to get on with the job. It underscores the most powerful forces for future growth: the increasing demand for more electric power, greater production at less cost, and lessening demand on themore » environment's resources. With half-century-old barriers to broader production finally down, the real action now belongs to the regulators. It's one thing to pass a bill. It's quite another to make it work. The reform bill does not deregulate, but essentially defines public policy objectives (competitive markets), creates a framework to develop them, and vest responsibility for the regulation of the generation and sale of power where it belongs: with state public utility commissions and the FERC. It is going to be up to them to set the limits of the market, and to set the pace of expansion; in other words, to rearrange the play to achieve the bill's objective.« less

AWOB: A Collaborative Workbench for Astronomers

NASA Astrophysics Data System (ADS)

Kim, J. W.; Lemson, G.; Bulatovic, N.; Makarenko, V.; Vogler, A.; Voges, W.; Yao, Y.; Kiefl, R.; Koychev, S.

2015-09-01

We present the Astronomers Workbench (AWOB1), a web-based collaboration and publication platform for a scientific project of any size, developed in collaboration between the Max-Planck institutes of Astrophysics (MPA) and Extra-terrestrial Physics (MPE) and the Max-Planck Digital Library (MPDL). AWOB facilitates the collaboration between geographically distributed astronomers working on a common project throughout its whole scientific life cycle. AWOB does so by making it very easy for scientists to set up and manage a collaborative workspace for individual projects, where data can be uploaded and shared. It supports inviting project collaborators, provides wikis, automated mailing lists, calendars and event notification and has a built in chat facility. It allows the definition and tracking of tasks within projects and supports easy creation of e-publications for the dissemination of data and images and other resources that cannot be added to submitted papers. AWOB extends the project concept to larger scale consortia, within which it is possible to manage working groups and sub-projects. The existing AWOB instance has so far been limited to Max-Planck members and their collaborators, but will be opened to the whole astronomical community. AWOB is an open-source project and its source code is available upon request. We intend to extend AWOB's functionality also to other disciplines, and would greatly appreciate contributions from the community.

36 CFR 1280.92 - When are the Presidential library museums open to the public?

Code of Federal Regulations, 2011 CFR

2011-07-01

... library museums open to the public? 1280.92 Section 1280.92 Parks, Forests, and Public Property NATIONAL... Use of Facilities in Presidential Libraries? § 1280.92 When are the Presidential library museums open to the public? (a) The Presidential library museums are open every day except Thanksgiving, December...

36 CFR 1280.92 - When are the Presidential library museums open to the public?

Code of Federal Regulations, 2012 CFR

2012-07-01

... library museums open to the public? 1280.92 Section 1280.92 Parks, Forests, and Public Property NATIONAL... Use of Facilities in Presidential Libraries? § 1280.92 When are the Presidential library museums open to the public? (a) The Presidential library museums are open every day except Thanksgiving, December...

36 CFR 1280.92 - When are the Presidential library museums open to the public?

Code of Federal Regulations, 2014 CFR

2014-07-01

... library museums open to the public? 1280.92 Section 1280.92 Parks, Forests, and Public Property NATIONAL... Use of Facilities in Presidential Libraries? § 1280.92 When are the Presidential library museums open to the public? (a) The Presidential library museums are open every day except Thanksgiving, December...

36 CFR 230.41 - Eligibility requirements for cost-share assistance.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Eligibility requirements for cost-share assistance. 230.41 Section 230.41 Parks, Forests, and Public Property FOREST SERVICE... of a responsible official, determines that significant public benefits would accrue from approval of...

78 FR 8456 - Coverage of Certain Preventive Services Under the Affordable Care Act

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-06

... 2713 of the Public Health Service Act requires coverage without cost sharing of certain preventive... Requirement to Cover Contraceptive Services Without Cost Sharing Under Section 2713 of the Public Health..., non-stock, public benefit, and similar types of corporations. However, for this purpose an...

SEEK: a systems biology data and model management platform.

PubMed

Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L; Mueller, Wolfgang; Goble, Carole

2015-07-11

Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.

Prototyping an online wetland ecosystem services model using open model sharing standards

USGS Publications Warehouse

Feng, M.; Liu, S.; Euliss, N.H.; Young, Caitlin; Mushet, D.M.

2011-01-01

Great interest currently exists for developing ecosystem models to forecast how ecosystem services may change under alternative land use and climate futures. Ecosystem services are diverse and include supporting services or functions (e.g., primary production, nutrient cycling), provisioning services (e.g., wildlife, groundwater), regulating services (e.g., water purification, floodwater retention), and even cultural services (e.g., ecotourism, cultural heritage). Hence, the knowledge base necessary to quantify ecosystem services is broad and derived from many diverse scientific disciplines. Building the required interdisciplinary models is especially challenging as modelers from different locations and times may develop the disciplinary models needed for ecosystem simulations, and these models must be identified and made accessible to the interdisciplinary simulation. Additional difficulties include inconsistent data structures, formats, and metadata required by geospatial models as well as limitations on computing, storage, and connectivity. Traditional standalone and closed network systems cannot fully support sharing and integrating interdisciplinary geospatial models from variant sources. To address this need, we developed an approach to openly share and access geospatial computational models using distributed Geographic Information System (GIS) techniques and open geospatial standards. We included a means to share computational models compliant with Open Geospatial Consortium (OGC) Web Processing Services (WPS) standard to ensure modelers have an efficient and simplified means to publish new models. To demonstrate our approach, we developed five disciplinary models that can be integrated and shared to simulate a few of the ecosystem services (e.g., water storage, waterfowl breeding) that are provided by wetlands in the Prairie Pothole Region (PPR) of North America.

OpenEIS. Users Guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Woohyun; Lutes, Robert G.; Katipamula, Srinivas

This document is a users guide for OpenEIS, a software code designed to provide standard methods for authoring, sharing, testing, using and improving algorithms for operational building energy efficiency.

HydroShare for iUTAH: Collaborative Publication, Interoperability, and Reuse of Hydrologic Data and Models for a Large, Interdisciplinary Water Research Project

NASA Astrophysics Data System (ADS)

Horsburgh, J. S.; Jones, A. S.

2016-12-01

Data and models used within the hydrologic science community are diverse. New research data and model repositories have succeeded in making data and models more accessible, but have been, in most cases, limited to particular types or classes of data or models and also lack the type of collaborative, and iterative functionality needed to enable shared data collection and modeling workflows. File sharing systems currently used within many scientific communities for private sharing of preliminary and intermediate data and modeling products do not support collaborative data capture, description, visualization, and annotation. More recently, hydrologic datasets and models have been cast as "social objects" that can be published, collaborated around, annotated, discovered, and accessed. Yet it can be difficult using existing software tools to achieve the kind of collaborative workflows and data/model reuse that many envision. HydroShare is a new, web-based system for sharing hydrologic data and models with specific functionality aimed at making collaboration easier and achieving new levels of interactive functionality and interoperability. Within HydroShare, we have developed new functionality for creating datasets, describing them with metadata, and sharing them with collaborators. HydroShare is enabled by a generic data model and content packaging scheme that supports describing and sharing diverse hydrologic datasets and models. Interoperability among the diverse types of data and models used by hydrologic scientists is achieved through the use of consistent storage, management, sharing, publication, and annotation within HydroShare. In this presentation, we highlight and demonstrate how the flexibility of HydroShare's data model and packaging scheme, HydroShare's access control and sharing functionality, and versioning and publication capabilities have enabled the sharing and publication of research datasets for a large, interdisciplinary water research project called iUTAH (innovative Urban Transitions and Aridregion Hydro-sustainability). We discuss the experiences of iUTAH researchers now using HydroShare to collaboratively create, curate, and publish datasets and models in a way that encourages collaboration, promotes reuse, and meets funding agency requirements.

Alternative Fuels Data Center: Ryder Opens Natural Gas Vehicle Maintenance

Science.gov Websites

Facility Ryder Opens Natural Gas Vehicle Maintenance Facility to someone by E-mail Share Alternative Fuels Data Center: Ryder Opens Natural Gas Vehicle Maintenance Facility on Facebook Tweet about Alternative Fuels Data Center: Ryder Opens Natural Gas Vehicle Maintenance Facility on Twitter Bookmark

Educators Assess "Open Content" Movement

ERIC Educational Resources Information Center

Trotter, Andrew

2009-01-01

This article discusses the open-content movement in education. A small but growing movement of K-12 educators is latching on to educational resources that are "open," or free for others to use, change, and republish on web sites that promote sharing. The open-content movement is fueled partly by digital creation tools that make it easy…

Periodicals Price Survey 2008: Embracing Openness

ERIC Educational Resources Information Center

Van Orsdel, Lee C.; Born, Kathleen

2008-01-01

Evidence for open access as an emergent, global state of mind is everywhere. The "New York Times" went "open" last September, and the "Wall Street Journal" is slated to follow. Increasingly, scholarly communities are breaking with tradition and calling for the open sharing of research, software, and data. Amongst these global initiatives is the…

Beyond Open Source: According to Jim Hirsch, Open Technology, Not Open Source, Is the Wave of the Future

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

This article presents an interview with Jim Hirsch, an associate superintendent for technology at Piano Independent School District in Piano, Texas. Hirsch serves as a liaison for the open technologies committee of the Consortium for School Networking. In this interview, he shares his opinion on the significance of open source in K-12.

Opening Teaching Landscapes: The Importance of Quality Assurance in the Delivery of Open Educational Resources

ERIC Educational Resources Information Center

Atenas, Javiera; Havemann, Leo; Priego, Ernesto

2014-01-01

Scholars are increasingly being asked to share teaching materials, publish in open access journals, network in social media, and reuse open educational resources (OER). The theoretical benefits of Open Educational Practices (OEP) have become understood in the academic community but thus far, the use of OER has not been rapidly adopted. We aim to…

Alternative Fuels Data Center: West Virginia CNG Corridor Now Open

Science.gov Websites

West Virginia CNG Corridor Now Open to someone by E-mail Share Alternative Fuels Data Center: West Virginia CNG Corridor Now Open on Facebook Tweet about Alternative Fuels Data Center: West Virginia CNG Corridor Now Open on Twitter Bookmark Alternative Fuels Data Center: West Virginia CNG Corridor Now Open on

Open by default: a proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals

PubMed Central

2012-01-01

Copyright and licensing of scientific data, internationally, are complex and present legal barriers to data sharing, integration and reuse, and therefore restrict the most efficient transfer and discovery of scientific knowledge. Much data are included within scientific journal articles, their published tables, additional files (supplementary material) and reference lists. However, these data are usually published under licenses which are not appropriate for data. Creative Commons CC0 is an appropriate and increasingly accepted method for dedicating data to the public domain, to enable data reuse with the minimum of restrictions. BioMed Central is committed to working towards implementation of open data-compliant licensing in its publications. Here we detail a protocol for implementing a combined Creative Commons Attribution license (for copyrightable material) and Creative Commons CC0 waiver (for data) agreement for content published in peer-reviewed open access journals. We explain the differences between legal requirements for attribution in copyright, and cultural requirements in scholarship for giving individuals credit for their work through citation. We argue that publishing data in scientific journals under CC0 will have numerous benefits for individuals and society, and yet will have minimal implications for authors and minimal impact on current publishing and research workflows. We provide practical examples and definitions of data types, such as XML and tabular data, and specific secondary use cases for published data, including text mining, reproducible research, and open bibliography. We believe this proposed change to the current copyright and licensing structure in science publishing will help clarify what users – people and machines – of the published literature can do, legally, with journal articles and make research using the published literature more efficient. We further believe this model could be adopted across multiple publishers, and invite comment on this article from all stakeholders in scientific research. PMID:22958225

Replication initiatives will not salvage the trustworthiness of psychology.

PubMed

Coyne, James C

2016-05-31

Replication initiatives in psychology continue to gather considerable attention from far outside the field, as well as controversy from within. Some accomplishments of these initiatives are noted, but this article focuses on why they do not provide a general solution for what ails psychology. There are inherent limitations to mass replications ever being conducted in many areas of psychology, both in terms of their practicality and their prospects for improving the science. Unnecessary compromises were built into the ground rules for design and publication of the Open Science Collaboration: Psychology that undermine its effectiveness. Some ground rules could actually be flipped into guidance for how not to conduct replications. Greater adherence to best publication practices, transparency in the design and publishing of research, strengthening of independent post-publication peer review and firmer enforcement of rules about data sharing and declarations of conflict of interest would make many replications unnecessary. Yet, it has been difficult to move beyond simple endorsement of these measures to consistent implementation. Given the strong institutional support for questionable publication practices, progress will depend on effective individual and collective use of social media to expose lapses and demand reform. Some recent incidents highlight the necessity of this.

Harvard Personal Genome Project: lessons from participatory public research

PubMed Central

2014-01-01

Background Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an ‘open consent’ framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Discussion Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project. Summary We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants. PMID:24713084