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1.  Eurocan plus report: feasibility study for coordination of national cancer research activities 
The EUROCAN+PLUS Project, called for by the European Parliament, was launched in October 2005 as a feasibility study for coordination of national cancer research activities in Europe. Over the course of the next two years, the Project process organized over 60 large meetings and countless smaller meetings that gathered in total over a thousand people, the largest Europe–wide consultation ever conducted in the field of cancer research.
Despite a strong tradition in biomedical science in Europe, fragmentation and lack of sustainability remain formidable challenges for implementing innovative cancer research and cancer care improvement. There is an enormous duplication of research effort in the Member States, which wastes time, wastes money and severely limits the total intellectual concentration on the wide cancer problem. There is a striking lack of communication between some of the biggest actors on the European scene, and there are palpable tensions between funders and those researchers seeking funds.
It is essential to include the patients’ voice in the establishment of priority areas in cancer research at the present time. The necessity to have dialogue between funders and scientists to establish the best mechanisms to meet the needs of the entire community is evident. A top priority should be the development of translational research (in its widest form), leading to the development of effective and innovative cancer treatments and preventive strategies. Translational research ranges from bench–to–bedside innovative cancer therapies and extends to include bringing about changes in population behaviours when a risk factor is established.
The EUROCAN+PLUS Project recommends the creation of a small, permanent and independent European Cancer Initiative (ECI). This should be a model structure and was widely supported at both General Assemblies of the project. The ECI should assume responsibility for stimulating innovative cancer research and facilitating processes, becoming the common voice of the cancer research community and serving as an interface between the cancer research community and European citizens, patients’ organizations, European institutions, Member States, industry and small and medium enterprises (SMEs), putting into practice solutions aimed at alleviating barriers to collaboration and coordination of cancer research activities in the European Union, and dealing with legal and regulatory issues. The development of an effective ECI will require time, but this entity should be established immediately. As an initial step, coordination efforts should be directed towards the creation of a platform on translational research that could encompass (1) coordination between basic, clinical and epidemiological research; (2) formal agreements of co–operation between comprehensive cancer centres and basic research laboratories throughout Europe and (3) networking between funding bodies at the European level.
The European Parliament and its instruments have had a major influence in cancer control in Europe, notably in tobacco control and in the implementation of effective population–based screening. To make further progress there is a need for novelty and innovation in cancer research and prevention in Europe, and having a platform such as the ECI, where those involved in all aspects of cancer research can meet, discuss and interact, is a decisive development for Europe.
Executive Summary
Cancer is one of the biggest public health crises facing Europe in the 21st century—one for which Europe is currently not prepared nor preparing itself. Cancer is a major cause of death in Europe with two million casualties and three million new cases diagnosed annually, and the situation is set to worsen as the population ages.
These facts led the European Parliament, through the Research Directorate-General of the European Commission, to call for initiatives for better coordination of cancer research efforts in the European Union. The EUROCAN+PLUS Project was launched in October 2005 as a feasibility study for coordination of national cancer research activities. Over the course of the next two years, the Project process organized over 60 large meetings and countless smaller meetings that gathered in total over a thousand people. In this respect, the Project became the largest Europe-wide consultation ever conducted in the field of cancer research, implicating researchers, cancer centres and hospitals, administrators, healthcare professionals, funding agencies, industry, patients’ organizations and patients.
The Project first identified barriers impeding research and collaboration in research in Europe. Despite a strong tradition in biomedical science in Europe, fragmentation and lack of sustainability remain the formidable challenges for implementing innovative cancer research and cancer care improvement. There is an enormous duplication of research effort in the Member States, which wastes time, wastes money and severely limits the total intellectual concentration on the wide cancer problem. There is a striking lack of communication between some of the biggest actors on the European scene, and there are palpable tensions between funders and those researchers seeking funds.
In addition, there is a shortage of leadership, a multiplicity of institutions each focusing on its own agenda, sub–optimal contact with industry, inadequate training, non–existent career paths, low personnel mobility in research especially among clinicians and inefficient funding—all conspiring against efficient collaboration in cancer care and research. European cancer research today does not have a functional translational research continuum, that is the process that exploits biomedical research innovations and converts them into prevention methods, diagnostic tools and therapies. Moreover, epidemiological research is not integrated with other types of cancer research, and the implementation of the European Directives on Clinical Trials 1 and on Personal Data Protection 2 has further slowed the innovation process in Europe. Furthermore, large inequalities in health and research exist between the EU–15 and the New Member States.
The picture is not entirely bleak, however, as the European cancer research scene presents several strengths, such as excellent basic research and clinical research and innovative etiological research that should be better exploited.
When considering recommendations, several priority dimensions had to be retained. It is essential that proposals include actions and recommendations that can benefit all Member States of the European Union and not just States with the elite centres. It is also essential to have a broader patient orientation to help provide the knowledge to establish cancer control possibilities when we exhaust what can be achieved by the implementation of current knowledge. It is vital that the actions proposed can contribute to the Lisbon Strategy to make Europe more innovative and competitive in (cancer) research.
The Project participants identified six areas for which consensus solutions should be implemented in order to obtain better coordination of cancer research activities. The required solutions are as follows. The proactive management of innovation, detection, facilitation of collaborations and maintenance of healthy competition within the European cancer research community.The establishment of an exchange portal of information for health professionals, patients and policy makers.The provision of guidance for translational and clinical research including the establishment of a translational research platform involving comprehensive cancer centres and cancer research centres.The coordination of calls and financial management of cancer research projects.The construction of a ‘one–stop shop’ as a contact interface between the industry, small and medium enterprises, scientists and other stakeholders.The support of greater involvement of healthcare professionals in translational research and multidisciplinary training.
In the course of the EUROCAN+PLUS consultative process, several key collaborative projects emerged between the various groups and institutes engaged in the consultation. There was a collaboration network established with Europe’s leading Comprehensive Cancer Centres; funding was awarded for a closer collaboration of Owners of Cancer Registries in Europe (EUROCOURSE); there was funding received from FP7 for an extensive network of leading Biological Resource Centres in Europe (BBMRI); a Working Group identified the special needs of Central, Eastern and South–eastern Europe and proposed a remedy (‘Warsaw Declaration’), and the concept of developing a one–stop shop for dealing with academia and industry including the Innovative Medicines Initiative (IMI) was discussed in detail.
Several other dimensions currently lacking were identified. There is an absolute necessity to include the patients’ voice in the establishment of priority areas in cancer research at the present time. It was a salutary lesson when it was recognized that all that is known about the quality of life of the cancer patient comes from the experience of a tiny proportion of cancer patients included in a few clinical trials. The necessity to have dialogue between funders and scientists to establish the best mechanisms to meet the needs of the entire community was evident. A top priority should be the development of translational research (in its widest form) and the development of effective and innovative cancer treatments and preventative strategies in the European Union. Translational research ranges from bench-to-bedside innovative cancer therapies and extends to include bringing about changes in population behaviours when a risk factor is established.
Having taken note of the barriers and the solutions and having examined relevant examples of existing European organizations in the field, it was agreed during the General Assembly of 19 November 2007 that the EUROCAN+PLUS Project had to recommend the creation of a small, permanent and neutral ECI. This should be a model structure and was widely supported at both General Assemblies of the project. The proposal is based on the successful model of the European Molecular Biology Organisation (EMBO), and its principal aims include providing a forum where researchers from all backgrounds and from all countries can meet with members of other specialities including patients, nurses, clinicians, funders and scientific administrators to develop priority programmes to make Europe more competitive in research and more focused on the cancer patient.
The ECI should assume responsibility for: stimulating innovative cancer research and facilitating processes;becoming the common voice of the cancer research community and serving as an interface between the cancer research community and European citizens, patients’ and organizations;European institutions, Member States, industry and small and medium enterprises;putting into practice the aforementioned solutions aimed at alleviating barriers and coordinating cancer research activities in the EU;dealing with legal and regulatory issues.
Solutions implemented through the ECI will lead to better coordination and collaboration throughout Europe, more efficient use of resources, an increase in Europe’s attractiveness to the biomedical industry and better quality of cancer research and education of health professionals.
The Project considered that European legal instruments currently available were inadequate for addressing many aspects of the barriers identified and for the implementation of effective, lasting solutions. Therefore, the legal environment that could shelter an idea like the ECI remains to be defined but should be done so as a priority. In this context, the initiative of the European Commission for a new legal entity for research infrastructure might be a step in this direction. The development of an effective ECI will require time, but this should be established immediately. As an initial step, coordination efforts should be directed towards the creation of a platform on translational research that could encompass: (1) coordination between basic, clinical and epidemiological research; (2) formal agreements of co-operation between comprehensive cancer centres and basic research laboratories throughout Europe; (3) networking between funding bodies at the European level. Another topic deserving immediate attention is the creation of a European database on cancer research projects and cancer research facilities.
Despite enormous progress in cancer control in Europe during the past two decades, there was an increase of 300,000 in the number of new cases of cancer diagnosed between 2004 and 2006. The European Parliament and its instruments have had a major influence in cancer control, notably in tobacco control and in the implementation of effective population–based screening. To make further progress there is a need for novelty and innovation in cancer research and prevention in Europe, and having a platform such as the ECI, where those involved in all aspects of cancer research can meet, discuss and interact, is a decisive development for Europe.
PMCID: PMC3234055  PMID: 22274749
2.  Facebook for Scientists: Requirements and Services for Optimizing How Scientific Collaborations Are Established 
As biomedical research projects become increasingly interdisciplinary and complex, collaboration with appropriate individuals, teams, and institutions becomes ever more crucial to project success. While social networks are extremely important in determining how scientific collaborations are formed, social networking technologies have not yet been studied as a tool to help form scientific collaborations. Many currently emerging expertise locating systems include social networking technologies, but it is unclear whether they make the process of finding collaborators more efficient and effective.
This study was conducted to answer the following questions: (1) Which requirements should systems for finding collaborators in biomedical science fulfill? and (2) Which information technology services can address these requirements?
The background research phase encompassed a thorough review of the literature, affinity diagramming, contextual inquiry, and semistructured interviews. This phase yielded five themes suggestive of requirements for systems to support the formation of collaborations. In the next phase, the generative phase, we brainstormed and selected design ideas for formal concept validation with end users. Then, three related, well-validated ideas were selected for implementation and evaluation in a prototype.
Five main themes of systems requirements emerged: (1) beyond expertise, successful collaborations require compatibility with respect to personality, work style, productivity, and many other factors (compatibility); (2) finding appropriate collaborators requires the ability to effectively search in domains other than your own using information that is comprehensive and descriptive (communication); (3) social networks are important for finding potential collaborators, assessing their suitability and compatibility, and establishing contact with them (intermediation); (4) information profiles must be complete, correct, up-to-date, and comprehensive and allow fine-grained control over access to information by different audiences (information quality and access); (5) keeping online profiles up-to-date should require little or no effort and be integrated into the scientist’s existing workflow (motivation). Based on the requirements, 16 design ideas underwent formal validation with end users. Of those, three were chosen to be implemented and evaluated in a system prototype, “Digital|Vita”: maintaining, formatting, and semi-automated updating of biographical information; searching for experts; and building and maintaining the social network and managing document flow.
In addition to quantitative and factual information about potential collaborators, social connectedness, personal and professional compatibility, and power differentials also influence whether collaborations are formed. Current systems only partially model these requirements. Services in Digital|Vita combine an existing workflow, maintaining and formatting biographical information, with collaboration-searching functions in a novel way. Several barriers to the adoption of systems such as Digital|Vita exist, such as potential adoption asymmetries between junior and senior researchers and the tension between public and private information. Developers and researchers may consider one or more of the services described in this paper for implementation in their own expertise locating systems.
PMCID: PMC2553246  PMID: 18701421
Expertise locating systems; computer supported collaborative work; information systems; collaborators; research; social networks; translational research
3.  The Impact of eHealth on the Quality and Safety of Health Care: A Systematic Overview 
PLoS Medicine  2011;8(1):e1000387.
Aziz Sheikh and colleagues report the findings of their systematic overview that assessed the impact of eHealth solutions on the quality and safety of health care.
There is considerable international interest in exploiting the potential of digital solutions to enhance the quality and safety of health care. Implementations of transformative eHealth technologies are underway globally, often at very considerable cost. In order to assess the impact of eHealth solutions on the quality and safety of health care, and to inform policy decisions on eHealth deployments, we undertook a systematic review of systematic reviews assessing the effectiveness and consequences of various eHealth technologies on the quality and safety of care.
Methods and Findings
We developed novel search strategies, conceptual maps of health care quality, safety, and eHealth interventions, and then systematically identified, scrutinised, and synthesised the systematic review literature. Major biomedical databases were searched to identify systematic reviews published between 1997 and 2010. Related theoretical, methodological, and technical material was also reviewed. We identified 53 systematic reviews that focused on assessing the impact of eHealth interventions on the quality and/or safety of health care and 55 supplementary systematic reviews providing relevant supportive information. This systematic review literature was found to be generally of substandard quality with regards to methodology, reporting, and utility. We thematically categorised eHealth technologies into three main areas: (1) storing, managing, and transmission of data; (2) clinical decision support; and (3) facilitating care from a distance. We found that despite support from policymakers, there was relatively little empirical evidence to substantiate many of the claims made in relation to these technologies. Whether the success of those relatively few solutions identified to improve quality and safety would continue if these were deployed beyond the contexts in which they were originally developed, has yet to be established. Importantly, best practice guidelines in effective development and deployment strategies are lacking.
There is a large gap between the postulated and empirically demonstrated benefits of eHealth technologies. In addition, there is a lack of robust research on the risks of implementing these technologies and their cost-effectiveness has yet to be demonstrated, despite being frequently promoted by policymakers and “techno-enthusiasts” as if this was a given. In the light of the paucity of evidence in relation to improvements in patient outcomes, as well as the lack of evidence on their cost-effectiveness, it is vital that future eHealth technologies are evaluated against a comprehensive set of measures, ideally throughout all stages of the technology's life cycle. Such evaluation should be characterised by careful attention to socio-technical factors to maximise the likelihood of successful implementation and adoption.
Please see later in the article for the Editors' Summary
Editors' Summary
There is considerable international interest in exploiting the potential of digital health care solutions, often referred to as eHealth—the use of information and communication technologies—to enhance the quality and safety of health care. Often accompanied by large costs, any large-scale expenditure on eHealth—such as electronic health records, picture archiving and communication systems, ePrescribing, associated computerized provider order entry systems, and computerized decision support systems—has tended to be justified on the grounds that these are efficient and cost-effective means for improving health care. In 2005, the World Health Assembly passed an eHealth resolution (WHA 58.28) that acknowledged, “eHealth is the cost-effective and secure use of information and communications technologies in support of health and health-related fields, including health-care services, health surveillance, health literature, and health education, knowledge and research,” and urged member states to develop and implement eHealth technologies. Since then, implementing eHealth technologies has become a main priority for many countries. For example, England has invested at least £12.8 billion in a National Programme for Information Technology for the National Health Service, and the Obama administration in the United States has committed to a US$38 billion eHealth investment in health care.
Why Was This Study Done?
Despite the wide endorsement of and support for eHealth, the scientific basis of its benefits—which are repeatedly made and often uncritically accepted—remains to be firmly established. A robust evidence-based perspective on the advantages on eHealth could help to suggest priority areas that have the greatest potential for benefit to patients and also to inform international eHealth deliberations on costs. Therefore, in order to better inform the international community, the authors systematically reviewed the published systematic review literature on eHealth technologies and evaluated the impact of these technologies on the quality and safety of health care delivery.
What Did the Researchers Do and Find?
The researchers divided eHealth technologies into three main categories: (1) storing, managing, and transmission of data; (2) clinical decision support; and (3) facilitating care from a distance. Then, implementing methods based on those developed by the Cochrane Collaboration and the NHS Service Delivery and Organisation Programme, the researchers used detailed search strategies and maps of health care quality, safety, and eHealth interventions to identify relevant systematic reviews (and related theoretical, methodological, and technical material) published between 1997 and 2010. Using these techniques, the researchers retrieved a total of 46,349 references from which they identified 108 reviews. The 53 reviews that the researchers finally selected (and critically reviewed) provided the main evidence base for assessing the impact of eHealth technologies in the three categories selected.
In their systematic review of systematic reviews, the researchers included electronic health records and picture archiving communications systems in their evaluation of category 1, computerized provider (or physician) order entry and e-prescribing in category 2, and all clinical information systems that, when used in the context of eHealth technologies, integrate clinical and demographic patient information to support clinician decision making in category 3.
The researchers found that many of the clinical claims made about the most commonly used eHealth technologies were not substantiated by empirical evidence. The evidence base in support of eHealth technologies was weak and inconsistent and importantly, there was insubstantial evidence to support the cost-effectiveness of these technologies. For example, the researchers only found limited evidence that some of the many presumed benefits could be realized; importantly, they also found some evidence that introducing these new technologies may on occasions also generate new risks such as prescribers becoming over-reliant on clinical decision support for e-prescribing, or overestimate its functionality, resulting in decreased practitioner performance.
What Do These Findings Mean?
The researchers found that despite the wide support for eHealth technologies and the frequently made claims by policy makers when constructing business cases to raise funds for large-scale eHealth projects, there is as yet relatively little empirical evidence to substantiate many of the claims made about eHealth technologies. In addition, even for the eHealth technology tools that have proven to be successful, there is little evidence to show that such tools would continue to be successful beyond the contexts in which they were originally developed. Therefore, in light of the lack of evidence in relation to improvements in patient outcomes, as well as the lack of evidence on their cost-effectiveness, the authors say that future eHealth technologies should be evaluated against a comprehensive set of measures, ideally throughout all stages of the technology's life cycle, and include socio-technical factors to maximize the likelihood of successful implementation and adoption in a given context. Furthermore, it is equally important that eHealth projects that have already been commissioned are subject to rigorous, multidisciplinary, and independent evaluation.
Additional Information
Please access these websites via the online version of this summary at
The authors' broader study is: Car J, Black A, Anandan C, Cresswell K, Pagliari C, McKinstry B, et al. (2008) The Impact of eHealth on the Quality and Safety of Healthcare. Available at:
More information is available on the World Health Assembly eHealth resolution
The World Health Organization provides information at the Global Observatory on eHealth, as well as a global insight into eHealth developments
The European Commission provides Information on eHealth in Europe and some examples of good eHealth practice
More information is provided on NHS Connecting for Health
PMCID: PMC3022523  PMID: 21267058
4.  Transforming Epidemiology for 21st Century Medicine and Public Health 
In 2012, the National Cancer Institute (NCI) engaged the scientific community to provide a vision for cancer epidemiology in the 21st century. Eight overarching thematic recommendations, with proposed corresponding actions for consideration by funding agencies, professional societies, and the research community emerged from the collective intellectual discourse. The themes are (i) extending the reach of epidemiology beyond discovery and etiologic research to include multilevel analysis, intervention evaluation, implementation, and outcomes research; (ii) transforming the practice of epidemiology by moving towards more access and sharing of protocols, data, metadata, and specimens to foster collaboration, to ensure reproducibility and replication, and accelerate translation; (iii) expanding cohort studies to collect exposure, clinical and other information across the life course and examining multiple health-related endpoints; (iv) developing and validating reliable methods and technologies to quantify exposures and outcomes on a massive scale, and to assess concomitantly the role of multiple factors in complex diseases; (v) integrating “big data” science into the practice of epidemiology; (vi) expanding knowledge integration to drive research, policy and practice; (vii) transforming training of 21st century epidemiologists to address interdisciplinary and translational research; and (viii) optimizing the use of resources and infrastructure for epidemiologic studies. These recommendations can transform cancer epidemiology and the field of epidemiology in general, by enhancing transparency, interdisciplinary collaboration, and strategic applications of new technologies. They should lay a strong scientific foundation for accelerated translation of scientific discoveries into individual and population health benefits.
PMCID: PMC3625652  PMID: 23462917
big data; clinical trials; cohort studies; epidemiology; genomics; medicine; public health; technologies; training; translational research
5.  Google Wave: Have CTSA-Minded Institutions Caught It? 
Google Wave was touted as the next big communication tool—combining e-mail, social networking, and chat within a single “wave”—with the potential to create a new world for collaboration. Information professionals who are knowledgeable of this tool and its capabilities could become uniquely situated to use it, evaluate it, and teach it. This seemed especially true for those working within Clinical and Translational Science Award (CTSA)-minded institutions, given the promise of interdisciplinary collaboration between investigators and the potential for creating new authorship models. This case study on Google Wave users who are affiliated with CTSA-minded institutions, was designed for and presented at the Evidence-Based Scholarly Communication Conference held by the University of New Mexico Health Sciences Library and Information Center. It provides an early evidence based evaluation of Google Wave's potential.
Two “waves” were created. The first consisted of five survey questions designed to collect demographic data on the respondents' roles, a general impression of Wave, the specific tools within Wave that might be useful, and potential collaborators with whom the respondents might use Wave. The second wave was a private, guided discussion on Wave's collaboration potential. Individuals from CTSA-minded institutions were invited to participate with messages on Twitter, forums, blogs, and electronic mail lists, although there were difficulties reaching out to these institutions as a group.
By the conclusion of the study, only a small number of people (n=11, with a viable n=9) had responded to the survey. Given this small result set, it made sense to group the responses by the respondents' roles (CTSA staff and researchers, support staff, medical librarian, or general public) and to treat them as individual cases. Most of the respondents were librarians and support staff who felt that Wave might have potential for collaboration; there were no CTSA researcher respondents. For the second part of the study, the discussion wave, only one participant explicitly expressed interest in joining. All were invited to join, but there was no participation in the discussion wave at the conclusion of the study.
The results of this study implied that Google Wave was not on the forefront of CTSA-minded institutions' communication strategies. However, it was being used, and it did demonstrate new collaboration and authorship capabilities. Being generally aware of these capabilities may be useful to information professionals who seek to be current and informed regarding developing technology and to those interested in scholarly communication practices. In addition, the difficulties encountered during this case study in attempting to reach out to CTSA-minded institutions raised the question of how members currently communicate with each other as institutions and as individuals. There was a lesson learned in the usefulness of doing case-study research to evaluate new technologies; the cost in terms of time was relatively low, and knowledge about the technology itself was gained while establishing a base level of evidence to potentially build on in the future.
PMCID: PMC3068201  PMID: 21461135
6.  Incorporating collaboratory concepts into informatics in support of translational interdisciplinary biomedical research 
Due to its complex nature, modern biomedical research has become increasingly interdisciplinary and collaborative in nature. Although a necessity, interdisciplinary biomedical collaboration is difficult. There is, however, a growing body of literature on the study and fostering of collaboration in fields such as computer supported cooperative work (CSCW) and information science (IS). These studies of collaboration provide insight into how to potentially alleviate the difficulties of interdisciplinary collaborative research. We, therefore, undertook a cross cutting study of science and engineering collaboratories to identify emergent themes. We review many relevant collaboratory concepts: (a) general collaboratory concepts across many domains: communication, common workspace and coordination, and data sharing and management, (b) specific collaboratory concepts of particular biomedical relevance: data integration and analysis, security structure, metadata and data provenance, and interoperability and data standards, (c) environmental factors that support collaboratories: administrative and management structure, technical support, and available funding as critical environmental factors, and (d) future considerations for biomedical collaboration: appropriate training and long-term planning. In our opinion, the collaboratory concepts we discuss can guide planning and design of future collaborative infrastructure by biomedical informatics researchers to alleviate some of the difficulties of interdisciplinary biomedical collaboration.
PMCID: PMC2606933  PMID: 18706852
Collaboration; Biomedical informatics; Computer supported collaborative work; Collaboratories; Social and technical issues; Bioinformatics
7.  How can scientists bring research to use: the HENVINET experience 
Environmental Health  2012;11(Suppl 1):S2.
Health concerns have driven the European environmental policies of the last 25 years, with issues becoming more complex. Addressing these concerns requires an approach that is both interdisciplinary and engages scientists with society. In response to this requirement, the FP6 coordination action “Health and Environment Network” HENVINET was set up to create a permanent inter-disciplinary network of professionals in the field of health and environment tasked to bridge the communication gap between science and society. In this paper we describe how HENVINET delivered on this task.
The HENVINET project approached the issue of inter-disciplinary collaboration in four ways. (1) The Drivers-Pressures-State-Exposure-Effect-Action framework was used to structure information gathering, collaboration and communication between scientists in the field of health and the environment. (2) Interactive web-based tools were developed to enhance methods for knowledge evaluation, and use these methods to formulate policy advice. (3) Quantification methods were adapted to measure scientific agreement. And (4) Open architecture web technology was used to develop an information repository and a web portal to facilitate collaboration and communication among scientists.
Twenty-five organizations from Europe and five from outside Europe participated in the Health and Environment Network HENVINET, which lasted for 3.5 years. The consortium included partners in environmental research, public health and veterinary medicine; included medical practitioners and representatives of local administrations; and had access to national policy making and EEA and WHO expertise. Dedicated web-based tools for visualisation of environmental health issues and knowledge evaluation allowed remote expert elicitation, and were used as a basis for developing policy advice in five health areas (asthma and allergies; cancer; neurodevelopmental disorders; endocrine disruption; and engineered nanoparticles in the environment). An open searchable database of decision support tools was established and populated. A web based social networking tool was developed to enhance collaboration and communication between scientists and society.
HENVINET addressed key issues that arise in inter-disciplinary research on health and environment and in communicating research results to policy makers and society. HENVINET went beyond traditional scientific tools and methods to bridge the communication gap between science and policy makers. The project identified the need for a common framework and delivered it. It developed and implemented a variety of novel methods and tools and, using several representative examples, demonstrated the process of producing politically relevant scientific advice based on an open participation of experts. It highlighted the need for, and benefits of, a liaison between health and environment professionals and professionals in the social sciences and liberal arts. By adopting critical complexity thinking, HENVINET extended the traditional approach to environment and health research, and set the standard for current approaches to bridge the gap between science and society.
PMCID: PMC3388450  PMID: 22759502
8.  Synergizing expectation and execution for stroke communities of practice innovations 
Regional networks have been recognized as an interesting model to support interdisciplinary and inter-organizational interactions that lead to meaningful care improvements. Existing communities of practice within the a regional network, the Montreal Stroke Network (MSN) offers a compelling structure to better manage the exponential growth of knowledge and to support care providers to better manage the complex cases they must deal with in their practices. This research project proposes to examine internal and external factors that influence individual and organisational readiness to adopt national stroke best practices and to assess the impact of an e-collaborative platform in facilitating knowledge translation activities.
We will develop an e-collaborative platform that will include various social networking and collaborative tools. We propose to create online brainstorming sessions ('jams') around each best practice recommendation. Jam postings will be analysed to identify emergent themes. Syntheses of these analyses will be provided to members to help them identify priority areas for practice change. Discussions will be moderated by clinical leaders, whose role will be to accelerate crystallizing of ideas around 'how to' implement selected best practices. All clinicians (~200) involved in stroke care among the MSN will be asked to participate. Activities during face-to-face meetings and on the e-collaborative platform will be documented. Content analysis of all activities will be performed using an observation grid that will use as outcome indicators key elements of communities of practice and of the knowledge creation cycle developed by Nonaka. Semi-structured interviews will be conducted among users of the e-collaborative platform to collect information on variables of the knowledge-to-action framework. All participants will be asked to complete three questionnaires: the typology questionnaire, which classifies individuals into one of four mutually exclusive categories of information seeking; the e-health state of readiness, which covers ten domains of the readiness to change; and a community of practice evaluation survey.
This project is expected to enhance our understanding of collaborative work across disciplines and organisations in accelerating implementation of best practices along the continuum of care, and how e-technologies influence access, sharing, creation, and application of knowledge.
PMCID: PMC2890694  PMID: 20529305
9.  The IGOR Cloud Platform: Collaborative, Scalable, and Peer-Reviewed NGS Data Analysis 
Technical challenges facing researchers performing next-generation sequencing (NGS) analysis threaten to slow the pace of discovery and delay clinical applications of genomics data. Particularly for core laboratories, these challenges include: (1) Computation and storage have to scale with the vase amount of data generated. (2) Analysis pipelines are complex to design, set up, and share. (3) Collaboration, reproducibility, and sharing are hampered by privacy concerns and the sheer volume of data involved. Based on hands-on experience from large-scale NGS projects such as the 1000 Genomes Project, Seven Bridges Genomics has developed IGOR, a comprehensive cloud platform for NGS Data analysis that fully addresses these challenges: IGOR is a cloud-based platform for researchers and facilities to manage NGS data, design and run complex analysis pipelines, and efficiently collaborate on projects.Over a dozen curated and peer-reviewed NGS data analysis pipelines are publicly available for free, including alignment, variant calling, and RNA-Seq. All pipelines are based on open source tools and built to peer-reviewed specifications in close collaboration with researchers at leading institutions such as the Harvard Stem Cell Institute.Without any command-line knowledge, NGS pipelines can be built and customized in an intuitive graphical editor choosing from over 50 open source tools.When executing pipelines, IGOR automatically takes care of all resource management. Resources are seamlessly and automatically made available from Amazon Web Services and optimized for time and cost.Collaboration is facilitated through a project structure that allows researchers working in and across institutions to share files and pipelines. Fine-grained permissions allow detailed access control on a user-by-user basis for each project. Pipelines can be embedded and accessed through web pages akin to YouTube videos.Extensive batch processing and parallelization capabilities mean that hundreds of samples can be analyzed in the same amount of time that a single sample can be processed. Using file metadata, batch processing can be automated, e.g., by file, library, sample or lane.
The IGOR platform enables NGS research as a “turnkey” solution: Researchers can set up and run complex pipelines without expertise in command-line utilities or cloud computing. From a lab and facility perspective, the cloud-based architecture also eliminates the need to set up and maintain a large-scale infrastructure, typically resulting in at least 50% cost savings on infrastructure. By facilitating collaboration and easing analysis replication, the IGOR platform frees up the time of core laboratories to emphasize and focus on the research questions that ultimately guide them.
PMCID: PMC3635388
10.  A digital repository with an extensible data model for biobanking and genomic analysis management 
BMC Genomics  2014;15(Suppl 3):S3.
Molecular biology laboratories require extensive metadata to improve data collection and analysis. The heterogeneity of the collected metadata grows as research is evolving in to international multi-disciplinary collaborations and increasing data sharing among institutions. Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management.
We developed a novel data model in JSON format to describe heterogeneous data in a generic biomedical science scenario. The model is built on two hierarchical entities: processes and events, roughly corresponding to research studies and analysis steps within a single study. A number of sequential events can be grouped in a process building up a hierarchical structure to track patient and sample history. Each event can produce new data. Data is described by a set of user-defined metadata, and may have one or more associated files. We integrated the model in a web based digital repository with a data grid storage to manage large data sets located in geographically distinct areas. We built a graphical interface that allows authorized users to define new data types dynamically, according to their requirements. Operators compose queries on metadata fields using a flexible search interface and run them on the database and on the grid. We applied the digital repository to the integrated management of samples, patients and medical history in the BIT-Gaslini biobank. The platform currently manages 1800 samples of over 900 patients. Microarray data from 150 analyses are stored on the grid storage and replicated on two physical resources for preservation. The system is equipped with data integration capabilities with other biobanks for worldwide information sharing.
Our data model enables users to continuously define flexible, ad hoc, and loosely structured metadata, for information sharing in specific research projects and purposes. This approach can improve sensitively interdisciplinary research collaboration and allows to track patients' clinical records, sample management information, and genomic data. The web interface allows the operators to easily manage, query, and annotate the files, without dealing with the technicalities of the data grid.
PMCID: PMC4083403  PMID: 25077808
11.  Data harmonization and federated analysis of population-based studies: the BioSHaRE project 
Individual-level data pooling of large population-based studies across research centres in international research projects faces many hurdles. The BioSHaRE (Biobank Standardisation and Harmonisation for Research Excellence in the European Union) project aims to address these issues by building a collaborative group of investigators and developing tools for data harmonization, database integration and federated data analyses.
Eight population-based studies in six European countries were recruited to participate in the BioSHaRE project. Through workshops, teleconferences and electronic communications, participating investigators identified a set of 96 variables targeted for harmonization to answer research questions of interest. Using each study’s questionnaires, standard operating procedures, and data dictionaries, harmonization potential was assessed. Whenever harmonization was deemed possible, processing algorithms were developed and implemented in an open-source software infrastructure to transform study-specific data into the target (i.e. harmonized) format. Harmonized datasets located on server in each research centres across Europe were interconnected through a federated database system to perform statistical analysis.
Retrospective harmonization led to the generation of common format variables for 73% of matches considered (96 targeted variables across 8 studies). Authenticated investigators can now perform complex statistical analyses of harmonized datasets stored on distributed servers without actually sharing individual-level data using the DataSHIELD method.
New Internet-based networking technologies and database management systems are providing the means to support collaborative, multi-center research in an efficient and secure manner. The results from this pilot project show that, given a strong collaborative relationship between participating studies, it is possible to seamlessly co-analyse internationally harmonized research databases while allowing each study to retain full control over individual-level data. We encourage additional collaborative research networks in epidemiology, public health, and the social sciences to make use of the open source tools presented herein.
PMCID: PMC4175511  PMID: 24257327
12.  C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training 
PLoS ONE  2008;3(2):e1621.
The need for effective collaboration tools is growing as multidisciplinary proteome-wide projects and distributed research teams become more common. The resulting data is often quite disparate, stored in separate locations, and not contextually related. Collaborative Molecular Modeling Environment (C-ME) is an interactive community-based collaboration system that allows researchers to organize information, visualize data on a two-dimensional (2-D) or three-dimensional (3-D) basis, and share and manage that information with collaborators in real time. C-ME stores the information in industry-standard databases that are immediately accessible by appropriate permission within the computer network directory service or anonymously across the internet through the C-ME application or through a web browser. The system addresses two important aspects of collaboration: context and information management. C-ME allows a researcher to use a 3-D atomic structure model or a 2-D image as a contextual basis on which to attach and share annotations to specific atoms or molecules or to specific regions of a 2-D image. These annotations provide additional information about the atomic structure or image data that can then be evaluated, amended or added to by other project members.
PMCID: PMC2229842  PMID: 18286178
13.  Guidelines, Editors, Pharma And The Biological Paradigm Shift 
Mens Sana Monographs  2007;5(1):27-30.
Private investment in biomedical research has increased over the last few decades. At most places it has been welcomed as the next best thing to technology itself. Much of the intellectual talent from academic institutions is getting absorbed in lucrative positions in industry. Applied research finds willing collaborators in venture capital funded industry, so a symbiotic growth is ensured for both.
There are significant costs involved too. As academia interacts with industry, major areas of conflict of interest especially applicable to biomedical research have arisen. They are related to disputes over patents and royalty, hostile encounters between academia and industry, as also between public and private enterprise, legal tangles, research misconduct of various types, antagonistic press and patient-advocate lobbies and a general atmosphere in which commercial interest get precedence over patient welfare.
Pharma image stinks because of a number of errors of omission and commission. A recent example is suppression of negative findings about Bayer's Trasylol (Aprotinin) and the marketing maneuvers of Eli Lilly's Xigris (rhAPC). Whenever there is a conflict between patient vulnerability and profit motives, pharma often tends to tilt towards the latter. Moreover there are documents that bring to light how companies frequently cross the line between patient welfare and profit seeking behaviour.
A voluntary moratorium over pharma spending to pamper drug prescribers is necessary. A code of conduct adopted recently by OPPI in India to limit pharma company expenses over junkets and trinkets is a welcome step.
Clinical practice guidelines (CPG) are considered important as they guide the diagnostic/therapeutic regimen of a large number of medical professionals and hospitals and provide recommendations on drugs, their dosages and criteria for selection. Along with clinical trials, they are another area of growing influence by the pharmaceutical industry. For example, in a relatively recent survey of 2002, it was found that about 60% of 192 authors of clinical practice guidelines reported they had financial connections with the companies whose drugs were under consideration. There is a strong case for making CPGs based not just on effectivity but cost effectivity. The various ramifications of this need to be spelt out. Work of bodies like the Appraisal of Guidelines Research and Evaluation (AGREE) Collaboration and Guidelines Advisory Committee (GAC) are also worth a close look.
Even the actions of Foundations that work for disease amelioration have come under scrutiny. The process of setting up ‘Best Practices’ Guidelines for interactions between the pharmaceutical industry and clinicians has already begun and can have important consequences for patient care. Similarly, Good Publication Practice (GPP) for pharmaceutical companies have also been set up aimed at improving the behaviour of drug companies while reporting drug trials
The rapidly increasing trend toward influence and control by industry has become a concern for many. It is of such importance that the Association of American Medical Colleges has issued two relatively new documents - one, in 2001, on how to deal with individual conflicts of interest; and the other, in 2002, on how to deal with institutional conflicts of interest in the conduct of clinical research. Academic Medical Centers (AMCs), as also medical education and research institutions at other places, have to adopt means that minimize their conflicts of interest.
Both medical associations and research journal editors are getting concerned with individual and institutional conflicts of interest in the conduct of clinical research and documents are now available which address these issues. The 2001 ICMJE revision calls for full disclosure of the sponsor's role in research, as well as assurance that the investigators are independent of the sponsor, are fully accountable for the design and conduct of the trial, have independent access to all trial data and control all editorial and publication decisions. However the findings of a 2002 study suggest that academic institutions routinely participate in clinical research that does not adhere to ICMJE standards of accountability, access to data and control of publication.
There is an inevitable slant to produce not necessarily useful but marketable products which ensure the profitability of industry and research grants outflow to academia. Industry supports new, not traditional, therapies, irrespective of what is effective. Whatever traditional therapy is supported is most probably because the company concerned has a product with a big stake there, which has remained a ‘gold standard’ or which that player thinks has still some ‘juice’ left.
Industry sponsorship is mainly for potential medications, not for trying to determine whether there may be non-pharmacological interventions that may be equally good, if not better. In the paradigm shift towards biological psychiatry, the role of industry sponsorship is not overt but probably more pervasive than many have realised, or the right thinking may consider good, for the health of the branch in the long run.
An issue of major concern is protection of the interests of research subjects. Patients agree to become research subjects not only for personal medical benefit but, as an extension, to benefit the rest of the patient population and also advance medical research.
We all accept that industry profits have to be made, and investment in research and development by the pharma industry is massive. However, we must also accept there is a fundamental difference between marketing strategies for other entities and those for drugs.
The ultimate barometer is patient welfare and no drug that compromises it can stand the test of time. So, how does it make even commercial sense in the long term to market substandard products? The greatest mistake long-term players in industry may make is try to adopt the shady techniques of the upstart new entrant. Secrecy of marketing/sales tactics, of the process of manufacture, of other strategies and plans of business expansion, of strategies to tackle competition are fine business tactics. But it is critical that secrecy as a tactic not extend to reporting of research findings, especially those contrary to one's product.
Pharma has no option but to make a quality product, do comprehensive adverse reaction profiles, and market it only if it passes both tests.
Why does pharma adopt questionable tactics? The reasons are essentially two:
What with all the constraints, a drug comes to the pharmacy after huge investments. There are crippling overheads and infrastructure costs to be recovered. And there are massive profit margins to be maintained. If these were to be dependent only on genuine drug discoveries, that would be taking too great a risk.Industry players have to strike the right balance between profit making and credibility. In profit making, the marketing champions play their role. In credibility ratings, researchers and paid spokes-persons play their role. All is hunky dory till marketing is based on credibility. When there is nothing available to make for credibility, something is projected as one and marketing carried out, in the calculated hope that profits can accrue, since profit making must continue endlessly. That is what makes pharma adopt even questionable means to make profits.
Essentially, there are four types of drugs. First, drugs that work and have minimal side-effects; second, drugs which work but have serious side-effects; third, drugs that do not work and have minimal side-effects; and fourth, drugs which work minimally but have serious side-effects. It is the second and fourth types that create major hassles for industry. Often, industry may try to project the fourth type as the second to escape censure.
The major cat and mouse game being played by conscientious researchers is in exposing the third and fourth for what they are and not allowing industry to palm them off as the first and second type respectively. The other major game is in preventing the second type from being projected as the first. The third type are essentially harmless, so they attract censure all right and some merriment at the antics to market them. But they escape anything more than a light rap on the knuckles, except when they are projected as the first type.
What is necessary for industry captains and long-term players is to realise:
Their major propelling force can only be producing the first type. 2. They accept the second type only till they can lay their hands on the first. 3. The third type can be occasionally played around with to shore up profits, but never by projecting them as the first type. 4. The fourth type are the laggards, real threat to credibility and therefore do not deserve any market hype or promotion.
In finding out why most pharma indulges in questionable tactics, we are lead to some interesting solutions to prevent such tactics with the least amount of hassles for all concerned, even as both profits and credibility are kept intact.
PMCID: PMC3192391  PMID: 22058616
Academia; Pharmaceutical Industry; Clinical Practice Guidelines; Best Practice Guidelines; Academic Medical Centers; Medical Associations; Research Journals; Clinical Research; Public Welfare; Pharma Image; Corporate Welfare; Biological Psychiatry; Law Suits Against Industry
14.  Achieving Holistic Health for the Individual through Person-Centered Collaborative Care Supported by Informatics 
This article seeks to describe the current state of informatics supported collaborative care and to point out areas of future research in this highly interdisciplinary field.
In this article, person-centered collaborative care is seen as a concept addressing both the provision of care over organizational borders between health and social care, and within care teams as well as the changed patient/client-care provider relationship characterized by increased patient/client involvement.
From a health systems perspective, there are several attempts to describe the conceptual and theoretical basis for collaborative care indicating that agreement on core concepts and terminology is difficult. From an informatics perspective, focus is on standardization of clinical content models and terminology to achieve interoperability of information technology systems and to support standardized care pathways. Few examples look into how ad-hoc collaborative care processes can be supported using information technology and informatics standards. Nevertheless, promising examples do exist showing that integrational Information Communication Technology services can be supportive for collaborative care developments. However, the current landscape consists of many fragmented, often technology-driven eHealth solutions targeting specific diagnostic groups in geographically and/or organizationally restricted settings.
A systematic approach incorporating organizational, clinical, informatics and social science knowledge is needed to perform further research in areas such as virtual team partnerships, new paradigms of care delivery, data and knowledge management as well as its secure sharing. Also organizational and legal aspects need to be further researched in order to facilitate the coordinated provision of health and social care to citizens including self-management, utilizing informatics support in a societal context.
PMCID: PMC3633169  PMID: 23626912
Social Welfare; Health Information Management; Integrated Delivery of Health Care; Cooperative Behavior
15.  PragmatiX: An Interactive Tool for Visualizing the Creation Process Behind Collaboratively Engineered Ontologies 
With the emergence of tools for collaborative ontology engineering, more and more data about the creation process behind collaborative construction of ontologies is becoming available. Today, collaborative ontology engineering tools such as Collaborative Protégé offer rich and structured logs of changes, thereby opening up new challenges and opportunities to study and analyze the creation of collaboratively constructed ontologies. While there exists a plethora of visualization tools for ontologies, they have primarily been built to visualize aspects of the final product (the ontology) and not the collaborative processes behind construction (e.g. the changes made by contributors over time). To the best of our knowledge, there exists no ontology visualization tool today that focuses primarily on visualizing the history behind collaboratively constructed ontologies. Since the ontology engineering processes can influence the quality of the final ontology, we believe that visualizing process data represents an important stepping-stone towards better understanding of managing the collaborative construction of ontologies in the future. In this application paper, we present a tool – PragmatiX – which taps into structured change logs provided by tools such as Collaborative Protégé to visualize various pragmatic aspects of collaborative ontology engineering. The tool is aimed at managers and leaders of collaborative ontology engineering projects to help them in monitoring progress, in exploring issues and problems, and in tracking quality-related issues such as overrides and coordination among contributors. The paper makes the following contributions: (i) we present PragmatiX, a tool for visualizing the creation process behind collaboratively constructed ontologies (ii) we illustrate the functionality and generality of the tool by applying it to structured logs of changes of two large collaborative ontology-engineering projects and (iii) we conduct a heuristic evaluation of the tool with domain experts to uncover early design challenges and opportunities for improvement. Finally, we hope that this work sparks a new line of research on visualization tools for collaborative ontology engineering projects.
PMCID: PMC3901413  PMID: 24465189
Collaborative Ontology Engineering; pragmatic analysis; ontology monitoring; ontology engineering visualization; ontology evaluation; ontology tool
16.  Enriched biodiversity data as a resource and service 
Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon.
Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists.
One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain.
Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts.
PMCID: PMC4092319  PMID: 25057255
Biodiversity informatics; Data enrichment; Hackathon; Intelligent openness; Linked data; Open source; Software; Semantic Web; Taxonomy; Web services
17.  RMS: a platform for managing cross-disciplinary and multi-institutional research project collaboration 
Cross-institutional cross-disciplinary collaboration has become a trend as researchers move toward building more productive and innovative teams for scientific research. Research collaboration is significantly changing the organizational structure and strategies used in the clinical and translational science domain. However, due to the obstacles of diverse administrative structures, differences in area of expertise, and communication barriers, establishing and managing a cross-institutional research project is still a challenging task. We address these challenges by creating an integrated informatics platform to reduce the barriers to biomedical research collaboration.
The Request Management System (RMS) is an informatics infrastructure designed to transform a patchwork of expertise and resources into an integrated support network. The RMS facilitates investigators’ initiation of new collaborative projects and supports the management of the collaboration process. In RMS, experts and their knowledge areas are categorized and managed structurally to provide consistent service. A role-based collaborative workflow is tightly integrated with domain experts and services to streamline and monitor the life-cycle of a research project. The RMS has so far tracked over 1,500 investigators with over 4,800 tasks. The research network based on the data collected in RMS illustrated that the investigators’ collaborative projects increased close to 3 times from 2009 to 2012. Our experience with RMS indicates that the platform reduces barriers for cross-institutional collaboration of biomedical research projects.
Building a new generation of infrastructure to enhance cross-disciplinary and multi-institutional collaboration has become an important yet challenging task. In this paper, we share the experience of developing and utilizing a collaborative project management system. The results of this study demonstrate that a web-based integrated informatics platform can facilitate and increase research interactions among investigators.
PMCID: PMC4264263  PMID: 25433526
Biomedical research; Organization & administration; Research collaboration; System design and development; Collaborative research; Communication networks; Systems integration; Data-driven analysis
18.  A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience 
Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience. It is even more difficult to provide extensible software environments able to effectively target the rapidly changing data requirements and structures of research experiments. There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using integrated bioinformatics services and tools; (ii) handling multimodal/multiscale data and metadata, enabling the injection of several different data types according to structured schemas; (iii) providing high extensibility, in order to address different requirements deriving from a large variety of applications simply through a user runtime configuration.
A dynamically extensible data structure supporting collaborative multidisciplinary research projects in neuroscience has been defined and implemented. We have considered extensibility issues from two different points of view. First, the improvement of data flexibility has been taken into account. This has been done through the development of a methodology for the dynamic creation and use of data types and related metadata, based on the definition of “meta” data model. This way, users are not constrainted to a set of predefined data and the model can be easily extensible and applicable to different contexts. Second, users have been enabled to easily customize and extend the experimental procedures in order to track each step of acquisition or analysis. This has been achieved through a process-event data structure, a multipurpose taxonomic schema composed by two generic main objects: events and processes. Then, a repository has been built based on such data model and structure, and deployed on distributed resources thanks to a Grid-based approach. Finally, data integration aspects have been addressed by providing the repository application with an efficient dynamic interface designed to enable the user to both easily query the data depending on defined datatypes and view all the data of every patient in an integrated and simple way.
The results of our work have been twofold. First, a dynamically extensible data model has been implemented and tested based on a “meta” data-model enabling users to define their own data types independently from the application context. This data model has allowed users to dynamically include additional data types without the need of rebuilding the underlying database. Then a complex process-event data structure has been built, based on this data model, describing patient-centered diagnostic processes and merging information from data and metadata. Second, a repository implementing such a data structure has been deployed on a distributed Data Grid in order to provide scalability both in terms of data input and data storage and to exploit distributed data and computational approaches in order to share resources more efficiently. Moreover, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.
Based on such repository, data managing has been made possible through a friendly web interface. The driving principle of not being forced to preconfigured data types has been satisfied. It is up to users to dynamically configure the data model for the given experiment or data acquisition program, thus making it potentially suitable for customized applications.
PMCID: PMC3560115  PMID: 23043673
Neuroscience; Data models; Multidisciplinary studies
19.  VAMPS: a website for visualization and analysis of microbial population structures 
BMC Bioinformatics  2014;15:41.
The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis of complex communities over time and space a tractable research pursuit for small research groups. However, the ability to generate 105–108 reads with relative ease brings with it many downstream complications. Beyond the computational resources and skills needed to process and analyze data, it is difficult to compare datasets in an intuitive and interactive manner that leads to hypothesis generation and testing.
We developed the free web service VAMPS (Visualization and Analysis of Microbial Population Structures, to address these challenges and to facilitate research by individuals or collaborating groups working on projects with large-scale sequencing data. Users can upload marker gene sequences and associated metadata; reads are quality filtered and assigned to both taxonomic structures and to taxonomy-independent clusters. A simple point-and-click interface allows users to select for analysis any combination of their own or their collaborators’ private data and data from public projects, filter these by their choice of taxonomic and/or abundance criteria, and then explore these data using a wide range of analytic methods and visualizations. Each result is extensively hyperlinked to other analysis and visualization options, promoting data exploration and leading to a greater understanding of data relationships.
VAMPS allows researchers using marker gene sequence data to analyze the diversity of microbial communities and the relationships between communities, to explore these analyses in an intuitive visual context, and to download data, results, and images for publication. VAMPS obviates the need for individual research groups to make the considerable investment in computational infrastructure and bioinformatic support otherwise necessary to process, analyze, and interpret massive amounts of next-generation sequence data. Any web-capable device can be used to upload, process, explore, and extract data and results from VAMPS. VAMPS encourages researchers to share sequence and metadata, and fosters collaboration between researchers of disparate biomes who recognize common patterns in shared data.
PMCID: PMC3922339  PMID: 24499292
Microbiome; Microbial ecology; Microbial diversity; Data visualization; Website; Bacteria; SSU rRNA; Next-generation sequencing
20.  Geospatial resources for supporting data standards, guidance and best practice in health informatics 
BMC Research Notes  2011;4:19.
The 1980s marked the occasion when Geographical Information System (GIS) technology was broadly introduced into the geo-spatial community through the establishment of a strong GIS industry. This technology quickly disseminated across many countries, and has now become established as an important research, planning and commercial tool for a wider community that includes organisations in the public and private health sectors.
The broad acceptance of GIS technology and the nature of its functionality have meant that numerous datasets have been created over the past three decades. Most of these datasets have been created independently, and without any structured documentation systems in place. However, search and retrieval systems can only work if there is a mechanism for datasets existence to be discovered and this is where proper metadata creation and management can greatly help.
This situation must be addressed through support mechanisms such as Web-based portal technologies, metadata editor tools, automation, metadata standards and guidelines and collaborative efforts with relevant individuals and organisations. Engagement with data developers or administrators should also include a strategy of identifying the benefits associated with metadata creation and publication.
The establishment of numerous Spatial Data Infrastructures (SDIs), and other Internet resources, is a testament to the recognition of the importance of supporting good data management and sharing practices across the geographic information community. These resources extend to health informatics in support of research, public services and teaching and learning.
This paper identifies many of these resources available to the UK academic health informatics community. It also reveals the reluctance of many spatial data creators across the wider UK academic community to use these resources to create and publish metadata, or deposit their data in repositories for sharing.
The Go-Geo! service is introduced as an SDI developed to provide UK academia with the necessary resources to address the concerns surrounding metadata creation and data sharing. The Go-Geo! portal, Geodoc metadata editor tool, ShareGeo spatial data repository, and a range of other support resources, are described in detail.
This paper describes a variety of resources available for the health research and public health sector to use for managing and sharing their data. The Go-Geo! service is one resource which offers an SDI for the eclectic range of disciplines using GIS in UK academia, including health informatics.
The benefits of data management and sharing are immense, and in these times of cost restraints, these resources can be seen as solutions to find cost savings which can be reinvested in more research.
PMCID: PMC3224535  PMID: 21269487
21.  Primary Care Research Team Assessment (PCRTA): development and evaluation. 
BACKGROUND: Since the early 1990s the United Kingdom (UK) Department of Health has explicitly promoted a research and development (R&D) strategy for the National Health Service (NHS). General practitioners (GPs) and other members of the primary care team are in a unique position to undertake research activity that will complement and inform the research undertaken by basic scientists and hospital-based colleagues and lead directly to a better evidence base for decision making by primary care professionals. Opportunities to engage in R&D in primary care are growing and the scope for those wishing to become involved is finally widening. Infrastructure funding for research-active practices and the establishment of a range of support networks have helped to improve the research capacity and blur some of the boundaries between academic departments and clinical practice. This is leading to a supportive environment for primary care research. There is thus a need to develop and validate nationally accepted quality standards and accreditation of performance to ensure that funders, collaborators and primary care professionals can deliver high quality primary care research. Several strategies have been described in national policy documents in order to achieve an improvement in teaching and clinical care, as well as enhancing research capacity in primary care. The development of both research practices and primary care research networks has been recognised as having an important contribution to make in enabling health professionals to devote more protected time to undertake research methods training and to undertake research in a service setting. The recognition and development of primary care research has also brought with it an emphasis on quality and standards, including an approach to the new research governance framework. PRIMARY CARE RESEARCH TEAM ASSESSMENT: In 1998, the NHS Executive South and West, and later the London Research and Development Directorate, provided funding for a pilot project based at the Royal College of General Practitioners (RCGP) to develop a scheme to accredit UK general practices undertaking primary care R&D. The pilot began with initial consultation on the development of the process, as well as the standards and criteria for assessment. The resulting assessment schedule allowed for assessment at one of two levels: Collaborative Research Practice (Level I), with little direct experience of gaining project or infrastructure funding Established Research Practice (Level II), with more experience of research funding and activity and a sound infrastructure to allow for growth in capacity. The process for assessment of practices involved the assessment of written documentation, followed by a half-day assessment visit by a multidisciplinary team of three assessors. IMPLEMENTATION--THE PILOT PROJECT: Pilot practices were sampled in two regions. Firstly, in the NHS Executive South West Region, where over 150 practices expressed an interest in participating. From these a purposive sample of 21 practices was selected, providing a range of research and service activity. A further seven practices were identified and included within the project through the East London and Essex Network of Researchers (ELENoR). Many in this latter group received funding and administrative support and advice from ELENoR in order to prepare written submissions for assessment. Some sample loss was encountered within the pilot project, which was attributable largely to conflicting demands on participants' time. Indeed, the preparation of written submissions within the South West coincided with the introduction of primary care groups (PCGs) in April 1999, which several practices cited as having a major impact on their participation in the pilot project. A final sample of 15 practices (nine in the South West and six through ELENoR) underwent assessment through the pilot project. EVALUATION: A formal evaluation of the Primary Care Research Team Assessment (PCRTA) pilot was undertaken by an independent researcher (FM). This was supplemented with feedback from the assessment team members. The qualitative aspect of the evaluation, which included face-to-face and telephone interviews with assessors, lead researchers and other practice staff within the pilot research practices, as well as members of the project management group, demonstrated a positive view of the pilot scheme. Several key areas were identified in relation to particular strengths of research practices and areas for development including: Strengths Level II practices were found to have a strong primary care team ethos in research. Level II practices tended to have a greater degree of strategic thinking in relation to research. Development areas Level I practices were found to lack a clear and explicit research strategy. Practices at both levels had scope to develop their communication processes for dissemination of research and also for patient involvement. Practices at both levels needed mechanisms for supporting professional development in research methodology. The evaluation demonstrated that practices felt that they had gained from their participation and assessors felt that the scheme had worked well. Some specific issues were raised by different respondents within the qualitative evaluation relating to consistency of interpretation of standards and also the possible overlap of the assessment scheme with other RCGP quality initiatives. NATIONAL IMPLEMENTATION OF THE PRIMARY CARE RESEARCH TEAM ASSESSMENT: The pilot project has been very successful and recommendations have been made to progress to a UK scheme. Management and review of the scheme will remain largely the same, with a few changes focusing on the assessment process and support for practices entering the scheme. Specific changes include: development of the support and mentoring role of the primary care research networks increased peer and external support and mentoring for research practices undergoing assessment development of assessor training in line with other schemes within the RCGP Assessment Network work to ensure consistency across RCGP accreditation schemes in relation to key criteria, thereby facilitating comparable assessment processes refinement of the definition of the two groups, with Level I practices referred to as Collaborators and Level II practices as Investigator-Led. The project has continued to generate much enthusiasm and support and continues to reflect current policy. Indeed, recent developments include the proposed new funding arrangements for primary care R&D, which refer to the RCGP assessment scheme and recognise it as a key component in the future R&D agenda. The assessment scheme will help primary care trusts (PCTs) and individual practices to prepare and demonstrate their approach to research governance in a systematic way. It will also provide a more explicit avenue for primary care trusts to explore local service and development priorities identified within health improvement programmes and the research priorities set nationally for the NHS.
PMCID: PMC2560501  PMID: 12049028
22.  A Framework for Building Research Partnerships with First Nations Communities 
Solutions to complex health and environmental issues experienced by First Nations communities in Canada require the adoption of collaborative modes of research. The traditional “helicopter” approach to research applied in communities has led to disenchantment on the part of First Nations people and has impeded their willingness to participate in research. University researchers have tended to develop projects without community input and to adopt short term approaches to the entire process, perhaps a reflection of granting and publication cycles and other realities of academia. Researchers often enter communities, collect data without respect for local culture, and then exit, having had little or no community interaction or consideration of how results generated could benefit communities or lead to sustainable solutions. Community-based participatory research (CBPR) has emerged as an alternative to the helicopter approach and is promoted here as a method to research that will meet the objectives of both First Nations and research communities. CBPR is a collaborative approach that equitably involves all partners in the research process. Although the benefits of CBPR have been recognized by segments of the University research community, there exists a need for comprehensive changes in approaches to First Nations centered research, and additional guidance to researchers on how to establish respectful and productive partnerships with First Nations communities beyond a single funded research project. This article provides a brief overview of ethical guidelines developed for researchers planning studies involving Aboriginal people as well as the historical context and principles of CBPR. A framework for building research partnerships with First Nations communities that incorporates and builds upon the guidelines and principles of CBPR is then presented. The framework was based on 10 years’ experience working with First Nations communities in Saskatchewan. The framework for research partnership is composed of five phases. They are categorized as the pre-research, community consultation, community entry, research and research dissemination phases. These phases are cyclical, non-linear and interconnected. Elements of, and opportunities for, exploration, discussion, engagement, consultation, relationship building, partnership development, community involvement, and information sharing are key components of the five phases within the framework. The phases and elements within this proposed framework have been utilized to build and implement sustainable collaborative environmental health research projects with Saskatchewan First Nations communities.
PMCID: PMC4024052  PMID: 24855374
Saskatchewan first nations; community-based participatory research; framework; engagement; consultation; ethical partnership
23.  Wikis and Collaborative Writing Applications in Health Care: A Scoping Review Protocol 
JMIR Research Protocols  2012;1(1):e1.
The rapid rise in the use of collaborative writing applications (eg, wikis, Google Documents, and Google Knol) has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors that affect their use. While researchers have conducted systematic reviews on a range of software-based information and communication technologies as well as other social media (eg, virtual communities of practice, virtual peer-to-peer communities, and electronic support groups), none have reviewed collaborative writing applications in the medical sector. The overarching goal of this project is to explore the depth and breadth of evidence for the use of collaborative writing applications in health care. Thus, the purposes of this scoping review will be to (1) map the literature on collaborative writing applications; (2) compare the applications’ features; (3) describe the evidence of each application’s positive and negative effects as a KT intervention in health care; (4) inventory and describe the barriers and facilitators that affect the applications’ use; and (5) produce an action plan and a research agenda. A six-stage framework for scoping reviews will be used: (1) identifying the research question; (2) identifying relevant studies within the selected databases (using the EPPI-Reviewer software to classify the studies); (3) selecting studies (an iterative process in which two reviewers search the literature, refine the search strategy, and review articles for inclusion); (4) charting the data (using EPPI-Reviewer’s data-charting form); (5) collating, summarizing, and reporting the results (performing a descriptive, numerical, and interpretive synthesis); and (6) consulting knowledge users during three planned meetings. Since this scoping review concerns the use of collaborative writing applications as KT interventions in health care, we will use the Knowledge to Action (KTA) framework to describe and compare the various studies and collaborative writing projects we find. In addition to guiding the use of collaborative writing applications in health care, this scoping review will advance the science of KT by testing tools that could be used to evaluate other social media. We also expect to identify areas that require further systematic reviews and primary research and to produce a highly relevant research agenda that explores and leverages the potential of collaborative writing software. To date, this is the first study to use the KTA framework to study the role collaborative writing applications in KT, and the first to involve three national and international institutional knowledge users as part of the research process.
PMCID: PMC3626140  PMID: 23612481
24.  Home Telehealth for Patients With Chronic Obstructive Pulmonary Disease (COPD) 
Executive Summary
In July 2010, the Medical Advisory Secretariat (MAS) began work on a Chronic Obstructive Pulmonary Disease (COPD) evidentiary framework, an evidence-based review of the literature surrounding treatment strategies for patients with COPD. This project emerged from a request by the Health System Strategy Division of the Ministry of Health and Long-Term Care that MAS provide them with an evidentiary platform on the effectiveness and cost-effectiveness of COPD interventions.
After an initial review of health technology assessments and systematic reviews of COPD literature, and consultation with experts, MAS identified the following topics for analysis: vaccinations (influenza and pneumococcal), smoking cessation, multidisciplinary care, pulmonary rehabilitation, long-term oxygen therapy, noninvasive positive pressure ventilation for acute and chronic respiratory failure, hospital-at-home for acute exacerbations of COPD, and telehealth (including telemonitoring and telephone support). Evidence-based analyses were prepared for each of these topics. For each technology, an economic analysis was also completed where appropriate. In addition, a review of the qualitative literature on patient, caregiver, and provider perspectives on living and dying with COPD was conducted, as were reviews of the qualitative literature on each of the technologies included in these analyses.
The Chronic Obstructive Pulmonary Disease Mega-Analysis series is made up of the following reports, which can be publicly accessed at the MAS website at:
Chronic Obstructive Pulmonary Disease (COPD) Evidentiary Framework
Influenza and Pneumococcal Vaccinations for Patients With Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Smoking Cessation for Patients With Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Community-Based Multidisciplinary Care for Patients With Stable Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Pulmonary Rehabilitation for Patients With Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Long-term Oxygen Therapy for Patients With Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Noninvasive Positive Pressure Ventilation for Acute Respiratory Failure Patients With Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Noninvasive Positive Pressure Ventilation for Chronic Respiratory Failure Patients With Stable Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Hospital-at-Home Programs for Patients With Acute Exacerbations of Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Home Telehealth for Patients With Chronic Obstructive Pulmonary Disease (COPD): An Evidence-Based Analysis
Cost-Effectiveness of Interventions for Chronic Obstructive Pulmonary Disease Using an Ontario Policy Model
Experiences of Living and Dying With COPD: A Systematic Review and Synthesis of the Qualitative Empirical Literature
For more information on the qualitative review, please contact Mita Giacomini at:
For more information on the economic analysis, please visit the PATH website:
The Toronto Health Economics and Technology Assessment (THETA) collaborative has produced an associated report on patient preference for mechanical ventilation. For more information, please visit the THETA website:
The objective of this analysis was to conduct an evidence-based assessment of home telehealth technologies for patients with chronic obstructive pulmonary disease (COPD) in order to inform recommendations regarding the access and provision of these services in Ontario. This analysis was one of several analyses undertaken to evaluate interventions for COPD. The perspective of this assessment was that of the Ontario Ministry of Health and Long-Term Care, a provincial payer of medically necessary health care services.
Clinical Need: Condition and Target Population
Canada is facing an increase in chronic respiratory diseases due in part to its aging demographic. The projected increase in COPD will put a strain on health care payers and providers. There is therefore an increasing demand for telehealth services that improve access to health care services while maintaining or improving quality and equality of care. Many telehealth technologies however are in the early stages of development or diffusion and thus require study to define their application and potential harms or benefits. The Medical Advisory Secretariat (MAS) therefore sought to evaluate telehealth technologies for COPD.
Telemedicine (or telehealth) refers to using advanced information and communication technologies and electronic medical devices to support the delivery of clinical care, professional education, and health-related administrative services.
Generally there are 4 broad functions of home telehealth interventions for COPD:
to monitor vital signs or biological health data (e.g., oxygen saturation),
to monitor symptoms, medication, or other non-biologic endpoints (e.g., exercise adherence),
to provide information (education) and/or other support services (such as reminders to exercise or positive reinforcement), and
to establish a communication link between patient and provider.
These functions often require distinct technologies, although some devices can perform a number of these diverse functions. For the purposes of this review, MAS focused on home telemonitoring and telephone only support technologies.
Telemonitoring (or remote monitoring) refers to the use of medical devices to remotely collect a patient’s vital signs and/or other biologic health data and the transmission of those data to a monitoring station for interpretation by a health care provider.
Telephone only support refers to disease/disorder management support provided by a health care provider to a patient who is at home via telephone or videoconferencing technology in the absence of transmission of patient biologic data.
Research Questions
What is the effectiveness, cost-effectiveness, and safety of home telemonitoring compared with usual care for patients with COPD?
What is the effectiveness, cost-effectiveness, and safety of telephone only support programs compared with usual care for patients with COPD?
Research Methods
Literature Search
Search Strategy
A literature search was performed on November 3, 2010 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cumulative Index to Nursing & Allied Health Literature (CINAHL), the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for studies published from January 1, 2000 until November 3, 2010. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria, full-text articles were obtained. Reference lists were also examined for any additional relevant studies not identified through the search. Articles with unknown eligibility were reviewed with a second clinical epidemiologist, and then a group of epidemiologists until consensus was established. The quality of evidence was assessed as high, moderate, low, or very low according to GRADE methodology.
Inclusion Criteria – Question #1
frequent transmission of a patient’s physiological data collected at home and without a health care professional physically present to health care professionals for routine monitoring through the use of a communication technology;
monitoring combined with a coordinated management and feedback system based on transmitted data;
telemonitoring as a key component of the intervention (subjective determination);
usual care as provided by the usual care provider for the control group;
randomized controlled trials (RCTs), controlled clinical trials (CCTs), systematic reviews, and/or meta-analyses;
published between January 1, 2000 and November 3, 2010.
Inclusion Criteria – Question #2
scheduled or frequent contact between patient and a health care professional via telephone or videoconferencing technology in the absence of transmission of patient physiological data;
monitoring combined with a coordinated management and feedback system based on transmitted data;
telephone support as a key component of the intervention (subjective determination);
usual care as provided by the usual care provider for the control group;
RCTs, CCTs, systematic reviews, and/or meta-analyses;
published between January 1, 2000 and November 3, 2010.
Exclusion Criteria
published in a language other than English;
intervention group (and not control) receiving some form of home visits by a medical professional, typically a nurse (i.e., telenursing) beyond initial technology set-up and education, to collect physiological data, or to somehow manage or treat the patient;
not recording patient or health system outcomes (e.g., technical reports testing accuracy, reliability or other development-related outcomes of a device, acceptability/feasibility studies, etc.);
not using an independent control group that received usual care (e.g., studies employing historical or periodic controls).
Outcomes of Interest
hospitalizations (primary outcome)
emergency department visits
length of stay
quality of life
other […]
Subgroup Analyses (a priori)
length of intervention (primary)
severity of COPD (primary)
Quality of Evidence
The quality of evidence assigned to individual studies was determined using a modified CONSORT Statement Checklist for Randomized Controlled Trials. (1) The CONSORT Statement was adapted to include 3 additional quality measures: the adequacy of control group description, significant differential loss to follow-up between groups, and greater than or equal to 30% study attrition. Individual study quality was defined based on total scores according to the CONSORT Statement checklist: very low (0 to < 40%), low (≥ 40 to < 60%), moderate (≥ 60 to < 80%), and high (≥ 80 to 100%).
The quality of the body of evidence was assessed as high, moderate, low, or very low according to the GRADE Working Group criteria. The following definitions of quality were used in grading the quality of the evidence:
Summary of Findings
Six publications, representing 5 independent trials, met the eligibility criteria for Research Question #1. Three trials were RCTs reported across 4 publications, whereby patients were randomized to home telemonitoring or usual care, and 2 trials were CCTs, whereby patients or health care centers were nonrandomly assigned to intervention or usual care.
A total of 310 participants were studied across the 5 included trials. The mean age of study participants in the included trials ranged from 61.2 to 74.5 years for the intervention group and 61.1 to 74.5 years for the usual care group. The percentage of men ranged from 40% to 64% in the intervention group and 46% to 72% in the control group.
All 5 trials were performed in a moderate to severe COPD patient population. Three trials initiated the intervention following discharge from hospital. One trial initiated the intervention following a pulmonary rehabilitation program. The final trial initiated the intervention during management of patients at an outpatient clinic.
Four of the 5 trials included oxygen saturation (i.e., pulse oximetry) as one of the biological patient parameters being monitored. Additional parameters monitored included forced expiratory volume in one second, peak expiratory flow, and temperature.
There was considerable clinical heterogeneity between trials in study design, methods, and intervention/control. In relation to the telemonitoring intervention, 3 of the 5 included studies used an electronic health hub that performed multiple functions beyond the monitoring of biological parameters. One study used only a pulse oximeter device alone with modem capabilities. Finally, in 1 study, patients measured and then forwarded biological data to a nurse during a televideo consultation. Usual care varied considerably between studies.
Only one trial met the eligibility criteria for Research Question #2. The included trial was an RCT that randomized 60 patients to nurse telephone follow-up or usual care (no telephone follow-up). Participants were recruited from the medical department of an acute-care hospital in Hong Kong and began receiving follow-up after discharge from the hospital with a diagnosis of COPD (no severity restriction). The intervention itself consisted of only two 10-to 20-minute telephone calls, once between days 3 to 7 and once between days 14 to 20, involving a structured, individualized educational and supportive programme led by a nurse that focused on 3 components: assessment, management options, and evaluation.
Regarding Research Question #1:
Low to very low quality evidence (according to GRADE) finds non-significant effects or conflicting effects (of significant or non-significant benefit) for all outcomes examined when comparing home telemonitoring to usual care.
There is a trend towards significant increase in time free of hospitalization and use of other health care services with home telemonitoring, but these findings need to be confirmed further in randomized trials of high quality.
There is severe clinical heterogeneity between studies that limits summary conclusions.
The economic impact of home telemonitoring is uncertain and requires further study.
Home telemonitoring is largely dependent on local information technologies, infrastructure, and personnel, and thus the generalizability of external findings may be low. Jurisdictions wishing to replicate home telemonitoring interventions should likely test those interventions within their jurisdictional framework before adoption, or should focus on home-grown interventions that are subjected to appropriate evaluation and proven effective.
Regarding Research Question #2:
Low quality evidence finds significant benefit in favour of telephone-only support for self-efficacy and emergency department visits when compared to usual care, but non-significant results for hospitalizations and hospital length of stay.
There are very serious issues with the generalizability of the evidence and thus additional research is required.
PMCID: PMC3384362  PMID: 23074421
25.  PoPLAR: Portal for Petascale Lifescience Applications and Research 
BMC Bioinformatics  2013;14(Suppl 9):S3.
We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches--such as proteomics, genomics, metabolomics, and meta-genomics--drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge.
The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community's most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal.
This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences.
This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.
PMCID: PMC3698029  PMID: 23902523

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