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1.  Eurocan plus report: feasibility study for coordination of national cancer research activities 
Summary
The EUROCAN+PLUS Project, called for by the European Parliament, was launched in October 2005 as a feasibility study for coordination of national cancer research activities in Europe. Over the course of the next two years, the Project process organized over 60 large meetings and countless smaller meetings that gathered in total over a thousand people, the largest Europe–wide consultation ever conducted in the field of cancer research.
Despite a strong tradition in biomedical science in Europe, fragmentation and lack of sustainability remain formidable challenges for implementing innovative cancer research and cancer care improvement. There is an enormous duplication of research effort in the Member States, which wastes time, wastes money and severely limits the total intellectual concentration on the wide cancer problem. There is a striking lack of communication between some of the biggest actors on the European scene, and there are palpable tensions between funders and those researchers seeking funds.
It is essential to include the patients’ voice in the establishment of priority areas in cancer research at the present time. The necessity to have dialogue between funders and scientists to establish the best mechanisms to meet the needs of the entire community is evident. A top priority should be the development of translational research (in its widest form), leading to the development of effective and innovative cancer treatments and preventive strategies. Translational research ranges from bench–to–bedside innovative cancer therapies and extends to include bringing about changes in population behaviours when a risk factor is established.
The EUROCAN+PLUS Project recommends the creation of a small, permanent and independent European Cancer Initiative (ECI). This should be a model structure and was widely supported at both General Assemblies of the project. The ECI should assume responsibility for stimulating innovative cancer research and facilitating processes, becoming the common voice of the cancer research community and serving as an interface between the cancer research community and European citizens, patients’ organizations, European institutions, Member States, industry and small and medium enterprises (SMEs), putting into practice solutions aimed at alleviating barriers to collaboration and coordination of cancer research activities in the European Union, and dealing with legal and regulatory issues. The development of an effective ECI will require time, but this entity should be established immediately. As an initial step, coordination efforts should be directed towards the creation of a platform on translational research that could encompass (1) coordination between basic, clinical and epidemiological research; (2) formal agreements of co–operation between comprehensive cancer centres and basic research laboratories throughout Europe and (3) networking between funding bodies at the European level.
The European Parliament and its instruments have had a major influence in cancer control in Europe, notably in tobacco control and in the implementation of effective population–based screening. To make further progress there is a need for novelty and innovation in cancer research and prevention in Europe, and having a platform such as the ECI, where those involved in all aspects of cancer research can meet, discuss and interact, is a decisive development for Europe.
Executive Summary
Cancer is one of the biggest public health crises facing Europe in the 21st century—one for which Europe is currently not prepared nor preparing itself. Cancer is a major cause of death in Europe with two million casualties and three million new cases diagnosed annually, and the situation is set to worsen as the population ages.
These facts led the European Parliament, through the Research Directorate-General of the European Commission, to call for initiatives for better coordination of cancer research efforts in the European Union. The EUROCAN+PLUS Project was launched in October 2005 as a feasibility study for coordination of national cancer research activities. Over the course of the next two years, the Project process organized over 60 large meetings and countless smaller meetings that gathered in total over a thousand people. In this respect, the Project became the largest Europe-wide consultation ever conducted in the field of cancer research, implicating researchers, cancer centres and hospitals, administrators, healthcare professionals, funding agencies, industry, patients’ organizations and patients.
The Project first identified barriers impeding research and collaboration in research in Europe. Despite a strong tradition in biomedical science in Europe, fragmentation and lack of sustainability remain the formidable challenges for implementing innovative cancer research and cancer care improvement. There is an enormous duplication of research effort in the Member States, which wastes time, wastes money and severely limits the total intellectual concentration on the wide cancer problem. There is a striking lack of communication between some of the biggest actors on the European scene, and there are palpable tensions between funders and those researchers seeking funds.
In addition, there is a shortage of leadership, a multiplicity of institutions each focusing on its own agenda, sub–optimal contact with industry, inadequate training, non–existent career paths, low personnel mobility in research especially among clinicians and inefficient funding—all conspiring against efficient collaboration in cancer care and research. European cancer research today does not have a functional translational research continuum, that is the process that exploits biomedical research innovations and converts them into prevention methods, diagnostic tools and therapies. Moreover, epidemiological research is not integrated with other types of cancer research, and the implementation of the European Directives on Clinical Trials 1 and on Personal Data Protection 2 has further slowed the innovation process in Europe. Furthermore, large inequalities in health and research exist between the EU–15 and the New Member States.
The picture is not entirely bleak, however, as the European cancer research scene presents several strengths, such as excellent basic research and clinical research and innovative etiological research that should be better exploited.
When considering recommendations, several priority dimensions had to be retained. It is essential that proposals include actions and recommendations that can benefit all Member States of the European Union and not just States with the elite centres. It is also essential to have a broader patient orientation to help provide the knowledge to establish cancer control possibilities when we exhaust what can be achieved by the implementation of current knowledge. It is vital that the actions proposed can contribute to the Lisbon Strategy to make Europe more innovative and competitive in (cancer) research.
The Project participants identified six areas for which consensus solutions should be implemented in order to obtain better coordination of cancer research activities. The required solutions are as follows. The proactive management of innovation, detection, facilitation of collaborations and maintenance of healthy competition within the European cancer research community.The establishment of an exchange portal of information for health professionals, patients and policy makers.The provision of guidance for translational and clinical research including the establishment of a translational research platform involving comprehensive cancer centres and cancer research centres.The coordination of calls and financial management of cancer research projects.The construction of a ‘one–stop shop’ as a contact interface between the industry, small and medium enterprises, scientists and other stakeholders.The support of greater involvement of healthcare professionals in translational research and multidisciplinary training.
In the course of the EUROCAN+PLUS consultative process, several key collaborative projects emerged between the various groups and institutes engaged in the consultation. There was a collaboration network established with Europe’s leading Comprehensive Cancer Centres; funding was awarded for a closer collaboration of Owners of Cancer Registries in Europe (EUROCOURSE); there was funding received from FP7 for an extensive network of leading Biological Resource Centres in Europe (BBMRI); a Working Group identified the special needs of Central, Eastern and South–eastern Europe and proposed a remedy (‘Warsaw Declaration’), and the concept of developing a one–stop shop for dealing with academia and industry including the Innovative Medicines Initiative (IMI) was discussed in detail.
Several other dimensions currently lacking were identified. There is an absolute necessity to include the patients’ voice in the establishment of priority areas in cancer research at the present time. It was a salutary lesson when it was recognized that all that is known about the quality of life of the cancer patient comes from the experience of a tiny proportion of cancer patients included in a few clinical trials. The necessity to have dialogue between funders and scientists to establish the best mechanisms to meet the needs of the entire community was evident. A top priority should be the development of translational research (in its widest form) and the development of effective and innovative cancer treatments and preventative strategies in the European Union. Translational research ranges from bench-to-bedside innovative cancer therapies and extends to include bringing about changes in population behaviours when a risk factor is established.
Having taken note of the barriers and the solutions and having examined relevant examples of existing European organizations in the field, it was agreed during the General Assembly of 19 November 2007 that the EUROCAN+PLUS Project had to recommend the creation of a small, permanent and neutral ECI. This should be a model structure and was widely supported at both General Assemblies of the project. The proposal is based on the successful model of the European Molecular Biology Organisation (EMBO), and its principal aims include providing a forum where researchers from all backgrounds and from all countries can meet with members of other specialities including patients, nurses, clinicians, funders and scientific administrators to develop priority programmes to make Europe more competitive in research and more focused on the cancer patient.
The ECI should assume responsibility for: stimulating innovative cancer research and facilitating processes;becoming the common voice of the cancer research community and serving as an interface between the cancer research community and European citizens, patients’ and organizations;European institutions, Member States, industry and small and medium enterprises;putting into practice the aforementioned solutions aimed at alleviating barriers and coordinating cancer research activities in the EU;dealing with legal and regulatory issues.
Solutions implemented through the ECI will lead to better coordination and collaboration throughout Europe, more efficient use of resources, an increase in Europe’s attractiveness to the biomedical industry and better quality of cancer research and education of health professionals.
The Project considered that European legal instruments currently available were inadequate for addressing many aspects of the barriers identified and for the implementation of effective, lasting solutions. Therefore, the legal environment that could shelter an idea like the ECI remains to be defined but should be done so as a priority. In this context, the initiative of the European Commission for a new legal entity for research infrastructure might be a step in this direction. The development of an effective ECI will require time, but this should be established immediately. As an initial step, coordination efforts should be directed towards the creation of a platform on translational research that could encompass: (1) coordination between basic, clinical and epidemiological research; (2) formal agreements of co-operation between comprehensive cancer centres and basic research laboratories throughout Europe; (3) networking between funding bodies at the European level. Another topic deserving immediate attention is the creation of a European database on cancer research projects and cancer research facilities.
Despite enormous progress in cancer control in Europe during the past two decades, there was an increase of 300,000 in the number of new cases of cancer diagnosed between 2004 and 2006. The European Parliament and its instruments have had a major influence in cancer control, notably in tobacco control and in the implementation of effective population–based screening. To make further progress there is a need for novelty and innovation in cancer research and prevention in Europe, and having a platform such as the ECI, where those involved in all aspects of cancer research can meet, discuss and interact, is a decisive development for Europe.
doi:10.3332/ecancer.2011.84
PMCID: PMC3234055  PMID: 22274749
2.  A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era 
BMC Genomics  2009;10(Suppl 3):S36.
Background
The development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements of various cellular and molecular phenomena pose considerable challenges in data processing and extraction of biological meaning. Moreover, it has created an unmet need for the effective integration of these datasets to achieve insights into biological systems. While it has increased the demand for bioinformatics experts who can interface with biologists, it has also raised the requirement for biologists to possess a basic capability in bioinformatics and to communicate seamlessly with these experts. This may be achieved by embedding in their undergraduate and graduate life science education, basic training in bioinformatics geared towards acquiring a minimum skill set in computation and informatics.
Results
Based on previous attempts to define curricula suitable for addressing the bioinformatics capability gap, an initiative was taken during the Workshops on Education in Bioinformatics and Computational Biology (WEBCB) in 2008 and 2009 to identify a minimum skill set for the training of future bioinformaticians and molecular biologists with informatics capabilities. The minimum skill set proposed is cross-disciplinary in nature, involving a combination of knowledge and proficiency from the fields of biology, computer science, mathematics and statistics, and can be tailored to the needs of the "-omics".
Conclusion
The proposed bioinformatics minimum skill set serves as a guideline for biology curriculum design and development in universities at both the undergraduate and graduate levels.
doi:10.1186/1471-2164-10-S3-S36
PMCID: PMC2788390  PMID: 19958501
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.
doi:10.1093/bib/bbt022
PMCID: PMC3771231  PMID: 23543352
training; next-generation sequencing; NGS; cloud; workshop
4.  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.
Background
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.
Conclusions
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
Background
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 http://dx.doi.org/10.1371/journal.pmed.1001037.
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.
doi:10.1371/journal.pmed.1001037
PMCID: PMC3101205  PMID: 21629685
5.  BioMoby extensions to the Taverna workflow management and enactment software 
BMC Bioinformatics  2006;7:523.
Background
As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface.
Results
The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate.
Conclusion
With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.
doi:10.1186/1471-2105-7-523
PMCID: PMC1693925  PMID: 17137515
6.  Professional Uncertainty and Disempowerment Responding to Ethnic Diversity in Health Care: A Qualitative Study 
PLoS Medicine  2007;4(11):e323.
Background
While ethnic disparities in health and health care are increasing, evidence on how to enhance quality of care and reduce inequalities remains limited. Despite growth in the scope and application of guidelines on “cultural competence,” remarkably little is known about how practising health professionals experience and perceive their work with patients from diverse ethnic communities. Using cancer care as a clinical context, we aimed to explore this with a range of health professionals to inform interventions to enhance quality of care.
Methods and Findings
We conducted a qualitative study involving 18 focus groups with a purposeful sample of 106 health professionals of differing disciplines, in primary and secondary care settings, working with patient populations of varying ethnic diversity in the Midlands of the UK. Data were analysed by constant comparison and we undertook processes for validation of analysis. We found that, as they sought to offer appropriate care, health professionals wrestled with considerable uncertainty and apprehension in responding to the needs of patients of ethnicities different from their own. They emphasised their perceived ignorance about cultural difference and were anxious about being culturally inappropriate, causing affront, or appearing discriminatory or racist. Professionals' ability to think and act flexibly or creatively faltered. Although trying to do their best, professionals' uncertainty was disempowering, creating a disabling hesitancy and inertia in their practice. Most professionals sought and applied a knowledge-based cultural expertise approach to patients, though some identified the risk of engendering stereotypical expectations of patients. Professionals' uncertainty and disempowerment had the potential to perpetuate each other, to the detriment of patient care.
Conclusions
This study suggests potential mechanisms by which health professionals may inadvertently contribute to ethnic disparities in health care. It identifies critical opportunities to empower health professionals to respond more effectively. Interventions should help professionals acknowledge their uncertainty and its potential to create inertia in their practice. A shift away from a cultural expertise model toward a greater focus on each patient as an individual may help.
From a qualitative study, Joe Kai and colleagues have identified opportunities to empower health professionals to respond more effectively to challenges in their work with patients from diverse ethnic communities.
Editors' Summary
Background.
Communities are increasingly diverse in terms of ethnicity (belonging to a group of people defined by social characteristics such as cultural tradition or national origin) and race (belonging to a group identified by inherited physical characteristics). Although health professionals and governments are striving to ensure that everybody has the same access to health care, there is increasing evidence of ethnic inequalities in health-care outcomes. Some of these inequalities reflect intrinsic differences between groups of people—Ashkenazi Jews, for example, often carry an altered gene that increases their chance of developing aggressive breast cancer. Often, however, these differences reflect inequalities in the health care received by different ethnic groups. To improve this situation, “cultural competence” has been promoted over recent years. Cultural competence is the development of skills by individuals and organizations that allow them to work effectively with people from different cultures. Health professionals are now taught about ethnic differences in health beliefs and practices, religion, and communication styles to help them provide the best service to all their patients.
Why Was This Study Done?
Numerous guidelines aim to improve cultural competency but little is known about how health professionals experience and perceive their work with patients from diverse ethnic groups. Is their behavior influenced by ethnicity in ways that might contribute to health care disparities? For example, do doctors sometimes avoid medical examinations for fear of causing offence because of cultural differences? If more were known about how health professionals handle ethnic diversity (a term used here to include both ethnicity and race) it might be possible to reduce ethnic inequalities in health care. In this qualitative study, the researchers have explored how health professionals involved in cancer care are affected by working with ethnically diverse patients. A qualitative study is one that collects nonquantitative data such as how doctors “feel” about treating people of different ethnic backgrounds; a quantitative study might compare clinical outcomes in different ethnic groups.
What Did the Researchers Do and Find?
The researchers enrolled 106 doctors, nurses, and other health-related professionals from different health-service settings in the Midlands, an ethnically diverse region of the UK. They organized 18 focus groups in which the health professionals described their experiences of caring for people from ethnic minority backgrounds. The participants were encouraged to recall actual cases and to identify what they saw as problems and strengths in their interactions with these patients. The researchers found that the health professionals wrestled with many challenges when providing health care for patients from diverse ethnic backgrounds. These challenges included problems with language and with general communication (for example, deciding when it was acceptable to touch a patient to show empathy). Health professionals also worried they did not know enough about cultural differences. As a result, they said they often felt uncertain of their ability to avoid causing affront or appearing racist. This uncertainty, the researchers report, disempowered the health professionals, sometimes making them hesitate or fail to do what was best for their patient.
What Do These Findings Mean?
These findings reveal that health professionals often experience considerable uncertainty when caring for ethnically diverse patients, even after training in cultural competency. They also show that this uncertainty can lead to hesitancy and inertia, which might contribute to ethnic health care inequalities. Because the study participants were probably already interested in ethnic diversity and health care, interviews with other health professionals (and investigations of patient experiences) are needed to confirm these findings. Nevertheless, the researchers suggest several interventions that might reduce health care inequalities caused by ethnic diversity. For example, health professionals should be encouraged to recognize their uncertainty and should have access to more information and training about ethnic differences. In addition, there should be a shift in emphasis away from relying on knowledge-based cultural information towards taking an “ethnographic” approach. In other words, health professionals should be helped to feel able to ask their patients about what matters most to them as individuals about their illness and treatment.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040323.
Information on cultural competence and health care is available from the US National Center for Cultural Competence (in English and Spanish) and DiversityRx
PROCEED (Professionals Responding to Cancer in Ethnic Diversity) is a multimedia training tool for educators within the health and allied professions developed from the results of this study; a press release on PROCEED is available from the University of Nottingham
Transcultural Health Care Practice: An educational resource for nurses and health care practitioners is available on the web site of the UK Royal College of Nursing
doi:10.1371/journal.pmed.0040323
PMCID: PMC2071935  PMID: 18001148
7.  The GMOD Drupal Bioinformatic Server Framework 
Bioinformatics  2010;26(24):3119-3124.
Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS).
Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community.
Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished.
Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com
Contact: alexie@butterflybase.org
doi:10.1093/bioinformatics/btq599
PMCID: PMC2995126  PMID: 20971988
8.  The Role of the Toxicologic Pathologist in the Post-Genomic Era# 
Journal of Toxicologic Pathology  2013;26(2):105-110.
An era can be defined as a period in time identified by distinctive character, events, or practices. We are now in the genomic era. The pre-genomic era: There was a pre-genomic era. It started many years ago with novel and seminal animal experiments, primarily directed at studying cancer. It is marked by the development of the two-year rodent cancer bioassay and the ultimate realization that alternative approaches and short-term animal models were needed to replace this resource-intensive and time-consuming method for predicting human health risk. Many alternatives approaches and short-term animal models were proposed and tried but, to date, none have completely replaced our dependence upon the two-year rodent bioassay. However, the alternative approaches and models themselves have made tangible contributions to basic research, clinical medicine and to our understanding of cancer and they remain useful tools to address hypothesis-driven research questions. The pre-genomic era was a time when toxicologic pathologists played a major role in drug development, evaluating the cancer bioassay and the associated dose-setting toxicity studies, and exploring the utility of proposed alternative animal models. It was a time when there was shortage of qualified toxicologic pathologists. The genomic era: We are in the genomic era. It is a time when the genetic underpinnings of normal biological and pathologic processes are being discovered and documented. It is a time for sequencing entire genomes and deliberately silencing relevant segments of the mouse genome to see what each segment controls and if that silencing leads to increased susceptibility to disease. What remains to be charted in this genomic era is the complex interaction of genes, gene segments, post-translational modifications of encoded proteins, and environmental factors that affect genomic expression. In this current genomic era, the toxicologic pathologist has had to make room for a growing population of molecular biologists. In this present era newly emerging DVM and MD scientists enter the work arena with a PhD in pathology often based on some aspect of molecular biology or molecular pathology research. In molecular biology, the almost daily technological advances require one’s complete dedication to remain at the cutting edge of the science. Similarly, the practice of toxicologic pathology, like other morphological disciplines, is based largely on experience and requires dedicated daily examination of pathology material to maintain a well-trained eye capable of distilling specific information from stained tissue slides - a dedicated effort that cannot be well done as an intermezzo between other tasks. It is a rare individual that has true expertise in both molecular biology and pathology. In this genomic era, the newly emerging DVM-PhD or MD-PhD pathologist enters a marketplace without many job opportunities in contrast to the pre-genomic era. Many face an identity crisis needing to decide to become a competent pathologist or, alternatively, to become a competent molecular biologist. At the same time, more PhD molecular biologists without training in pathology are members of the research teams working in drug development and toxicology. How best can the toxicologic pathologist interact in the contemporary team approach in drug development, toxicology research and safety testing? Based on their biomedical training, toxicologic pathologists are in an ideal position to link data from the emerging technologies with their knowledge of pathobiology and toxicology. To enable this linkage and obtain the synergy it provides, the bench-level, slide-reading expert pathologist will need to have some basic understanding and appreciation of molecular biology methods and tools. On the other hand, it is not likely that the typical molecular biologist could competently evaluate and diagnose stained tissue slides from a toxicology study or a cancer bioassay. The post-genomic era: The post-genomic era will likely arrive approximately around 2050 at which time entire genomes from multiple species will exist in massive databases, data from thousands of robotic high throughput chemical screenings will exist in other databases, genetic toxicity and chemical structure-activity-relationships will reside in yet other databases. All databases will be linked and relevant information will be extracted and analyzed by appropriate algorithms following input of the latest molecular, submolecular, genetic, experimental, pathology and clinical data. Knowledge gained will permit the genetic components of many diseases to be amenable to therapeutic prevention and/or intervention. Much like computerized algorithms are currently used to forecast weather or to predict political elections, computerized sophisticated algorithms based largely on scientific data mining will categorize new drugs and chemicals relative to their health benefits versus their health risks for defined human populations and subpopulations. However, this form of a virtual toxicity study or cancer bioassay will only identify probabilities of adverse consequences from interaction of particular environmental and/or chemical/drug exposure(s) with specific genomic variables. Proof in many situations will require confirmation in intact in vivo mammalian animal models. The toxicologic pathologist in the post-genomic era will be the best suited scientist to confirm the data mining and its probability predictions for safety or adverse consequences with the actual tissue morphological features in test species that define specific test agent pathobiology and human health risk.
doi:10.1293/tox.26.105
PMCID: PMC3695332  PMID: 23914052
genomic era; history of toxicologic pathology; molecular biology
9.  The Instituto Gulbenkian de Ciência and its Outreach 
The Instituto Gulbenkian de Ciência (IGC) is biomedical research institute that acts as a host institution for small research groups, in Portugal. Most of its activities reach out to the scientific community in several ways. The IGC organizes regular series of seminars with invited international speakers, workshops, courses and conferences, and an in-house PhD programme. Specific outreach needs had to be met in the two instances that are described here.
GTPB
The Gulbenkian Training Programme in Bioinformatics (GTPB) started as a regular activity in 1999 in response to the demand of users seeking opportunities to acquire hands-on practical skills in Bioinformatics in an effective way. Training provision in Bioinformatics requires the conciliation of a variety of interests into a series of highly effective training events, in which scientists can acquire skills and a high degree of independence in their usage. The GTPB programme currently offers more than 30 themes, of which 15 to 20 are chosen for single events in each year. The GTPB has provided training to more than 2000 researchers and students, so far.
IGC Outreach
A dedicated outreach programme targets science education and public engagement in science, for different audience groups. The aim of the outreach programme is to promote scientific literacy, foster careers in science and empower citizens to engage in cutting-edge biomedical research. Activities include Open Days, seminars and laboratory workshops for teachers, development of online, multimedia and hard-copy resources and experimental protocols to be used in schools, visits to schools with hands-on experiments and career talks by researchers and facility staff. Less conventional outreach activities include direct participation in venues for the general public (such a a music festival, for example) have created unexpected opportunities for fundraising and direct financial support for students engaged in research projects.
PMCID: PMC3630688
10.  Chapter 3: Small Molecules and Disease 
PLoS Computational Biology  2012;8(12):e1002805.
“Big” molecules such as proteins and genes still continue to capture the imagination of most biologists, biochemists and bioinformaticians. “Small” molecules, on the other hand, are the molecules that most biologists, biochemists and bioinformaticians prefer to ignore. However, it is becoming increasingly apparent that small molecules such as amino acids, lipids and sugars play a far more important role in all aspects of disease etiology and disease treatment than we realized. This particular chapter focuses on an emerging field of bioinformatics called “chemical bioinformatics” – a discipline that has evolved to help address the blended chemical and molecular biological needs of toxicogenomics, pharmacogenomics, metabolomics and systems biology. In the following pages we will cover several topics related to chemical bioinformatics. First, a brief overview of some of the most important or useful chemical bioinformatic resources will be given. Second, a more detailed overview will be given on those particular resources that allow researchers to connect small molecules to diseases. This section will focus on describing a number of recently developed databases or knowledgebases that explicitly relate small molecules – either as the treatment, symptom or cause – to disease. Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease.
doi:10.1371/journal.pcbi.1002805
PMCID: PMC3531289  PMID: 23300405
11.  Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers 
Briefings in Bioinformatics  2011;13(3):383-389.
Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.
doi:10.1093/bib/bbr064
PMCID: PMC3357490  PMID: 22110242
Bioinformatics; training; end users; bioinformatics courses; learning bioinformatics
12.  The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability 
Briefings in Bioinformatics  2013;14(5):548-555.
Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.
doi:10.1093/bib/bbt045
PMCID: PMC3771235  PMID: 23793381
next-generation sequencing; bioinformatics; training; collaborative learning; best practice
13.  Visualising biological data: a semantic approach to tool and database integration 
BMC Bioinformatics  2009;10(Suppl 6):S19.
Motivation
In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held remotely on the internet or locally on in-house servers. Supporting these tasks are ad hoc collections of data-manipulation tools, scripting languages and visualisation software, which are often combined in arcane ways to create cumbersome systems that have been customised for a particular purpose, and are consequently not readily adaptable to other uses. For many day-to-day bioinformatics tasks, the sizes of current databases, and the scale of the analyses necessary, now demand increasing levels of automation; nevertheless, the unique experience and intuition of human researchers is still required to interpret the end results in any meaningful biological way. Putting humans in the loop requires tools to support real-time interaction with these vast and complex data-sets. Numerous tools do exist for this purpose, but many do not have optimal interfaces, most are effectively isolated from other tools and databases owing to incompatible data formats, and many have limited real-time performance when applied to realistically large data-sets: much of the user's cognitive capacity is therefore focused on controlling the software and manipulating esoteric file formats rather than on performing the research.
Methods
To confront these issues, harnessing expertise in human-computer interaction (HCI), high-performance rendering and distributed systems, and guided by bioinformaticians and end-user biologists, we are building reusable software components that, together, create a toolkit that is both architecturally sound from a computing point of view, and addresses both user and developer requirements. Key to the system's usability is its direct exploitation of semantics, which, crucially, gives individual components knowledge of their own functionality and allows them to interoperate seamlessly, removing many of the existing barriers and bottlenecks from standard bioinformatics tasks.
Results
The toolkit, named Utopia, is freely available from .
doi:10.1186/1471-2105-10-S6-S19
PMCID: PMC2697642  PMID: 19534744
14.  The U.S. training institute for dissemination and implementation research in health 
Background
The science of dissemination and implementation (D&I) is advancing the knowledge base for how best to integrate evidence-based interventions within clinical and community settings and how to recast the nature or conduct of the research itself to make it more relevant and actionable in those settings. While the field is growing, there are only a few training programs for D&I research; this is an important avenue to help build the field’s capacity. To improve the United States’ capacity for D&I research, the National Institutes of Health and Veterans Health Administration collaborated to develop a five-day training institute for postdoctoral level applicants aspiring to advance this science.
Methods
We describe the background, goals, structure, curriculum, application process, trainee evaluation, and future plans for the Training in Dissemination and Implementation Research in Health (TIDIRH).
Results
The TIDIRH used a five-day residential immersion to maximize opportunities for trainees and faculty to interact. The train-the-trainer-like approach was intended to equip participants with materials that they could readily take back to their home institutions to increase interest and further investment in D&I. The TIDIRH curriculum included a balance of structured large group discussions and interactive small group sessions.
Thirty-five of 266 applicants for the first annual training institute were accepted from a variety of disciplines, including psychology (12 trainees); medicine (6 trainees); epidemiology (5 trainees); health behavior/health education (4 trainees); and 1 trainee each from education & human development, health policy and management, health services research, public health studies, public policy and social work, with a maximum of two individuals from any one institution. The institute was rated as very helpful by attendees, and by six months after the institute, a follow-up survey (97% return rate) revealed that 72% had initiated a new grant proposal in D&I research; 28% had received funding, and 77% had used skills from TIDIRH to influence their peers from different disciplines about D&I research through building local research networks, organizing formal presentations and symposia, teaching and by leading interdisciplinary teams to conduct D&I research.
Conclusions
The initial TIDIRH training was judged successful by trainee evaluation at the conclusion of the week’s training and six-month follow-up, and plans are to continue and possibly expand the TIDIRH in coming years. Strengths are seen as the residential format, quality of the faculty and their flexibility in adjusting content to meet trainee needs, and the highlighting of concrete D&I examples by the local host institution, which rotates annually. Lessons learned and plans for future TIDIRH trainings are summarized.
doi:10.1186/1748-5908-8-12
PMCID: PMC3564839  PMID: 23347882
Training; Dissemination; Implementation
15.  Attitudes and experiences of residents in pursuit of postgraduate fellowships: A national survey of Canadian trainees 
Introduction:
There have been significant pressures on urology training in North America over the last decade due to both the constantly evolving skill set required and the external demands around delivery of urological care, particularly in Canada. We explore the attitudes and experience of Canadian urology residents toward their postgraduate decisions on fellowship opportunities.
Methods:
The study consisted of a self-report questionnaire of 4 separate cohorts of graduating urology residents from 2008 to 2011. The first cohort graduating in 2008 and 2009 were sent surveys through SurveyMonkey.com after graduation from residency; those graduating in 2010 and 2011 were prospectively invited as a convenience sample attending a Queen’s Urology Examination Skills Training Program review course just prior to graduation. The survey included both open- and closed-ended questions, employing a 5-point Likert scale, and explored the attitudes and experience of fellowship choices. Likert scores for each question were reported as means ± standard deviation (SD). Descriptive and correlative statistics were used to analyze the responses. In addition, an agreement score was created for those responding with “strongly agree” and “agree” on the Likert scale.
Results:
A total of 104 surveys were administered, with 84 respondents (80.8% response rate). As a whole, 84.9% of respondents agreed that they pursued fellowships; oncology and minimally invasive urology were the most popular choices throughout the 4 years. Respondents stated that reasons for pursuing a fellowship included: interest in pursuing an academic career (mean 3.73± 1.1 (SD): agreement score 61.1%) as well as acquiring marketable skills to obtain an urology position (3.59 ± 1.3: 64.4%). Most agreed or strongly agreed (84.9%) that a reason for pursing a fellowship was an interest in focusing their practice to this sub-specialty area. In comparison, most graduates disagreed that a reason for pursuing a fellowship was that residency did not equip them with the necessary skills to practice urology (2.49 ± 1.2: 19%). Most (81.2%) of graduates agreed they knew enough about academic urology to know if it would be a suitable career choice for them versus 54.7% regarding community urology (p < 0.0001). Surprisingly, only 61.7% of residents agreed that they completed a community elective during training, and most felt they would have benefited from additional elective time in the community.
Conclusions:
Urology residents graduating from Canadian programs pursue postgraduate training to enhance their surgical skill set and to achieve marketability, but also to facilitate a potential academic career. Responses from the trainees suggest that exposure to community practice appears suboptimal and may be an area of focus for programs to aid in career counselling and professional development.
doi:10.5489/cuaj.2136
PMCID: PMC4277525  PMID: 25553159
16.  Perspectives on an Education in Computational Biology and Medicine 
The mainstream application of massively parallel, high-throughput assays in biomedical research has created a demand for scientists educated in Computational Biology and Bioinformatics (CBB). In response, formalized graduate programs have rapidly evolved over the past decade. Concurrently, there is increasing need for clinicians trained to oversee the responsible translation of CBB research into clinical tools. Physician-scientists with dedicated CBB training can facilitate such translation, positioning themselves at the intersection between computational biomedical research and medicine. This perspective explores key elements of the educational path to such a position, specifically addressing: 1) evolving perceptions of the role of the computational biologist and the impact on training and career opportunities; 2) challenges in and strategies for obtaining the core skill set required of a biomedical researcher in a computational world; and 3) how the combination of CBB with medical training provides a logical foundation for a career in academic medicine and/or biomedical research.
PMCID: PMC3447197  PMID: 23012581
computational biology; bioinformatics; graduate education; MD/PhD
17.  A Quick Guide for Building a Successful Bioinformatics Community 
PLoS Computational Biology  2015;11(2):e1003972.
“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).
doi:10.1371/journal.pcbi.1003972
PMCID: PMC4318577  PMID: 25654371
18.  Mathematics and evolutionary biology make bioinformatics education comprehensible 
Briefings in Bioinformatics  2013;14(5):599-609.
The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.
doi:10.1093/bib/bbt046
PMCID: PMC3771232  PMID: 23821621
bioinformatics education; discrete mathematics; quantitative reasoning; off-line downloadable free and open-source software; evolutionary problem solving
19.  Everything you were afraid to ask about communication skills 
‘Communication skills’ is now very well established in medical education as an area that needs to be taught at both undergraduate and postgraduate level. But it is a discipline with a low level of challenge — it allows itself constantly to take seriously questions about its fundamentals (such as whether it works at all) although common sense and everyday experience tell us that skills are indeed improved through training and practice. This slows progress. Much research has also concentrated on listing and defining a set of skills, yet although all doctors must understand and utilise a range of skills as a precondition for good communication, the findings themselves are often equally common-sensical, and are not, in any case, restricted to medicine. They often tend to form part of a general consensus in favour of lay-centredness, which has been studied in other types of professional encounter, particularly the language of teachers and pupils. Moreover, insofar as teachers of medical communication limit their aims and their own classroom language to terms associated with skills, they offer little scope for more important questions about how these skills should be deployed, and about the attitudes to medicine and professional life that underpin them. A central educational question is: should we concentrate on teaching skills in the belief that attitudes will follow, or attitudes in the belief that they will generate appropriate skills?
PMCID: PMC1266242  PMID: 15667765
attitudes; communication; education
20.  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.
doi:10.1186/1471-2164-10-S3-S1
PMCID: PMC2788361  PMID: 19958472
21.  Influence of a National Cancer Institute transdisciplinary research and training initiative on trainees' transdisciplinary research competencies and scholarly productivity 
ABSTRACT
Over the past several decades, there has been burgeoning interest and investment in large transdisciplinary (TD) team science initiatives that aim to address complex societal problems. Despite this trend, TD training opportunities in the health sciences remain limited, and evaluations of these opportunities are even more uncommon due to funding constraints. We had the unique opportunity to conduct an exploratory study to examine the potential outcomes and impacts of TD training in a National Cancer Institute-supported initiative for TD research and training—the Transdisciplinary Research on Energetics and Cancer I (TREC I) initiative. This study used a retrospective mixed-methods approach leveraging secondary analysis of existing data sources to learn about TREC trainees' experiences with TREC training, TD research competencies, changes in scholarly productivity, and the associations among these domains. Results indicated that, on average, TREC trainees were satisfied with their TREC mentoring experiences and believed that TREC training processes were effective, in general. Participation in TREC training was associated with TD research competencies, including TD research orientation, positive general attitude toward TD training, development of scientific skills for TD research, and intrapersonal/interpersonal competencies for collaboration. There was also a significant increase in trainees' scholarly productivity from before to after starting in TREC training, as indicated by average annual number of publications and presentations and average number of coauthors per publication. Perceived effectiveness of TREC training was positively correlated with change in average annual number of research presentations from before to after starting in TREC training (r = 0.65, p < 0.05, N = 12), as well as TD research orientation (r = 0.36, p < 0.05), general attitude toward TD training (0.39, p < 0.05), scientific skills for TD research (r = 0.45–0.48, p < 0.05), and perceived collaborative productivity at one's TREC center (r = 0.47, p < 0.01). Finally, a significant positive correlation was observed between multi-mentoring experiences and both TD research orientation (r = 0.58, p < 0.05) and perceived collaborative productivity at one's TREC center (r = 0.44, p < 0.05). This exploratory study had methodological constraints including the absence of a comparison group and cross-sectional rather than longitudinal data related to TD research competencies. Despite these limitations, the study provided an opportunity to use existing data sources to explore potential outcomes and impacts of TD training and inform development of future rigorous evaluations of TD training. Overall, findings suggest that TD training in the context of a TD research initiative can provide satisfying training opportunities that support the development of TD research competencies and promote scholarly productivity.
doi:10.1007/s13142-012-0173-0
PMCID: PMC3717930  PMID: 24073146
Transdisciplinary; Interdisciplinary; Education; Training; Multi-mentoring
22.  BUILDING THE NEXT GENERATION OF QUANTITATIVE BIOLOGISTS 
Many colleges and universities across the globe now offer bachelors, masters, and doctoral degrees, along with certificate programs in bioinformatics. While there is some consensus surrounding curricula competencies, programs vary greatly in their core foci, with some leaning heavily toward the biological sciences and others toward quantitative areas. This allows prospective students to choose a program that best fits their interests and career goals. In the digital age, most scientific fields are facing an enormous growth of data, and as a consequence, the goals and challenges of bioinformatics are rapidly changing; this requires that bioinformatics education also change. In this workshop, we seek to ascertain current trends in bioinformatics education by asking the question, “What are the core competencies all bioinformaticians should have at the end of their training, and how successful have programs been in placing students in desired careers?”
PMCID: PMC3935419  PMID: 24297567
23.  Research capacity and training needs for non-communicable diseases in the public health arena in Turkey 
Background
The aim of this study is to define the research capacity and training needs for professionals working on non-communicable diseases (NCDs) in the public health arena in Turkey.
Methods
This study was part of a comparative cross-national research capacity-building project taking place across Turkey and the Mediterranean Middle East (RESCAP-Med, funded by the EU). Identification of research capacity and training needs took place in three stages. The first stage involved mapping health institutions engaged in NCD research, based on a comprehensive literature review. The second stage entailed in-depth interviews with key informants (KIs) with an overview of research capacity in public health and the training needs of their staff. The third stage required interviewing junior researchers, identified by KIs in stage two, to evaluate their perceptions of their own training needs. The approach we have taken was based upon a method devised by Hennessy&Hicks. In total, 55 junior researchers identified by 10 KIs were invited to participate, of whom 46 researchers agreed to take part (84%). The specific disciplines in public health identified in advance by RESCAP-MED for training were: advanced epidemiology, health economics, environmental health, medical sociology-anthropology, and health policy.
Results
The initial literature review showed considerable research on NCDs, but concentrated in a few areas of NCD research. The main problems listed by KIs were inadequate opportunities for specialization due to heavy teaching workloads, the lack of incentives to pursue research, a lack of financial resources even when interest existed, and insufficient institutional mechanisms for dialogue between policy makers and researchers over national research priorities. Among junior researchers, there was widespread competence in basic epidemiological skills, but an awareness of gaps in knowledge of more advanced epidemiological skills, and the opportunities to acquire these skills were lacking. Self-assessed competencies in each of the four other disciplines considered revealed greater training needs, especially regarding familiarity with the qualitative research skills for medical anthropology/sociology.
Conclusions
In Turkey there are considerable strengths to build upon. But a combination of institutional disincentives for research, and the lack of opportunities for the rising generation of researchers to acquire advanced training skills.
doi:10.1186/1472-6963-14-373
PMCID: PMC4165910  PMID: 25193671
Training needs assessment; Research capacity; Mapping; Non-communicable diseases; Public health
24.  Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation 
PLoS Computational Biology  2012;8(11):e1002751.
In systems and computational biology, much effort is devoted to functional identification of systems and networks at the molecular-or cellular scale. However, similarly important networks exist at anatomical scales such as the tendon network of human fingers: the complex array of collagen fibers that transmits and distributes muscle forces to finger joints. This network is critical to the versatility of the human hand, and its function has been debated since at least the 16th century. Here, we experimentally infer the structure (both topology and parameter values) of this network through sparse interrogation with force inputs. A population of models representing this structure co-evolves in simulation with a population of informative future force inputs via the predator-prey estimation-exploration algorithm. Model fitness depends on their ability to explain experimental data, while the fitness of future force inputs depends on causing maximal functional discrepancy among current models. We validate our approach by inferring two known synthetic Latex networks, and one anatomical tendon network harvested from a cadaver's middle finger. We find that functionally similar but structurally diverse models can exist within a narrow range of the training set and cross-validation errors. For the Latex networks, models with low training set error [<4%] and resembling the known network have the smallest cross-validation errors [∼5%]. The low training set [<4%] and cross validation [<7.2%] errors for models for the cadaveric specimen demonstrate what, to our knowledge, is the first experimental inference of the functional structure of complex anatomical networks. This work expands current bioinformatics inference approaches by demonstrating that sparse, yet informative interrogation of biological specimens holds significant computational advantages in accurate and efficient inference over random testing, or assuming model topology and only inferring parameters values. These findings also hold clues to both our evolutionary history and the development of versatile machines.
Author Summary
In science and medicine alike, one of the critical steps to understand the working of organisms is to identify how a given individual is similar or different from others. Only then can the specific features of an individual be distinguished from the general properties of that species. However, doing enough input-output experiments on a given organism to obtain a reliable description of its function (i.e., a model) can often harm the organism, or require too much time when testing perishable tissues or human subjects. We have met this challenge by demonstrating that our novel algorithm can accelerate the extraction of accurate functional models in complex tissues by continually tailoring each successive experiment to be more informative. We apply this new method to the problem of describing how the tendons of the fingers interact, which has puzzled scientists and clinicians since the time of Da Vinci. This new computational-experimental method now enables fresh research directions in biological and medical research by allowing the experimental extraction of accurate functional models with minimal damage to the organism. For example, it will allow a better understanding of similarities and differences among related species, and the development of personalized medical treatment.
doi:10.1371/journal.pcbi.1002751
PMCID: PMC3493461  PMID: 23144601
25.  Wound Care Specialization: The Current Status and Future Plans to Move Wound Care into the Medical Community 
Advances in Wound Care  2012;1(5):184-188.
Background
There has been an explosion of basic science results in the field of wound care over the past 20 years. Initially, wound dressings were the only therapeutic option available to the wound practitioner. With advanced basic science knowledge, technical innovation, and the recent participation of pharmaceutical companies, the wound clinician now has an arsenal of dressings, biological tissue replacements, gene therapy, and cell-based treatment options. What has not, however, kept pace with these changes is the education and practical training for those treating nonhealing wounds. The pace of innovation in wound diagnostic tools has also lagged, creating even more pressure on the clinician to use experience, skill, and training to properly diagnose the root cause for the nonhealing wound. As wound healing is not considered a medical specialty, there is no formal training process for physicians, and subsequently, allied health practitioners are often the only ones available to provide care for these complex patients. Wound care training, however, is also not part of any formal curriculum for these healthcare providers as well, creating confusion for patients, payors, regulators, researchers, and product manufacturers.
The Problem
In all other fields of medicine there is a formal process in place for physicians to train, certify, and credential. Medicine is constantly evolving and there have been several new fields of specialty care created over the past two decades that can serve as examples for the wound care field to follow. Without academic-based, clinical residency/fellowship training in wound healing ultimately leading to formal certification, the field will be unable to achieve an appropriate status in the medical establishment. Achieving this goal will impact product innovation, payment, and the sustainability of the field.
Basic/Clinical Science Advances
The enhanced understanding of normal and dysregulated wound healing processes, which have been uncovered by basic scientists, has translated to the bedside through the creation of multiple advanced biological solutions for patients with nonhealing wounds.
Clinical Care Relevance
These advanced wound care therapeutics will require physician involvement in a way not previously seen in wound care. It will no longer be possible to practice wound care “part time” in the near future. The amount of new information and massive base of core knowledge required will mandate a full-time commitment. The increase in patients with this condition because of an aging population, increased numbers of diabetic patients, and the ever growing epidemic of obesity will mandate that all clinicians providing wound care will need to increase their skill sets through formal training. In addition, underserved patient populations are disproportionately affected and their outcomes are comparatively worse, further complicating the problem at a healthcare structural and policy level.
Conclusion
The American College of Wound Healing and Tissue Repair was founded in Illinois as a nonprofit organization whose express function is to organize university-based medical school programs around a common curriculum for physicians who want to specialize in wound healing. Currently, two wound care fellows have graduated from the University of Illinois at Chicago and other programs are under development. The ultimate process will be achieved when certification is accredited by an organization such as the American Board of Medical Specialties. This article outlines the current process in place to achieve this goal within 10 years.
doi:10.1089/wound.2011.0346
PMCID: PMC3839023  PMID: 24527303

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