ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.
Ontology highlight
ABSTRACT:
SUBMITTER: Larcombe L
PROVIDER: S-EPMC5521157 | biostudies-literature | 2017
REPOSITORIES: biostudies-literature
Publications
ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.
Larcombe L L Hendricusdottir R R Attwood T K TK Bacall F F Beard N N Bellis L J LJ Dunn W B WB Hancock J M JM Nenadic A A Orengo C C Overduin B B Sansone S-A SA Thurston M M Viant M R MR Winder C L CL Goble C A CA Ponting C P CP Rustici G G
F1000Research 20170621
ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform's coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-imp ...[more]
Similar Datasets
Project description:ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR's framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course.
| S-EPMC7377377 | biostudies-literature
Project description:ELIXIR is the European infrastructure established specifically for the sharing and sustainability of life science data. To provide up-to-date resources and services, ELIXIR needs to undergo a continuous process of refreshing the services provided by its national Nodes. Here we present the approach taken by ELIXIR-UK to address the advice by the ELIXIR Scientific Advisory Board that Nodes need to develop " mechanisms to ensure that each Node continues to be representative of the Bioinformatics efforts within the country". ELIXIR-UK put in place an open and transparent process to identify potential ELIXIR resources within the UK during late 2015 and early to mid-2016. Areas of strategic strength were identified and Expressions of Interest in these priority areas were requested from the UK community. Criteria were established, in discussion with the ELIXIR Hub, and prospective ELIXIR-UK resources were assessed by an independent committee set up by the Node for this purpose. Of 19 resources considered, 14 were judged to be immediately ready to be included in the UK ELIXIR Node's portfolio. A further five were placed on the Node's roadmap for future consideration for inclusion. ELIXIR-UK expects to repeat this process regularly to ensure its portfolio continues to reflect its community's strengths.
| S-EPMC5265702 | biostudies-literature
Project description:BACKGROUND:The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the "Big Data" era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians. Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center. RESULTS:Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call "ELIXIR-IT HPC@CINECA", offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of ~?8 Millions of CPU/hours and, for data storage, ~?100?TB of permanent and?~?300?TB of temporary space. CONCLUSIONS:Three years after the beginning of the ELIXIR-IT HPC@CINECA program, we can appreciate its impact over the Italian bioinformatics community and draw some considerations. Several Italian researchers who applied to the program have gained access to one of the top-ranking public scientific supercomputing facilities in Europe. Those investigators had the opportunity to sensibly reduce computational turnaround times in their research projects and to process massive amounts of data, pursuing research approaches that would have been otherwise difficult or impossible to undertake. Moreover, by taking advantage of the wealth of documentation and training material provided by CINECA, participants had the opportunity to improve their skills in the usage of HPC systems and be better positioned to apply to similar EU programs of greater scale, such as PRACE. To illustrate the effective usage and impact of the resources awarded by the program - in different research applications - we report five successful use cases, which have already published their findings in peer-reviewed journals.
| S-EPMC7446135 | biostudies-literature
Project description:Demand for training life scientists in bioinformatics skills led to the development of a train-the-trainer collaboration between the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-the-trainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors.
| S-EPMC6597034 | biostudies-literature
Project description:OBJECTIVES:To determine the operative experience of UK general surgery trainees and assess the changing procedural supervision and acquisition of competency assessments through the course of training. BACKGROUND:Competency assessment is changing with concepts of trainee autonomy decisions (termed entrustment decisions) being introduced to surgical training. METHODS:Data from the Intercollegiate Surgical Curriculum Programme and the eLogbook databases for all UK General Surgery trainees registered from August 1, 2007 who had completed training were used. Total and index procedures (IP) were counted and variation by year of training assessed. Recorded supervision codes and competency assessment outcomes for IPs were assessed by year of training. RESULTS:We identified 311 trainees with complete data. Appendicectomy was the most frequently undertaken IP during first year of training [mean procedures (mp) = 26] and emergency laparotomy during final year of training (mp = 27). The proportion of all IPs recorded as unsupervised increased through training (P < 0.05) and varied between IPs with 91.2% of appendicectomies (mp = 20), 40.6% of emergency laparotomies (mp = 27), and 17.4% of segmental colectomies (mp = 15) recorded as unsupervised during the final year of training. Acquisition of competency assessments increased through training and varied by IP. CONCLUSIONS:The changing autonomy of trainees through the course of an entire training scheme, alongside formal competency assessments, may provide evidence of changing entrustment decisions made by trainers for different key procedures. Other countries utilizing electronic logbooks could adopt similar techniques to further understanding of competency attainment amongst their surgical trainees.
| S-EPMC6369871 | biostudies-other
Project description:The aim of the project was to define transcriptional signatures in whole blood of TB patients (before drug treatment) and healthy controls to distinguish the signature of Latent and Active TB patients from each other and from healthy controls. This will help in diagnosis of active tuberculosis which normally relies on culture of the bacilli, which can take up to 6 wks, and sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). In some cases the bacill cannot be grown from sputum or BAL. Secondly the aim was to determine whether Latent patients have a homogeneous or heterogeneous signature, one may expect the latter since it is not possible to determine by the present tests (Tuberculin skin test - TST - or MTb antigen responsiveness of blood cells to produce IFN-gamma - IGRA assay) whether the mycobacteria has been cleared, is still present but is controlled, or if patients are recently infected or reactivated and will develop active TB. The latter situation may be determined if Latent patients have a blood transcriptional signature similar to that in Active patients. The transcriptional signature in Active TB patients may also provide information as to the factors leading to immunopathogenesis, thus possibly identifying therapeutic targets. The transcriptional profile in Latent TB may give information as to the protective factors controlling the infection, thus important for monitoring vaccine development. A further aim was to examine the transcriptional blood profile of active TB patients at the time of recruitment (before drug treatment) and then subsequently at specific time points after drug treatment to determine whether the signature is extingsuihed with treatment and when. London is a site of intermediate burden of TB - the study was initiated in London, across a broad range of ethnicities to obtain a robust signature that could be used in different developing countries where there is a high burden TB disease.
2010-08-11 | GSE19439 | GEO
Project description:Developments in advanced polypectomy technique provide an alternative to surgery in the management of large and complex colorectal polyps. These endoscopic techniques require expertise and can potentially incur high complication rates. This survey evaluates current UK practice, attitudes and training in advanced polypectomy.Anonymous online questionnaire.Colonoscopists within the UK were asked about their approach to large polyps (>2 cm).Among the 268 respondents (64% of whom were BCSP accredited), 86% were confident in removing lesions >2 cm by endoscopic mucosal resection (EMR). Of these, 27% were classed as low volume operators (<10 lesions resected/annum) and 14% as high volume operators (>50/annum). By comparison, only 3% currently performed endoscopic submucosal dissection (ESD). Referring one or more benign polyps for surgery a year was common among responders of all levels (11-68%). Training deficiencies were common: only 21% of responders had received a period of training dedicated to advanced polypectomy; 58% of responders would welcome a national training scheme and a majority supported the implementation of advanced polypectomy accreditation with national guidelines. However, while 41% wanted nominated regional EMR experts, only 18% would welcome an integrated national referral network for large/complex polyps.EMR is practised widely while ESD service provision is very limited. Most experienced colonoscopists are confident to perform piecemeal EMR, even if their training is suboptimal and annual numbers low. Practices and attitudes were variable, even among self-defined level 4 operators. Improving training and implementation of accreditation were welcomed, but there was little appetite for mandated referral to subspecialist 'experts' and national networks.
| S-EPMC5369560 | biostudies-other
Project description:One of the main goals of the ELIXIR-EXCELERATE project from the European Union's Horizon 2020 programme is to support a pan-European training programme to increase bioinformatics capacity and competency across ELIXIR Nodes. To this end, a Train-the-Trainer (TtT) programme has been developed by the TtT subtask of EXCELERATE's Training Platform, to try to expose bioinformatics instructors to aspects of pedagogy and evidence-based learning principles, to help them better design, develop and deliver high-quality training in future. As a first step towards such a programme, an ELIXIR-EXCELERATE TtT (EE-TtT) pilot was developed, drawing on existing 'instructor training' models, using input both from experienced instructors and from experts in bioinformatics, the cognitive sciences and educational psychology. This manuscript describes the process of defining the pilot programme, illustrates its goals, structure and contents, and discusses its outcomes. From Jan 2016 to Jan 2017, we carried out seven pilot EE-TtT courses (training more than sixty new instructors), collaboratively drafted the training materials, and started establishing a network of trainers and instructors within the ELIXIR community. The EE-TtT pilot represents an essential step towards the development of a sustainable and scalable ELIXIR TtT programme. Indeed, the lessons learned from the pilot, the experience gained, the materials developed, and the analysis of the feedback collected throughout the seven pilot courses have both positioned us to consolidate the programme in the coming years, and contributed to the development of an enthusiastic and expanding ELIXIR community of instructors and trainers.
| S-EPMC5596339 | biostudies-literature
Project description:IntroductionKnowledge about allocation of doctors into postgraduate training programmes is essential in terms of workforce planning, transparency and equity issues. However, this is a rarely examined topic. To address this gap in the literature, the current study examines the relationships between applicants' sociodemographic characteristics and outcomes on the UK Foundation Training selection process.MethodsA longitudinal, cohort study of trainees who applied for the first stage of UK postgraduate medical training in 2013-2014. We used UK Medical Education Database (UKMED) to access linked data from different sources, including medical school admissions, assessments and postgraduate training. Multivariable ordinal regression analyses were used to predict the odds of applicants being allocated to their preferred foundation schools.ResultsApplicants allocated to their first-choice foundation school scored on average a quarter of an SD above the average of all applicants in the sample. After adjusting for Foundation Training application score, no statistically significant effects were observed for gender, socioeconomic status (as determined by income support) or whether applicants entered medical school as graduates or not. Ethnicity and place of medical qualification were strong predictors of allocation to preferred foundation school. Applicants who graduated from medical schools in Wales, Scotland and Northern Ireland were 1.17 times, 3.33 times and 12.64 times (respectively), the odds of applicants who graduated from a medical school in England to be allocated to a foundation school of their choice.ConclusionsThe data provide supportive evidence for the fairness of the allocation process but highlight some interesting findings relating to 'push-pull' factors in medical careers decision-making. These findings should be considered when designing postgraduate training policy.
| S-EPMC6042613 | biostudies-literature
Project description:To establish the perceived adequacy of the hepatology training component of the unified gastroenterology and hepatology training programme in the UK by assessing the attitudes and experiences of trainees in the programme.Online cross-sectional questionnaire survey linked to the annual British Society of Gastroenterology/Trainee in Gastroenterology survey in 2010.National survey of all specialist gastroenterology trainees in the UK.283/489 (58%) trainees responded, 68% were male. 54% of all trainees wanted to deliver liver services as consultants. 25% of trainees complete training without exposure to a liver unit providing comprehensive specialist hepatology services. Median time spent in such a unit for the others was 8 months (IQR 6). Significantly fewer trainees lacked confidence in managing liver-related conditions if they had spent time training in a specialist liver unit and with increasing years in training. One in three trainees is dissuaded from a career in hepatology. One in five trainees wished to work part time as consultants-an option preferred significantly more by women.Hepatology training in the UK is perceived by trainees as being suboptimal. A national strategy aimed at improving and standardising hepatology training and making specialist liver unit experience available for every trainee is required.
| S-EPMC5517250 | biostudies-other