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1.  Extending Asia Pacific bioinformatics into new realms in the "-omics" era 
BMC Genomics  2009;10(Suppl 3):S1.
The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.
PMCID: PMC2788361  PMID: 19958472
2.  E-Learning as New Method of Medical Education 
Acta Informatica Medica  2008;16(2):102-117.
Distance learning refers to use of technologies based on health care delivered on distance and covers areas such as electronic health, tele-health (e-health), telematics, telemedicine, tele-education, etc. For the need of e-health, telemedicine, tele-education and distance learning there are various technologies and communication systems from standard telephone lines to the system of transmission digitalized signals with modem, optical fiber, satellite links, wireless technologies, etc. Tele-education represents health education on distance, using Information Communication Technologies (ICT), as well as continuous education of a health system beneficiaries and use of electronic libraries, data bases or electronic data with data bases of knowledge. Distance learning (E-learning) as a part of tele-education has gained popularity in the past decade; however, its use is highly variable among medical schools and appears to be more common in basic medical science courses than in clinical education. Distance learning does not preclude traditional learning processes; frequently it is used in conjunction with in-person classroom or professional training procedures and practices. Tele-education has mostly been used in biomedical education as a blended learning method, which combines tele-education technology with traditional instructor-led training, where, for example, a lecture or demonstration is supplemented by an online tutorial. Distance learning is used for self-education, tests, services and for examinations in medicine i.e. in terms of self-education and individual examination services. The possibility of working in the exercise mode with image files and questions is an attractive way of self education. Automated tracking and reporting of learners’ activities lessen faculty administrative burden. Moreover, e-learning can be designed to include outcomes assessment to determine whether learning has occurred. This review article evaluates the current status and level of tele-education development in Bosnia and Herzegovina outlining its components, faculty development needs for implementation and the possibility of its integration as official learning standard in biomedical curricula in Bosnia and Herzegovina. Tele-education refers to the use of information and communication technologies (ICT) to enhance knowledge and performance. Tele-education in biomedical education is widely accepted in the medical education community where it is mostly integrated into biomedical curricula forming part of a blended learning strategy. There are many biomedical digital repositories of e-learning materials worldwide, some peer reviewed, where instructors or developers can submit materials for widespread use. First pilot project with the aim to introduce tele-education in biomedical curricula in Bosnia and Herzegovina was initiated by Department for Medical Informatics at Medical Faculty in Sarajevo in 2002 and has been developing since. Faculty member’s skills in creating tele-education differ from those needed for traditional teaching and faculty rewards must recognize this difference and reward the effort. Tele-education and use of computers will have an impact of future medical practice in a life long learning. Bologna process, which started last years in European countries, provide us to promote and introduce modern educational methods of education at biomedical faculties in Bosnia and Herzegovina. Cathedra of Medical informatics and Cathedra of Family medicine at Medical Faculty of University of Sarajevo started to use Web based education as common way of teaching of medical students. Satisfaction with this method of education within the students is good, but not yet suitable for most of medical disciplines at biomedical faculties in Bosnia and Herzegovina.
PMCID: PMC3789161  PMID: 24109154
Medical education; Distance learning; Bosnia and Herzegovina
3.  Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia 
Briefings in Bioinformatics  2013;14(5):563-574.
The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show–style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.
PMCID: PMC3771231  PMID: 23543352
training; next-generation sequencing; NGS; cloud; workshop
4.  Computational Biology and Bioinformatics in Nigeria 
PLoS Computational Biology  2014;10(4):e1003516.
Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.
PMCID: PMC3998874  PMID: 24763310
5.  Physician Emigration from Sub-Saharan Africa to the United States: Analysis of the 2011 AMA Physician Masterfile 
PLoS Medicine  2013;10(9):e1001513.
Siankam Tankwanchi and colleagues used the AMA Physician Masterfile and the WHO Global Health Workforce Statistics on physicians in sub-Saharan Africa to determine trends in physician emigration to the United States.
Please see later in the article for the Editors' Summary
The large-scale emigration of physicians from sub-Saharan Africa (SSA) to high-income nations is a serious development concern. Our objective was to determine current emigration trends of SSA physicians found in the physician workforce of the United States.
Methods and Findings
We analyzed physician data from the World Health Organization (WHO) Global Health Workforce Statistics along with graduation and residency data from the 2011 American Medical Association Physician Masterfile (AMA-PM) on physicians trained or born in SSA countries who currently practice in the US. We estimated emigration proportions, year of US entry, years of practice before emigration, and length of time in the US. According to the 2011 AMA-PM, 10,819 physicians were born or trained in 28 SSA countries. Sixty-eight percent (n = 7,370) were SSA-trained, 20% (n = 2,126) were US-trained, and 12% (n = 1,323) were trained outside both SSA and the US. We estimated active physicians (age ≤70 years) to represent 96% (n = 10,377) of the total. Migration trends among SSA-trained physicians increased from 2002 to 2011 for all but one principal source country; the exception was South Africa whose physician migration to the US decreased by 8% (−156). The increase in last-decade migration was >50% in Nigeria (+1,113) and Ghana (+243), >100% in Ethiopia (+274), and >200% (+244) in Sudan. Liberia was the most affected by migration to the US with 77% (n = 175) of its estimated physicians in the 2011 AMA-PM. On average, SSA-trained physicians have been in the US for 18 years. They practiced for 6.5 years before US entry, and nearly half emigrated during the implementation years (1984–1999) of the structural adjustment programs.
Physician emigration from SSA to the US is increasing for most SSA source countries. Unless far-reaching policies are implemented by the US and SSA countries, the current emigration trends will persist, and the US will remain a leading destination for SSA physicians emigrating from the continent of greatest need.
Please see later in the article for the Editors' Summary
Editors' Summary
Population growth and aging and increasingly complex health care interventions, as well as existing policies and market forces, mean that many countries are facing a shortage of health care professionals. High-income countries are addressing this problem in part by encouraging the immigration of foreign health care professionals from low- and middle-income countries. In the US, for example, international medical graduates (IMGs) can secure visas and permanent residency by passing examinations provided by the Educational Commission of Foreign Medical Graduates and by agreeing to provide care in areas that are underserved by US physicians. Inevitably, the emigration of physicians from low- and middle-income countries undermines health service delivery in the emigrating physicians' country of origin because physician supply is already inadequate in those countries. Physician emigration from sub-Saharan Africa, which has only 2% of the global physician workforce but a quarter of the global burden of disease, is particularly worrying. Since 1970, as a result of large-scale emigration and limited medical education, there has been negligible or negative growth in the density of physicians in many countries in sub-Saharan Africa. In Liberia, for example, in 1973, there were 7.76 physicians per 100,000 people but by 2008 there were only 1.37 physicians per 100,000 people; in the US, there are 250 physicians per 100,000 people.
Why Was This Study Done?
Before policy proposals can be formulated to address global inequities in physician distribution, a clear picture of the patterns of physician emigration from resource-limited countries is needed. In this study, the researchers use data from the 2011 American Medical Association Physician Masterfile (AMA-PM) to investigate the “brain drain” of physicians from sub-Saharan Africa to the US. The AMA-PM collects annual demographic, academic, and professional data on all residents (physicians undergoing training in a medical specialty) and licensed physicians who practice in the US.
What Did the Researchers Do and Find?
The researchers used data from the World Health Organization (WHO) Global Health Workforce Statistics and graduation and residency data from the 2011 AMA-PM to estimate physician emigration rates from sub-Saharan African countries, year of US entry, years of service provided before emigration to the US, and length of time in the US. There were 10,819 physicians who were born or trained in 28 sub-Saharan African countries in the 2011 AMA-PM. By using a published analysis of the 2002 AMA-PM, the researchers estimated that US immigration among sub-Saharan African-trained physicians had increased over the past decade for all the countries examined except South Africa, where physician emigration had decreased by 8%. Overall, the number of sub-Saharan African IMGs in the US had increased by 38% since 2002. More than half of this increase was accounted for by Nigerian IMGs. Liberia was the country most affected by migration of its physicians to the US—77% of its estimated 226 physicians were in the 2011 AMA-PM. On average, sub-Saharan African IMGs had been in the US for 18 years and had practiced for 6.5 years before emigration. Finally, nearly half of the sub-Saharan African IMGs had migrated to US between 1984 and 1995, years during which structural adjustment programs, which resulted in deep cuts to public health care services, were implemented in developing countries by international financial institutions as conditions for refinancing.
What Do These Findings Mean?
Although the sub-Saharan African IMGs in the 2011 AMA-PM only represent about 1% of all the physicians and less than 5% of the IMGs in the AMA-PM, these findings reveal a major loss of physicians from sub-Saharan Africa. They also suggest that emigration of physicians from sub-Saharan Africa is a growing problem and is likely to continue unless job satisfaction for physicians is improved in their country of origin. Moreover, because the AMA-PM only lists physicians who qualify for a US residency position, more physicians may have moved from sub-Saharan Africa to the US than reported here and may be working in other jobs incommensurate with their medical degrees (“brain waste”). The researchers suggest that physician emigration from sub-Saharan Africa to the US reflects the complexities in the labor markets for health care professionals in both Africa and the US and can be seen as low- and middle-income nations subsidizing the education of physicians in high-income countries. Policy proposals to address global inequities in physician distribution will therefore need both to encourage the recruitment, training, and retention of health care professionals in resource-limited countries and to persuade high-income countries to train more home-grown physicians to meet the needs of their own populations.
Additional Information
Please access these websites via the online version of this summary at
The Foundation for Advancement of International Medical Education and Research is a non-profit foundation committed to improving world health through education that was established in 2000 by the Educational Commission for Foreign Medical Graduates
The Global Health Workforce Alliance is a partnership of national governments, civil society, international agencies, finance institutions, researchers, educators, and professional associations dedicated to identifying, implementing and advocating for solutions to the chronic global shortage of health care professionals (available in several languages)
Information on the American Medical Association Physician Masterfile and the providers of physician data lists is available via the American Medical Associations website
The World Health Organization (WHO) annual World Health Statistics reports present the most recent health statistics for the WHO Member States
The Medical Education Partnership Initiative is a US-sponsored initiative that supports medical education and research in sub-Saharan African institutions, aiming to increase the quantity, quality, and retention of graduates with specific skills addressing the health needs of their national populations
CapacityPlus is the USAID-funded global project uniquely focused on the health workforce needed to achieve the Millennium Development Goals
Seed Global Health cultivates the next generation of health professionals by allying medical and nursing volunteers with their peers in resource-limited settings
"America is Stealing the Worlds Doctors", a 2012 New York Times article by Matt McAllester, describes the personal experience of a young doctor who emigrated from Zambia to the US
Path to United States Practice Is Long Slog to Foreign Doctors, a 2013 New York Times article by Catherine Rampell, describes the hurdles that immigrant physicians face in practicing in the US
PMCID: PMC3775724  PMID: 24068894
6.  Conflict of Interest Reporting by Authors Involved in Promotion of Off-Label Drug Use: An Analysis of Journal Disclosures 
PLoS Medicine  2012;9(8):e1001280.
Aaron Kesselheim and colleagues investigate conflict of interest disclosures in articles authored by physicians and scientists identified in whistleblower complaints alleging illegal off-label marketing by pharmaceutical companies.
Litigation documents reveal that pharmaceutical companies have paid physicians to promote off-label uses of their products through a number of different avenues. It is unknown whether physicians and scientists who have such conflicts of interest adequately disclose such relationships in the scientific publications they author.
Methods and Findings
We collected whistleblower complaints alleging illegal off-label marketing from the US Department of Justice and other publicly available sources (date range: 1996–2010). We identified physicians and scientists described in the complaints as having financial relationships with defendant manufacturers, then searched Medline for articles they authored in the subsequent three years. We assessed disclosures made in articles related to the off-label use in question, determined the frequency of adequate disclosure statements, and analyzed characteristics of the authors (specialty, author position) and articles (type, connection to off-label use, journal impact factor, citation count/year). We identified 39 conflicted individuals in whistleblower complaints. They published 404 articles related to the drugs at issue in the whistleblower complaints, only 62 (15%) of which contained an adequate disclosure statement. Most articles had no disclosure (43%) or did not mention the pharmaceutical company (40%). Adequate disclosure rates varied significantly by article type, with commentaries less likely to have adequate disclosure compared to articles reporting original studies or trials (adjusted odds ratio [OR] = 0.10, 95%CI = 0.02–0.67, p = 0.02). Over half of the authors (22/39, 56%) made no adequate disclosures in their articles. However, four of six authors with ≥25 articles disclosed in about one-third of articles (range: 10/36–8/25 [28%–32%]).
One in seven authors identified in whistleblower complaints as involved in off-label marketing activities adequately disclosed their conflict of interest in subsequent journal publications. This is a much lower rate of adequate disclosure than has been identified in previous studies. The non-disclosure patterns suggest shortcomings with authors and the rigor of journal practices.
Please see later in the article for the Editors' Summary
Editor's Summary
Off-label use of pharmaceuticals is the practice of prescribing a drug for a condition or age group, or in a dose or form of administration, that has not been specifically approved by a formal regulatory body, such as the US Food and Drug Administration (FDA). Off-label prescribing is common all over the world. In the US, although it is legal for doctors to prescribe drugs off-label and discuss such clinical uses with colleagues, it is illegal for pharmaceutical companies to directly promote off-label uses of any of their products. Revenue from off-label uses can be lucrative for drug companies and even surpass the income from approved uses. Therefore, many pharmaceutical companies have paid physicians and scientists to promote off-label use of their products as part of their marketing programs.
Why Was This Study Done?
Recently, a number of pharmaceutical companies have been investigated in the US for illegal marketing programs that promote off-label uses of their products and have had to pay billions of dollars in court settlements. As part of these investigations, doctors and scientists were identified who were paid by the companies to deliver lectures and conduct other activities to support off-label uses. When the same physicians and scientists also wrote articles about these drugs for medical journals, their financial relationships would have constituted clear conflicts of interest that should have been declared alongside the journal articles. So, in this study, the researchers identified such authors, examined their publications, and assessed the adequacy of conflict of interest disclosures made in these publications.
What Did the Researchers Do and Find?
The researchers used disclosed information from the US Department of Justice, media reports, and data from a non-governmental organization that tracks federal fraud actions, to find whistleblower complaints alleging illegal off-label promotion. Then they identified the doctors and scientists described in the complaints as having financial relationships with the defendant drug companies and searched Medline for articles authored by these experts in the subsequent three years. Using a four step approach, the researchers assessed the adequacy of conflict of interest disclosures made in articles relating to the off-label uses in question.
Using these methods, the researchers examined 26 complaints alleging illegal off-label promotion and identified the 91 doctors and scientists recorded as being involved in this practice. The researchers found 39 (43%) of these 91 experts had authored 404 related publications. In the complaints, these 39 experts were alleged to have engaged in 42 relationships with the relevant drug company: the most common activity was acting as a paid speaker (n = 26, 62%) but also writing reviews or articles on behalf of the company (n = 7), acting as consultants or advisory board members (n = 3), and receiving gifts/honoraria (n = 3), research support funds (n = 2), and educational support funds (n = 1). However, the researchers found that only 62 (15%) of the 404 related articles had adequate disclosures—43% (148) had no disclosure at all, 4% had statements denying any conflicts of interest, 40% had disclosures that did not mention the drug manufacturer, and 13% had disclosures that mentioned the manufacturer but inadequately conveyed the nature of the relationship between author and drug manufacturer reported in the complaint. The researchers also found that adequate disclosure rates varied significantly by article type, with commentaries significantly less likely to have adequate disclosure compared to articles reporting studies or trials.
What Do These Findings Mean?
These findings show the substantial deficiencies in the adequacy of conflict-of-interest disclosures made by authors who had been paid by pharmaceutical manufacturers as part of off-label marketing activities: only one in seven authors fully disclosed their conflict of interest in their published articles. This low figure is troubling and suggests that approaches to controlling the effects of conflicts of interest that rely on author candidness are inadequate and furthermore, journal practices are not robust enough and need to be improved. In the meantime, readers have no option but to interpret conflict of interest disclosures, particularly in relation to off-label uses, with caution.
Additional Information
Please access these Web sites via the online version of this summary at
The US FDA provides a guide on the use of off-label drugs
The US Agency for Healthcare Research and Quality offers a patient guide to off-label drugs
ProPublica offers a web-based tool to identify physicians who have financial relationships with certain pharmaceutical companies
Wikipedia has a good description of off-label drug use (note that Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
The Institute for Medicine as a Profession maintains a list of policies regulating physicians' financial relationships that are in place at US-based academic medical centers
PMCID: PMC3413710  PMID: 22899894
7.  Portuguese Coaches’ Perceptions of and Preferences for Knowledge Sources Related to their Professional Background 
The purpose of this study was to analyse Portuguese coaches’ perceptions of, and preferences for, knowledge sources as related to professional background; namely academic education level, coach education level and coaching experience. The study’s participants comprised 336 Portuguese coaches from twenty-two sports. A questionnaire was used to identify coaches’ demographic characteristics and representations about their preferred sources of coaching knowledge. MANOVA using Tukey’s HSD test was used to compare groups. The results highlighted that coaches perceived that coaching knowledge is built from a broad range of sources from personal coaching and playing experiences to more explicit formal, informal and non-formal learning situations. Results indicated that the coaches ascribed more importance to experiential sources such as working with experts, learning by doing, interacting with peer coaches and attending informal seminars and clinics, than to the formal learning situations provided by the national coaching certification programs. Differences, however, were found in that coaches who had a greater background within higher education (physical) and sport valued informal and non-formal learning sources more than did coaches who were defined as not coming from an academic background. The findings point to the importance of developing new learning, experientially-based, opportunities within the Portuguese context, where curricula content continues to be delivered via didactic means.
Key pointsCoaches recognized that learning is obtained from a broad range of sources of coaching knowledge and each source has a particular role in the development of a coach.Experiential guided sources reached more importance to coaches as working with experts, learning by doing, attending seminars/clinics outside of the formal system and interaction with peers were the most acknowledged.The only source that is related to formal learning, national certification programs, was recognized as the less importance than all informal and non-formal learning situations.The profile of the source of coaching knowledge showed to be stable among coaches as only the academic education level differentiated the coaches’ perceptions.
PMCID: PMC3761720  PMID: 24149644
coaching science; coaching education; coaches’ perceptions; learning situations
8.  Explorative search of distributed bio-data to answer complex biomedical questions 
BMC Bioinformatics  2014;15(Suppl 1):S3.
The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are most reliable and most related to the biomedical questions to be answered, which are increasingly complex and often involve many different biomedical-molecular aspects. Such questions can be addressed only by comprehensively searching and exploring different types of data, which frequently are ordered and provided by different data sources. Search Computing has been proposed for the management and integration of ranked results from heterogeneous search services. Here, we present its novel application to the explorative search of distributed biomedical-molecular data and the integration of the search results to answer complex biomedical questions.
A set of available bioinformatics search services has been modelled and registered in the Search Computing framework, and a Bioinformatics Search Computing application (Bio-SeCo) using such services has been created and made publicly available at It offers an integrated environment which eases search, exploration and ranking-aware combination of heterogeneous data provided by the available registered services, and supplies global results that can support answering complex multi-topic biomedical questions.
By using Bio-SeCo, scientists can explore the very large and very heterogeneous biomedical-molecular data available. They can easily make different explorative search attempts, inspect obtained results, select the most appropriate, expand or refine them and move forward and backward in the construction of a global complex biomedical query on multiple distributed sources that could eventually find the most relevant results. Thus, it provides an extremely useful automated support for exploratory integrated bio search, which is fundamental for Life Science data driven knowledge discovery.
PMCID: PMC4015759  PMID: 24564278
9.  Effect of an Educational Toolkit on Quality of Care: A Pragmatic Cluster Randomized Trial 
PLoS Medicine  2014;11(2):e1001588.
In a pragmatic cluster-randomized trial, Baiju Shah and colleagues evaluated the effectiveness of printed educational materials for clinician education focusing on cardiovascular disease screening and risk reduction in people with diabetes.
Please see later in the article for the Editors' Summary
Printed educational materials for clinician education are one of the most commonly used approaches for quality improvement. The objective of this pragmatic cluster randomized trial was to evaluate the effectiveness of an educational toolkit focusing on cardiovascular disease screening and risk reduction in people with diabetes.
Methods and Findings
All 933,789 people aged ≥40 years with diagnosed diabetes in Ontario, Canada were studied using population-level administrative databases, with additional clinical outcome data collected from a random sample of 1,592 high risk patients. Family practices were randomly assigned to receive the educational toolkit in June 2009 (intervention group) or May 2010 (control group). The primary outcome in the administrative data study, death or non-fatal myocardial infarction, occurred in 11,736 (2.5%) patients in the intervention group and 11,536 (2.5%) in the control group (p = 0.77). The primary outcome in the clinical data study, use of a statin, occurred in 700 (88.1%) patients in the intervention group and 725 (90.1%) in the control group (p = 0.26). Pre-specified secondary outcomes, including other clinical events, processes of care, and measures of risk factor control, were also not improved by the intervention. A limitation is the high baseline rate of statin prescribing in this population.
The educational toolkit did not improve quality of care or cardiovascular outcomes in a population with diabetes. Despite being relatively easy and inexpensive to implement, printed educational materials were not effective. The study highlights the need for a rigorous and scientifically based approach to the development, dissemination, and evaluation of quality improvement interventions.
Trial Registration NCT01411865 and NCT01026688
Please see later in the article for the Editors' Summary
Editors' Summary
Clinical practice guidelines help health care providers deliver the best care to patients by combining all the evidence on disease management into specific recommendations for care. However, the implementation of evidence-based guidelines is often far from perfect. Take the example of diabetes. This common chronic disease, which is characterized by high levels of sugar (glucose) in the blood, impairs the quality of life of patients and shortens life expectancy by increasing the risk of cardiovascular diseases (conditions that affect the heart and circulation) and other life-threatening conditions. Patients need complex care to manage the multiple risk factors (high blood sugar, high blood pressure, high levels of fat in the blood) that are associated with the long-term complications of diabetes, and they need to be regularly screened and treated for these complications. Clinical practice guidelines for diabetes provide recommendations on screening and diagnosis, drug treatment, and cardiovascular disease risk reduction, and on helping patients self-manage their disease. Unfortunately, the care delivered to patients with diabetes frequently fails to meet the standards laid down in these guidelines.
Why Was This Study Done?
How can guideline adherence and the quality of care provided to patients be improved? A common approach is to send printed educational materials to clinicians. For example, when the Canadian Diabetes Association (CDA) updated its clinical practice guidelines in 2008, it mailed educational toolkits that contained brochures and other printed materials targeting key themes from the guidelines to family physicians. In this pragmatic cluster randomized trial, the researchers investigate the effect of the CDA educational toolkit that targeted cardiovascular disease screening and treatment on the quality of care of people with diabetes. A pragmatic trial asks whether an intervention works under real-life conditions and whether it works in terms that matter to the patient; a cluster randomized trial randomly assigns groups of people to receive alternative interventions and compares outcomes in the differently treated “clusters.”
What Did the Researchers Do and Find?
The researchers randomly assigned family practices in Ontario, Canada to receive the educational toolkit in June 2009 (intervention group) or in May 2010 (control group). They examined outcomes between July 2009 and April 2010 in all patients with diabetes in Ontario aged over 40 years (933,789 people) using population-level administrative data. In Canada, administrative databases record the personal details of people registered with provincial health plans, information on hospital visits and prescriptions, and physician service claims for consultations, assessments, and diagnostic and therapeutic procedures. They also examined clinical outcome data from a random sample of 1,592 patients at high risk of cardiovascular complications. In the administrative data study, death or non-fatal heart attack (the primary outcome) occurred in about 11,500 patients in both the intervention and control group. In the clinical data study, the primary outcome―use of a statin to lower blood fat levels―occurred in about 700 patients in both study groups. Secondary outcomes, including other clinical events, processes of care, and measures of risk factor control were also not improved by the intervention. Indeed, in the administrative data study, some processes of care outcomes related to screening for heart disease were statistically significantly worse in the intervention group than in the control group, and in the clinical data study, fewer patients in the intervention group reached blood pressure targets than in the control group.
What Do These Findings Mean?
These findings suggest that the CDA cardiovascular diseases educational toolkit did not improve quality of care or cardiovascular outcomes in a population with diabetes. Indeed, the toolkit may have led to worsening in some secondary outcomes although, because numerous secondary outcomes were examined, this may be a chance finding. Limitations of the study include its length, which may have been too short to see an effect of the intervention on clinical outcomes, and the possibility of a ceiling effect—the control group in the clinical data study generally had good care, which left little room for improvement of the quality of care in the intervention group. Overall, however, these findings suggest that printed educational materials may not be an effective way to improve the quality of care for patients with diabetes and other complex conditions and highlight the need for a rigorous, scientific approach to the development, dissemination, and evaluation of quality improvement interventions.
Additional Information
Please access these websites via the online version of this summary at
The US National Diabetes Information Clearinghouse provides information about diabetes for patients, health care professionals, and the general public (in English and Spanish)
The UK National Health Service Choices website provides information (including some personal stories) for patients and carers about type 2 diabetes, the commonest form of diabetes
The Canadian Diabetes Association also provides information about diabetes for patients (including some personal stories about living with diabetes) and health care professionals; its latest clinical practice guidelines are available on its website
The UK National Institute for Health and Care Excellence provides general information about clinical guidelines and about health care quality standards in the UK
The US Agency for Healthcare Research and Quality aims to improve the quality, safety, efficiency, and effectiveness of health care for all Americans (information in English and Spanish); the US National Guideline Clearinghouse is a searchable database of clinical practice guidelines
The International Diabetes Federation provides information about diabetes for patients and health care professionals, along with international statistics on the burden of diabetes
PMCID: PMC3913553  PMID: 24505216
10.  Development and evaluation of an innovative model of inter-professional education focused on asthma medication use 
BMC Medical Education  2014;14:72.
Inter-professional learning has been promoted as the solution to many clinical management issues. One such issue is the correct use of asthma inhaler devices. Up to 80% of people with asthma use their inhaler device incorrectly. The implications of this are poor asthma control and quality of life. Correct inhaler technique can be taught, however these educational instructions need to be repeated if correct technique is to be maintained. It is important to maximise the opportunities to deliver this education in primary care. In light of this, it is important to explore how health care providers, in particular pharmacists and general medical practitioners, can work together in delivering inhaler technique education to patients, over time. Therefore, there is a need to develop and evaluate effective inter-professional education, which will address the need to educate patients in the correct use of their inhalers as well as equip health care professionals with skills to engage in collaborative relationships with each other.
This mixed methods study involves the development and evaluation of three modules of continuing education, Model 1, Model 2 and Model 3. A fourth group, Model 4, acting as a control.
Model 1 consists of face-to-face continuing professional education on asthma inhaler technique, aimed at pharmacists, general medical practitioners and their practice nurses.
Model 2 is an electronic online continuing education module based on Model 1 principles.
Model 3 is also based on asthma inhaler technique education but employs a learning intervention targeting health care professional relationships and is based on sociocultural theory.
This study took the form of a parallel group, repeated measure design. Following the completion of continuing professional education, health care professionals recruited people with asthma and followed them up for 6 months. During this period, inhaler device technique training was delivered and data on patient inhaler technique, clinical and humanistic outcomes were collected. Outcomes related to professional collaborative relationships were also measured.
Challenges presented included the requirement of significant financial resources for development of study materials and limited availability of validated tools to measure health care professional collaboration over time.
PMCID: PMC4234384  PMID: 24708800
11.  Medical Students' Exposure to and Attitudes about the Pharmaceutical Industry: A Systematic Review 
PLoS Medicine  2011;8(5):e1001037.
A systematic review of published studies reveals that undergraduate medical students may experience substantial exposure to pharmaceutical marketing, and that this contact may be associated with positive attitudes about marketing.
The relationship between health professionals and the pharmaceutical industry has become a source of controversy. Physicians' attitudes towards the industry can form early in their careers, but little is known about this key stage of development.
Methods and Findings
We performed a systematic review reported according to PRISMA guidelines to determine the frequency and nature of medical students' exposure to the drug industry, as well as students' attitudes concerning pharmaceutical policy issues. We searched MEDLINE, EMBASE, Web of Science, and ERIC from the earliest available dates through May 2010, as well as bibliographies of selected studies. We sought original studies that reported quantitative or qualitative data about medical students' exposure to pharmaceutical marketing, their attitudes about marketing practices, relationships with industry, and related pharmaceutical policy issues. Studies were separated, where possible, into those that addressed preclinical versus clinical training, and were quality rated using a standard methodology. Thirty-two studies met inclusion criteria. We found that 40%–100% of medical students reported interacting with the pharmaceutical industry. A substantial proportion of students (13%–69%) were reported as believing that gifts from industry influence prescribing. Eight studies reported a correlation between frequency of contact and favorable attitudes toward industry interactions. Students were more approving of gifts to physicians or medical students than to government officials. Certain attitudes appeared to change during medical school, though a time trend was not performed; for example, clinical students (53%–71%) were more likely than preclinical students (29%–62%) to report that promotional information helps educate about new drugs.
Undergraduate medical education provides substantial contact with pharmaceutical marketing, and the extent of such contact is associated with positive attitudes about marketing and skepticism about negative implications of these interactions. These results support future research into the association between exposure and attitudes, as well as any modifiable factors that contribute to attitudinal changes during medical education.
Please see later in the article for the Editors' Summary
Editors' Summary
The complex relationship between health professionals and the pharmaceutical industry has long been a subject of discussion among physicians and policymakers. There is a growing body of evidence that suggests that physicians' interactions with pharmaceutical sales representatives may influence clinical decision making in a way that is not always in the best interests of individual patients, for example, encouraging the use of expensive treatments that have no therapeutic advantage over less costly alternatives. The pharmaceutical industry often uses physician education as a marketing tool, as in the case of Continuing Medical Education courses that are designed to drive prescribing practices.
One reason that physicians may be particularly susceptible to pharmaceutical industry marketing messages is that doctors' attitudes towards the pharmaceutical industry may form early in their careers. The socialization effect of professional schooling is strong, and plays a lasting role in shaping views and behaviors.
Why Was This Study Done?
Recently, particularly in the US, some medical schools have limited students' and faculties' contact with industry, but some have argued that these restrictions are detrimental to students' education. Given the controversy over the pharmaceutical industry's role in undergraduate medical training, consolidating current knowledge in this area may be useful for setting priorities for changes to educational practices. In this study, the researchers systematically examined studies of pharmaceutical industry interactions with medical students and whether such interactions influenced students' views on related topics.
What Did the Researchers Do and Find?
The researchers did a comprehensive literature search using appropriate search terms for all relevant quantitative and qualitative studies published before June 2010. Using strict inclusion criteria, the researchers then selected 48 articles (from 1,603 abstracts) for full review and identified 32 eligible for analysis—giving a total of approximately 9,850 medical students studying at 76 medical schools or hospitals.
Most students had some form of interaction with the pharmaceutical industry but contact increased in the clinical years, with up to 90% of all clinical students receiving some form of educational material. The highest level of exposure occurred in the US. In most studies, the majority of students in their clinical training years found it ethically permissible for medical students to accept gifts from drug manufacturers, while a smaller percentage of preclinical students reported such attitudes. Students justified their entitlement to gifts by citing financial hardship or by asserting that most other students accepted gifts. In addition, although most students believed that education from industry sources is biased, students variably reported that information obtained from industry sources was useful and a valuable part of their education.
Almost two-thirds of students reported that they were immune to bias induced by promotion, gifts, or interactions with sales representatives but also reported that fellow medical students or doctors are influenced by such encounters. Eight studies reported a relationship between exposure to the pharmaceutical industry and positive attitudes about industry interactions and marketing strategies (although not all included supportive statistical data). Finally, student opinions were split on whether physician–industry interactions should be regulated by medical schools or the government.
What Do These Findings Mean?
This analysis shows that students are frequently exposed to pharmaceutical marketing, even in the preclinical years, and that the extent of students' contact with industry is generally associated with positive attitudes about marketing and skepticism towards any negative implications of interactions with industry. Therefore, strategies to educate students about interactions with the pharmaceutical industry should directly address widely held misconceptions about the effects of marketing and other biases that can emerge from industry interactions. But education alone may be insufficient. Institutional policies, such as rules regulating industry interactions, can play an important role in shaping students' attitudes, and interventions that decrease students' contact with industry and eliminate gifts may have a positive effect on building the skills that evidence-based medical practice requires. These changes can help cultivate strong professional values and instill in students a respect for scientific principles and critical evidence review that will later inform clinical decision-making and prescribing practices.
Additional Information
Please access these Web sites via the online version of this summary at
Further information about the influence of the pharmaceutical industry on doctors and medical students can be found at the American Medical Students Association PharmFree campaign and PharmFree Scorecard, Medsin-UKs PharmAware campaign, the nonprofit organization Healthy Skepticism, and the Web site of No Free Lunch.
PMCID: PMC3101205  PMID: 21629685
12.  Mobyle: a new full web bioinformatics framework 
Bioinformatics  2009;25(22):3005-3011.
Motivation: For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services: it is the user, again, who has to cope with data copy among a number of different services. A framework enabling portal administrators to build a network of cooperating services would therefore clearly be beneficial.
Results: We have designed a system, Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software. While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions.
Availability: The Mobyle system is distributed under the terms of the GNU GPLv2 on the project web site ( It is already deployed on three servers:, and The PlayMOBY companion is distributed under the terms of the CeCILL license, and is available at
Supplementary information:Supplementary data are available at Bioinformatics online.
PMCID: PMC2773253  PMID: 19689959
13.  InCoB2012 Conference: from biological data to knowledge to technological breakthroughs 
BMC Bioinformatics  2012;13(Suppl 17):S1.
Ten years ago when Asia-Pacific Bioinformatics Network held the first International Conference on Bioinformatics (InCoB) in Bangkok its theme was North-South Networking. At that time InCoB aimed to provide biologists and bioinformatics researchers in the Asia-Pacific region a forum to meet, interact with, and disseminate knowledge about the burgeoning field of bioinformatics. Meanwhile InCoB has evolved into a major regional bioinformatics conference that attracts not only talented and established scientists from the region but increasingly also from East Asia, North America and Europe. Since 2006 InCoB yielded 114 articles in BMC Bioinformatics supplement issues that have been cited nearly 1,000 times to date. In part, these developments reflect the success of bioinformatics education and continuous efforts to integrate and utilize bioinformatics in biotechnology and biosciences in the Asia-Pacific region. A cross-section of research leading from biological data to knowledge and to technological applications, the InCoB2012 theme, is introduced in this editorial. Other highlights included sessions organized by the Pan-Asian Pacific Genome Initiative and a Machine Learning in Immunology competition. InCoB2013 is scheduled for September 18-21, 2013 at Suzhou, China.
PMCID: PMC3521245  PMID: 23281929
14.  Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program 
Setting: Purdue University is a major agricultural, engineering, biomedical, and applied life science research institution with an increasing focus on bioinformatics research that spans multiple disciplines and campus academic units. The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus.
Program Components: After an extended period of information needs assessment and environmental scanning, the specialist developed a week of focused bioinformatics instruction (Bioinformatics Week) to launch system-wide, library-based bioinformatics services.
Evaluation Mechanisms: The specialist employed a two-tiered approach to assess user information requirements and expectations. The first phase involved careful observation and collection of information needs in-context throughout the campus, attending laboratory meetings, interviewing department chairs and individual researchers, and engaging in strategic planning efforts. Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning.
Next Steps/Future Directions: Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing bioinformatics support services for the Purdue community. The specialist is also engaged in training PUL faculty librarians in bioinformatics to provide a sustaining culture of library-based bioinformatics support and understanding of Purdue's bioinformatics-related decision and policy making.
PMCID: PMC1525331  PMID: 16888666
15.  The Long-Term Effects of a Peer-Led Sex Education Programme (RIPPLE): A Cluster Randomised Trial in Schools in England 
PLoS Medicine  2008;5(11):e224.
Peer-led sex education is widely believed to be an effective approach to reducing unsafe sex among young people, but reliable evidence from long-term studies is lacking. To assess the effectiveness of one form of school-based peer-led sex education in reducing unintended teenage pregnancy, we did a cluster (school) randomised trial with 7 y of follow-up.
Methods and Findings
Twenty-seven representative schools in England, with over 9,000 pupils aged 13–14 y at baseline, took part in the trial. Schools were randomised to either peer-led sex education (intervention) or to continue their usual teacher-led sex education (control). Peer educators, aged 16–17 y, were trained to deliver three 1-h classroom sessions of sex education to 13- to 14-y-old pupils from the same schools. The sessions used participatory learning methods designed to improve the younger pupils' skills in sexual communication and condom use and their knowledge about pregnancy, sexually transmitted infections (STIs), contraception, and local sexual health services. Main outcome measures were abortion and live births by age 20 y, determined by anonymised linkage of girls to routine (statutory) data. Assessment of these outcomes was blind to sex education allocation. The proportion of girls who had one or more abortions before age 20 y was the same in each arm (intervention, 5.0% [95% confidence interval (CI) 4.0%–6.3%]; control, 5.0% [95% CI 4.0%–6.4%]). The odds ratio (OR) adjusted for randomisation strata was 1.07 (95% CI 0.80–1.42, p = 0.64, intervention versus control). The proportion of girls with one or more live births by 20.5 y was 7.5% (95% CI 5.9%–9.6%) in the intervention arm and 10.6% (95% CI 6.8%–16.1%) in the control arm, adjusted OR 0.77 (0.51–1.15). Fewer girls in the peer-led arm self-reported a pregnancy by age 18 y (7.2% intervention versus 11.2% control, adjusted OR 0.62 [95% CI 0.42–0.91], weighted for non-response; response rate 61% intervention, 45% control). There were no significant differences for girls or boys in self-reported unprotected first sex, regretted or pressured sex, quality of current sexual relationship, diagnosed sexually transmitted diseases, or ability to identify local sexual health services.
Compared with conventional school sex education at age 13–14 y, this form of peer-led sex education was not associated with change in teenage abortions, but may have led to fewer teenage births and was popular with pupils. It merits consideration within broader teenage pregnancy prevention strategies.
Trial registration:
ISRCTN (ISRCTN94255362).
Judith Stephenson and colleagues report on a cluster randomized trial in London of school-based peer-led sex education and whether it reduced unintended teenage pregnancy.
Editors' Summary
Teenage pregnancies are fraught with problems. Children born to teenage mothers are often underweight, which can affect their long-term health; young mothers have a high risk of poor mental health after the birth; and teenage parents and their children are at increased risk of living in poverty. Little wonder, then, that faced with one of the highest teenage pregnancy rates in Western Europe, the Department of Health in England launched a national Teenage Pregnancy Strategy in 2000 to reduce teenage pregnancies. The main goal of the strategy is to halve the 1998 under-18 pregnancy rate—there were 46.6 pregnancies for every 1,000 young women in this age group in that year—by 2010. Approaches recommended in the strategy to achieve this goal include the provision of effective sexual health advice services for young people, active engagement of health, social, youth support, and other services in the reduction of teenage pregnancies, and the improvement of sex and relationships education (SRE).
Why Was This Study Done?
Although the annual under-18 pregnancy rate in England is falling, it is still very high, and it is extremely unlikely that the main goal of the Teenage Pregnancy Strategy will be achieved. Experts are, therefore, looking for better ways to reduce both teenage pregnancy rates and the high rates of sexual transmitted diseases among teenagers. Many believe that peer-led SRE—the teaching (sharing) of sexual health information, values, and behaviours by people of a similar age or status group—might be a good approach to try. Peers, they suggest, might convey information about sexual health and relationships better than teachers. However, little is known about the long-term effectiveness of peer-led SRE. In this randomized cluster trial, the researchers compare the effects of a peer-led SRE program and teacher-led sex education given to13- to 14-y-old pupils on abortion and live birth numbers among young women up to age 20 y. In a cluster randomized trial, participants are randomly assigned to the interventions being compared in “clusters”; in this trial, each “cluster” is a school.
What Did the Researchers Do and Find?
Twenty-seven schools in England (about 9,000 13- to 14-y-old pupils) participated in the RIPPLE (Randomized Intervention of PuPil-Led sex Education) trial. Each school was randomly assigned to peer-led SRE (the intervention arm) or to existing teacher-led SRE (the control arm). For peer-led SRE, trained 16- to 17-y-old peer educators gave three 1-h SRE sessions to the younger pupils in their schools. These sessions included practice with condoms, role play to improve sexual negotiating skills, and exercises to improve knowledge about sexual health. The researchers then used routine data on abortions and live births to find out how many female study participants had had an unintended pregnancy before the age of 20 y. One in 20 girls in both study arms had had one or more abortions. Slightly more girls in the control arm than in the intervention arm had had live births, but the difference was small and might have occurred by chance. However, significantly more girls in the intervention arm (11.2%) self-reported a pregnancy by age 18 than in the intervention arm (7.2%). There were no differences between the two arms for girls or boys in any other aspect of sexual health, including sexually transmitted diseases.
What Do These Findings Mean?
These findings indicate that the peer-led SRE program used in this trial had no effect on the number of teenage abortions but may have led to slightly fewer live births among the young women in the study. This particular peer-led SRE program was very short so a more extended program might have had a more marked effect on teenage pregnancy rates; this possibility needs to be tested, particularly since the pupils preferred peer-led SRE to teacher-led SRE. Even though peer-led SRE requires more resources than teacher-led SRE, this form of SRE should probably still be considered as part of a broad teenage prevention strategy, suggest the researchers. But, they warn, their findings should also “temper high expectations about the long-term impact of peer-led approaches” on young people's sexual health.
Additional Information.
Please access these Web sites via the online version of this summary at
This study is further discussed in a PLoS Medicine Perspective by David Ross
Every Child Matters, a Web site produced by the UK government, includes information on teenage pregnancy, the Teenage Pregnancy Strategy, and teenage pregnancy statistics in England
Directgov, an official government Web site for UK citizens, provides advice for parents on talking to children about sex and teenage pregnancyand advice for young people on sexual health and preventing pregnancy
Teachernet, a UK source of online publications for schools, also provides information for parents about sex and relationships education and the UK government's current guidance on SRE in schools
Avert, an international AIDS charity, also provides a fact sheet on sex education
The Sex Education Forum in the UK is the national authority on Sex and Relationships Education
PMCID: PMC2586352  PMID: 19067478
16.  Workflow management systems for gene sequence analysis and evolutionary studies – A Review 
Bioinformation  2013;9(13):663-672.
Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.
PMCID: PMC3732438  PMID: 23930017
Analysis; bioinformatics; databases; phylogeny; integration; workflows
17.  PowerPoint in the Classroom 
Cell Biology Education  2004;3(3):155-161.
Note from the Editors
Points of View (POV) addresses issues faced within life science education. Cell Biology Education has launched the POV feature to present two or more opinions published in tandem on a common topic. We consider POVs to be “Op-Ed” pieces designed to stimulate thought and dialog on significant educational issues. Each author has the opportunity to revise a POV after reading drafts of the other POVs. In this issue, we ask the question, “Is PowerPoint the best instructional medium to use in your class?” Everyone seems to have an opinion on Microsoft, but the intellectual merits of using PowerPoint (or similar software) is a growing question as states and institutions put more and more money into information technology and distance learning. Four POVs are presented: 1) David Keefe and James Willett provide their case why PowerPoint is an ideal teaching software. Keefe is an educational researcher at the Center for Technology in Learning at SRI International. Willett is a professor at George Mason University in the Departments of Microbial and Molecular Bioscience; as well as Bioinformatics and Computational Biology. 2) Kim McDonald highlights the causes of PowerPointlessness, a term which indicates the frequent use of PowerPoint as a crutch rather than a tool. She is a Bioscience Educator at the Shodor Education Foundation, Inc. 3) Diana Voss asks readers if PowerPoint is really necessary to present the material effectively or not. Voss is a Instructional Computing Support Specialist at SUNY Stony Brook. 4) Cynthia Lanius takes a light-hearted approach to ask whether PowerPoint is a technological improvement or just a change of pace for teacher and student presentations. Lanius is a Technology Integration Specialist in the Sinton (Texas) Independent School District. The authors span the range of teaching experiences and settings from which they bring different points of view to the debate. Readers are encouraged to participate in the online discussion forum hosted by CBE at and/or contact the authors directly.
PMCID: PMC520839  PMID: 15526063
18.  Social Networks in Education of Health Professionals in Bosnia and Herzegovina – the Role of Pubmed/Medline in Improvement of Medical Sciences 
Acta Informatica Medica  2011;19(4):196-202.
Social network is a social structure made up of individuals and organizations that represent “nodes”, and they are associated with one or more types of interdependency; such as: friendship, common interests, work, knowledge, prestige and many other interests. Beginning with the late twentieth and early twenty-first century, the Internet was a significant additional tool in the education of teenagers. Later, it takes more and more significant role in educating students and professionals.
The aim of this paper is to investigate, to what extent and how effectively the Internet is used today. In addition, more specifically, this paper will research the implications of the well-known social networks in education of students and health professionals in Bosnia and Herzegovina (B&H).
Material and methods:
We compared the ratio of using Medline, as the largest biomedical data base system for spreading medical information, as basics for health education at biomedical faculties at five universities in B&H.
Results and discussion:
According to data from the CRA (i.e. Communications Regulatory Agency) in B&H, in 2010, there were 522,364 internet access accounts, with about 2 million Internet users, representing about 52% of the total population. The Internet users’ preference is dominated by the users of fast broadband access (e.g. xDSL) with 42.8%, and elsewhere, still with dialup access, with 25.2%. The results showed that only 11.6% of professors use Facebook type of social network, 49.3% of them have a profile on BiomedExperts scientific social network and 79% have available articles in the largest biomedical literature database MEDLINE. Students are also frequent users of general social networks and educational clips from You Tube, which they prefer to utilize considerably more than the other types of professionals. Students rarely use the facilities of professional social networks, because they contain mainly data and information needed for further, postgraduate professional education. In our research, we analized cited published papers in the journal Medical Archives, the oldest medical journal in B&H (established in 1947) of randomly included 151 full and part time professors, authors from five medical faculties in B&H and B&H authors who currently work in the EU and USA.. ANOVA showed that there was no significant difference in the number of articles published between the Universities in Bosnia, but there was significant difference in the number of articles published on MEDLINE, between all faculties in B&H and a group of scientists who work around the world. Students’ tests showed that there was a statistically significant difference in the average number of papers published on Medline, between groups of part-time and full time professors. However, there were no statistically significant differences, between the professors for preclinical and clinical subjects.
In B&H there are decent conditions for the use of online social networks in the education of health professionals. While students enthusiastically embraced these opportunities, this is not so much a case with health care professionals in practice; while scientific health care workers have not shown greater interest in the use of social networks, both for purposes of scientific research and in terms of self-education and training of students. There is much more use of the advantages offered by online social networks, both in education and in support of the scientific research.
PMCID: PMC3564181  PMID: 23408513
Social networks; education; health professionals; students; Bosnia and Herzegovina.
19.  Implementing the 2009 Institute of Medicine recommendations on resident physician work hours, supervision, and safety 
Long working hours and sleep deprivation have been a facet of physician training in the US since the advent of the modern residency system. However, the scientific evidence linking fatigue with deficits in human performance, accidents and errors in industries from aeronautics to medicine, nuclear power, and transportation has mounted over the last 40 years. This evidence has also spawned regulations to help ensure public safety across safety-sensitive industries, with the notable exception of medicine.
In late 2007, at the behest of the US Congress, the Institute of Medicine embarked on a year-long examination of the scientific evidence linking resident physician sleep deprivation with clinical performance deficits and medical errors. The Institute of Medicine’s report, entitled “Resident duty hours: Enhancing sleep, supervision and safety”, published in January 2009, recommended new limits on resident physician work hours and workload, increased supervision, a heightened focus on resident physician safety, training in structured handovers and quality improvement, more rigorous external oversight of work hours and other aspects of residency training, and the identification of expanded funding sources necessary to implement the recommended reforms successfully and protect the public and resident physicians themselves from preventable harm.
Given that resident physicians comprise almost a quarter of all physicians who work in hospitals, and that taxpayers, through Medicare and Medicaid, fund graduate medical education, the public has a deep investment in physician training. Patients expect to receive safe, high-quality care in the nation’s teaching hospitals. Because it is their safety that is at issue, their voices should be central in policy decisions affecting patient safety. It is likewise important to integrate the perspectives of resident physicians, policy makers, and other constituencies in designing new policies. However, since its release, discussion of the Institute of Medicine report has been largely confined to the medical education community, led by the Accreditation Council for Graduate Medical Education (ACGME).
To begin gathering these perspectives and developing a plan to implement safer work hours for resident physicians, a conference entitled “Enhancing sleep, supervision and safety: What will it take to implement the Institute of Medicine recommendations?” was held at Harvard Medical School on June 17–18, 2010. This White Paper is a product of a diverse group of 26 representative stakeholders bringing relevant new information and innovative practices to bear on a critical patient safety problem. Given that our conference included experts from across disciplines with diverse perspectives and interests, not every recommendation was endorsed by each invited conference participant. However, every recommendation made here was endorsed by the majority of the group, and many were endorsed unanimously. Conference members participated in the process, reviewed the final product, and provided input before publication. Participants provided their individual perspectives, which do not necessarily represent the formal views of any organization.
In September 2010 the ACGME issued new rules to go into effect on July 1, 2011. Unfortunately, they stop considerably short of the Institute of Medicine’s recommendations and those endorsed by this conference. In particular, the ACGME only applied the limitation of 16 hours to first-year resident physicans. Thus, it is clear that policymakers, hospital administrators, and residency program directors who wish to implement safer health care systems must go far beyond what the ACGME will require. We hope this White Paper will serve as a guide and provide encouragement for that effort.
Resident physician workload and supervision
By the end of training, a resident physician should be able to practice independently. Yet much of resident physicians’ time is dominated by tasks with little educational value. The caseload can be so great that inadequate reflective time is left for learning based on clinical experiences. In addition, supervision is often vaguely defined and discontinuous. Medical malpractice data indicate that resident physicians are frequently named in lawsuits, most often for lack of supervision. The recommendations are: The ACGME should adjust resident physicians workload requirements to optimize educational value. Resident physicians as well as faculty should be involved in work redesign that eliminates nonessential and noneducational activity from resident physician dutiesMechanisms should be developed for identifying in real time when a resident physician’s workload is excessive, and processes developed to activate additional providersTeamwork should be actively encouraged in delivery of patient care. Historically, much of medical training has focused on individual knowledge, skills, and responsibility. As health care delivery has become more complex, it will be essential to train resident and attending physicians in effective teamwork that emphasizes collective responsibility for patient care and recognizes the signs, both individual and systemic, of a schedule and working conditions that are too demanding to be safeHospitals should embrace the opportunities that resident physician training redesign offers. Hospitals should recognize and act on the potential benefits of work redesign, eg, increased efficiency, reduced costs, improved quality of care, and resident physician and attending job satisfactionAttending physicians should supervise all hospital admissions. Resident physicians should directly discuss all admissions with attending physicians. Attending physicians should be both cognizant of and have input into the care patients are to receive upon admission to the hospitalInhouse supervision should be required for all critical care services, including emergency rooms, intensive care units, and trauma services. Resident physicians should not be left unsupervised to care for critically ill patients. In settings in which the acuity is high, physicians who have completed residency should provide direct supervision for resident physicians. Supervising physicians should always be physically in the hospital for supervision of resident physicians who care for critically ill patientsThe ACGME should explicitly define “good” supervision by specialty and by year of training. Explicit requirements for intensity and level of training for supervision of specific clinical scenarios should be providedCenters for Medicare and Medicaid Services (CMS) should use graduate medical education funding to provide incentives to programs with proven, effective levels of supervision. Although this action would require federal legislation, reimbursement rules would help to ensure that hospitals pay attention to the importance of good supervision and require it from their training programs
Resident physician work hours
Although the IOM “Sleep, supervision and safety” report provides a comprehensive review and discussion of all aspects of graduate medical education training, the report’s focal point is its recommendations regarding the hours that resident physicians are currently required to work. A considerable body of scientific evidence, much of it cited by the Institute of Medicine report, describes deteriorating performance in fatigued humans, as well as specific studies on resident physician fatigue and preventable medical errors.
The question before this conference was what work redesign and cultural changes are needed to reform work hours as recommended by the Institute of Medicine’s evidence-based report? Extensive scientific data demonstrate that shifts exceeding 12–16 hours without sleep are unsafe. Several principles should be followed in efforts to reduce consecutive hours below this level and achieve safer work schedules. The recommendations are: Limit resident physician work hours to 12–16 hour maximum shiftsA minimum of 10 hours off duty should be scheduled between shiftsResident physician input into work redesign should be actively solicitedSchedules should be designed that adhere to principles of sleep and circadian science; this includes careful consideration of the effects of multiple consecutive night shifts, and provision of adequate time off after night work, as specified in the IOM reportResident physicians should not be scheduled up to the maximum permissible limits; emergencies frequently occur that require resident physicians to stay longer than their scheduled shifts, and this should be anticipated in scheduling resident physicians’ work shiftsHospitals should anticipate the need for iterative improvement as new schedules are initiated; be prepared to learn from the initial phase-in, and change the plan as neededAs resident physician work hours are redesigned, attending physicians should also be considered; a potential consequence of resident physician work hour reduction and increased supervisory requirements may be an increase in work for attending physicians; this should be carefully monitored, and adjustments to attending physician work schedules made as needed to prevent unsafe work hours or working conditions for this group“Home call” should be brought under the overall limits of working hours; work load and hours should be monitored in each residency program to ensure that resident physicians and fellows on home call are getting sufficient sleepMedicare funding for graduate medical education in each hospital should be linked with adherence to the Institute of Medicine limits on resident physician work hours
Moonlighting by resident physicians
The Institute of Medicine report recommended including external as well as internal moonlighting in working hour limits. The recommendation is: All moonlighting work hours should be included in the ACGME working hour limits and actively monitored. Hospitals should formalize a moonlighting policy and establish systems for actively monitoring resident physician moonlighting
Safety of resident physicians
The “Sleep, supervision and safety” report also addresses fatigue-related harm done to resident physicians themselves. The report focuses on two main sources of physical injury to resident physicians impaired by fatigue, ie, needle-stick exposure to blood-borne pathogens and motor vehicle crashes. Providing safe transportation home for resident physicians is a logistical and financial challenge for hospitals. Educating physicians at all levels on the dangers of fatigue is clearly required to change driving behavior so that safe hospital-funded transport home is used effectively. Fatigue-related injury prevention (including not driving while drowsy) should be taught in medical school and during residency, and reinforced with attending physicians; hospitals and residency programs must be informed that resident physicians’ ability to judge their own level of impairment is impaired when they are sleep deprived; hence, leaving decisions about the capacity to drive to impaired resident physicians is not recommendedHospitals should provide transportation to all resident physicians who report feeling too tired to drive safely; in addition, although consecutive work should not exceed 16 hours, hospitals should provide transportation for all resident physicians who, because of unforeseen reasons or emergencies, work for longer than consecutive 24 hours; transportation under these circumstances should be automatically provided to house staff, and should not rely on self-identification or request
Training in effective handovers and quality improvement
Handover practice for resident physicians, attendings, and other health care providers has long been identified as a weak link in patient safety throughout health care settings. Policies to improve handovers of care must be tailored to fit the appropriate clinical scenario, recognizing that information overload can also be a problem. At the heart of improving handovers is the organizational effort to improve quality, an effort in which resident physicians have typically been insufficiently engaged. The recommendations are: Hospitals should train attending and resident physicians in effective handovers of careHospitals should create uniform processes for handovers that are tailored to meet each clinical setting; all handovers should be done verbally and face-to-face, but should also utilize written toolsWhen possible, hospitals should integrate hand-over tools into their electronic medical records (EMR) systems; these systems should be standardized to the extent possible across residency programs in a hospital, but may be tailored to the needs of specific programs and services; federal government should help subsidize adoption of electronic medical records by hospitals to improve signoutWhen feasible, handovers should be a team effort including nurses, patients, and familiesHospitals should include residents in their quality improvement and patient safety efforts; the ACGME should specify in their core competency requirements that resident physicians work on quality improvement projects; likewise, the Joint Commission should require that resident physicians be included in quality improvement and patient safety programs at teaching hospitals; hospital administrators and residency program directors should create opportunities for resident physicians to become involved in ongoing quality improvement projects and root cause analysis teams; feedback on successful quality improvement interventions should be shared with resident physicians and broadly disseminatedQuality improvement/patient safety concepts should be integral to the medical school curriculum; medical school deans should elevate the topics of patient safety, quality improvement, and teamwork; these concepts should be integrated throughout the medical school curriculum and reinforced throughout residency; mastery of these concepts by medical students should be tested on the United States Medical Licensing Examination (USMLE) stepsFederal government should support involvement of resident physicians in quality improvement efforts; initiatives to improve quality by including resident physicians in quality improvement projects should be financially supported by the Department of Health and Human Services
Monitoring and oversight of the ACGME
While the ACGME is a key stakeholder in residency training, external voices are essential to ensure that public interests are heard in the development and monitoring of standards. Consequently, the Institute of Medicine report recommended external oversight and monitoring through the Joint Commission and Centers for Medicare and Medicaid Services (CMS). The recommendations are: Make comprehensive fatigue management a Joint Commission National Patient Safety Goal; fatigue is a safety concern not only for resident physicians, but also for nurses, attending physicians, and other health care workers; the Joint Commission should seek to ensure that all health care workers, not just resident physicians, are working as safely as possibleFederal government, including the Centers for Medicare and Medicaid Services and the Agency for Healthcare Research and Quality, should encourage development of comprehensive fatigue management programs which all health systems would eventually be required to implementMake ACGME compliance with working hours a “ condition of participation” for reimbursement of direct and indirect graduate medical education costs; financial incentives will greatly increase the adoption of and compliance with ACGME standards
Future financial support for implementation
The Institute of Medicine’s report estimates that $1.7 billion (in 2008 dollars) would be needed to implement its recommendations. Twenty-five percent of that amount ($376 million) will be required just to bring hospitals into compliance with the existing 2003 ACGME rules. Downstream savings to the health care system could potentially result from safer care, but these benefits typically do not accrue to hospitals and residency programs, who have been asked historically to bear the burden of residency reform costs. The recommendations are: The Institute of Medicine should convene a panel of stakeholders, including private and public funders of health care and graduate medical education, to lay down the concrete steps necessary to identify and allocate the resources needed to implement the recommendations contained in the IOM “Resident duty hours: Enhancing sleep, supervision and safety” report. Conference participants suggested several approaches to engage public and private support for this initiativeEfforts to find additional funding to implement the Institute of Medicine recommendations should focus more broadly on patient safety and health care delivery reform; policy efforts focused narrowly upon resident physician work hours are less likely to succeed than broad patient safety initiatives that include residency redesign as a key componentHospitals should view the Institute of Medicine recommendations as an opportunity to begin resident physician work redesign projects as the core of a business model that embraces safety and ultimately saves resourcesBoth the Secretary of Health and Human Services and the Director of the Centers for Medicare and Medicaid Services should take the Institute of Medicine recommendations into consideration when promulgating rules for innovation grantsThe National Health Care Workforce Commission should consider the Institute of Medicine recommendations when analyzing the nation’s physician workforce needs
Recommendations for future research
Conference participants concurred that convening the stakeholders and agreeing on a research agenda was key. Some observed that some sectors within the medical education community have been reluctant to act on the data. Several logical funders for future research were identified. But above all agencies, Centers for Medicare and Medicaid Services is the only stakeholder that funds graduate medical education upstream and will reap savings downstream if preventable medical errors are reduced as a result of reform of resident physician work hours.
PMCID: PMC3630963  PMID: 23616719
resident; hospital; working hours; safety
20.  Bringing Web 2.0 to bioinformatics 
Briefings in Bioinformatics  2008;10(1):1-10.
Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.
PMCID: PMC2638627  PMID: 18842678
Web 2.0; bioinformatics; scientific social community; web service; pipelines
21.  TimeTree2: species divergence times on the iPhone 
Bioinformatics  2011;27(14):2023-2024.
Summary: Scientists, educators and the general public often need to know times of divergence between species. But they rarely can locate that information because it is buried in the scientific literature, usually in a format that is inaccessible to text search engines. We have developed a public knowledgebase that enables data-driven access to the collection of peer-reviewed publications in molecular evolution and phylogenetics that have reported estimates of time of divergence between species. Users can query the TimeTree resource by providing two names of organisms (common or scientific) that can correspond to species or groups of species. The current TimeTree web resource (TimeTree2) contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree2 interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website. Published time estimates are now readily accessible to the scientific community, K–12 and college educators, and the general public, without requiring knowledge of evolutionary nomenclature.
Availability: TimeTree2 is accessible from the URL, with an iPhone app available from iTunes ( and a YouTube tutorial (
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3129528  PMID: 21622662
22.  Online eLearning for undergraduates in health professions: A systematic review of the impact on knowledge, skills, attitudes and satisfaction 
Journal of Global Health  2014;4(1):010406.
Health systems worldwide are facing shortages in health professional workforce. Several studies have demonstrated the direct correlation between the availability of health workers, coverage of health services, and population health outcomes. To address this shortage, online eLearning is increasingly being adopted in health professionals’ education. To inform policy–making, in online eLearning, we need to determine its effectiveness.
We performed a systematic review of the effectiveness of online eLearning through a comprehensive search of the major databases for randomised controlled trials that compared online eLearning to traditional learning or alternative learning methods. The search period was from January 2000 to August 2013. We included articles which primarily focused on students' knowledge, skills, satisfaction and attitudes toward eLearning and cost-effectiveness and adverse effects as secondary outcomes. Two reviewers independently extracted data from the included studies. Due to significant heterogeneity among the included studies, we presented our results as a narrative synthesis.
Fifty–nine studies, including 6750 students enrolled in medicine, dentistry, nursing, physical therapy and pharmacy studies, met the inclusion criteria. Twelve of the 50 studies testing knowledge gains found significantly higher gains in the online eLearning intervention groups compared to traditional learning, whereas 27 did not detect significant differences or found mixed results. Eleven studies did not test for differences. Six studies detected significantly higher skill gains in the online eLearning intervention groups, whilst 3 other studies testing skill gains did not detect differences between groups and 1 study showed mixed results. Twelve studies tested students' attitudes, of which 8 studies showed no differences in attitudes or preferences for online eLearning. Students' satisfaction was measured in 29 studies, 4 studies showed higher satisfaction for online eLearning and 20 studies showed no difference in satisfaction between online eLearning and traditional learning. Risk of bias was high for several of the included studies.
The current evidence base suggests that online eLearning is equivalent, possibly superior to traditional learning. These findings present a potential incentive for policy makers to cautiously encourage its adoption, while respecting the heterogeneity among the studies.
PMCID: PMC4073252  PMID: 24976965
23.  The iPlant Collaborative: Cyberinfrastructure for Plant Biology 
The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.
PMCID: PMC3355756  PMID: 22645531
cyberinfrastructure; bioinformatics; plant biology; computational biology
24.  Promoting synergistic research and education in genomics and bioinformatics 
BMC Genomics  2008;9(Suppl 1):I1.
Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.
High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine ( and its official journals, the International Journal of Functional Informatics and Personalized Medicine ( and the International Journal of Computational Biology and Drug Design ( in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and scientific achievements by bridging these two very important disciplines into an interactive and attractive forum. Keeping this objective in mind, Biocomp 2007 aims to promote interdisciplinary and multidisciplinary education and research. 25 high quality peer-reviewed papers were selected from 400+ submissions for this supplementary issue of BMC Genomics. Those papers contributed to a wide-range of important research fields including gene expression data analysis and applications, high-throughput genome mapping, sequence analysis, gene regulation, protein structure prediction, disease prediction by machine learning techniques, systems biology, database and biological software development. We always encourage participants submitting proposals for genomics sessions, special interest research sessions, workshops and tutorials to Professor Hamid R. Arabnia ( in order to ensure that Biocomp continuously plays the leadership role in promoting inter/multidisciplinary research and education in the fields. Biocomp received top conference ranking with a high score of 0.95/1.00. Biocomp is academically co-sponsored by the International Society of Intelligent Biological Medicine and the Research Laboratories and Centers of Harvard University – Massachusetts Institute of Technology, Indiana University - Purdue University, Georgia Tech – Emory University, UIUC, UCLA, Columbia University, University of Texas at Austin and University of Iowa etc. Biocomp - Worldcomp brings leading scientists together across the nation and all over the world and aims to promote synergistic components such as keynote lectures, special interest sessions, workshops and tutorials in response to the advances of cutting-edge research.
PMCID: PMC3226105  PMID: 18366597
25.  Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community 
BMC Bioinformatics  2012;13:42.
A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure.
Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds.
Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.
PMCID: PMC3372431  PMID: 22429538

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