ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.
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ABSTRACT:
SUBMITTER: Larcombe L
PROVIDER: S-EPMC5521157 | biostudies-literature | 2017
REPOSITORIES: biostudies-literature
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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]
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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.
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Project description:BackgroundAdequate training of anaesthetists in regional anaesthesia is important to ensure optimal patient access to regional anaesthesia.MethodsWe undertook a national survey of UK trainee anaesthetists and Royal College of Anaesthetists (RCoA) tutors to assess experiences of training in regional anaesthesia. We performed descriptive statistics for baseline characteristics, and logistic regression of training indices and tutor confidence that their hospital could provide regional anaesthesia training at all three stages of the RCoA 2021 curriculum.ResultsA total of 492 trainees (19.2%) and 114 tutors (45.2%) completed the survey. Trainees were less likely to have received training in chest/abdominal wall compared with upper/lower limb blocks {erector spinae vs femoral block (odds ratio [OR] 0.25, 95% confidence interval [CI] 0.16-0.39), P<0.001}, or achieved >20 chest/abdominal wall blocks by Stage 3 of training (chest vs lower limb block [OR 0.09, 95% CI 0.05-0.15, P<0.001]. There was a strong association between training received, number of blocks performed (>20 vs 0-5 blocks), and self-reported ability to perform blocks independently, OR 20.9 (95% CI 9.38-53.2). 24/182 (13%) and 10/182 (5.5%) of trainees had performed ≥50 non-obstetric lumbar and thoracic epidurals, respectively, by Stage 3 training. There was a positive association between having a lead clinician for regional anaesthesia, particularly those with paid sessions, and reported confidence to provide regional anaesthesia training at all stages of the curriculum (Stage 3 OR 7.27 [95% CI 2.64-22.0]).ConclusionOur results confirm the importance of clinical experience and access to training in regional anaesthesia, and support the introduction of departmental regional anaesthesia leads to improve equity and quality in training opportunities.
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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
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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.
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Project description:ObjectivesTo 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.BackgroundCompetency assessment is changing with concepts of trainee autonomy decisions (termed entrustment decisions) being introduced to surgical training.MethodsData 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.ResultsWe 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.ConclusionsThe 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.
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Project description:BackgroundPlastic surgery training in the UK continues to evolve towards an outcome-based rather than time-served curriculum. UK plastic surgery trainees are appointed nationally, and are assessed according to national standards, but training is delivered regionally. This study sought opinion from current UK plastic surgery trainees in order to highlight strengths and shortcomings of the higher surgical training programme.MethodA cross-sectional study was designed and administered by the UK Plastic Surgery Trainees Association (PLASTA). A questionnaire was distributed to all UK plastic surgery trainees holding a National Training Number, using the REDCap web-based application.ResultsOf the 320 UK plastic surgery trainees, 131 (41%) participated in this survey, with responses from all 12 UK training regions. The most common subspecialty career aspirations for trainees were hand surgery, cleft lip and palate, lower limb and oncoplastic breast reconstruction. The survey highlighted regional variation in teaching programmes, the ability to achieve indicative operative logbook numbers, and training in aesthetic surgery. Of the trainees, 82% expressed a desire to undertake a fellowship within their training, but most did not know whether their deanery would support this. Fifteen per cent of the respondents were currently training flexibly and the majority of these had experienced negative behaviours towards their less than full time working status. Of the respondents, 44% reported stress, 25% reported a lack of autonomy and 17% reported feeling burnt out at work at least once a week. A total of 85% perceived that they did not have access to a mentoring service.ConclusionsPlastic surgery remains a popular and highly competitive surgical speciality in the UK, and many trainees reported high levels of satisfaction during their training. Aspects of training that could be improved have been highlighted and recommendations made accordingly.
| S-EPMC7394739 | biostudies-literature
Project description:Background: The adoption of palliative care as an integral component of health care has led to the need for generalist level providers, especially important in serious illnesses such as cancer. Objectives: The goals of this National Cancer Institute-funded training program were to (1) identify the eight domains of quality palliative care applied to oncology practice, (2) demonstrate skills for oncology advanced practice registered nurses (APRNs) in the domains of palliative care, and (3) develop goals for implementing the skills training in practice through process improvement, staff education, and clinical care. Design: The training program led by the End of Life Nursing Education Consortium (ELNEC) project included oncology APRNs in a three-day training course with one-year follow-up for ongoing support and to assess impact. Settings: Five training courses included 430 APRNs from 46 U.S states including both pediatric and adult oncology settings. The project included 25% minority participants. Measurement: Measures included participant goal implementation, course evaluations, and surveys to assess implementation and palliative care practices (precourse, 6 and 12 months postcourse). Results: The ELNEC oncology APRN training course resulted in changes in practice across domains, improved perceived effectiveness in clinical practice, and valuable insight regarding the challenges in generalist level palliative care implementation. Conclusion: The ELNEC oncology APRN course serves as a model for the palliative care field to advance generalist level practice. Future training efforts can build on this project to reach more oncology professionals and those in other areas of serious illness care.
| S-EPMC9894595 | biostudies-literature