Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.
Ontology highlight
ABSTRACT:
SUBMITTER: Pawlik A
PROVIDER: S-EPMC5516217 | biostudies-other | 2017
REPOSITORIES: biostudies-other
Publications
Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.
Pawlik Aleksandra A van Gelder Celia W G CWG Nenadic Aleksandra A Palagi Patricia M PM Korpelainen Eija E Lijnzaad Philip P Marek Diana D Sansone Susanna-Assunta SA Hancock John J Goble Carole C
F1000Research 20170703
Quality training in computational skills for life scientists is essential to allow them to deliver robust, reproducible and cutting-edge research. A pan-European bioinformatics programme, ELIXIR, has adopted a well-established and progressive programme of computational lab and data skills training from Software and Data Carpentry, aimed at increasing the number of skilled life scientists and building a sustainable training community in this field. This article describes the Pilot action, which i ...[more]
Similar Datasets
Project description:BACKGROUND: The advantages of using simulators in skills training are generally recognized, but simulators are often too expensive for medical schools in developing countries. Cheaper locally-made models (or part-task trainers) could be the answer, especially when teachers are involved in design and production (teacher-made models, TM). METHODS: We evaluated the effectiveness of a TM in training and assessing intravenous injection skills in comparison to an available commercial model (CM) in a randomized, blind, pretest-posttest study with 144 undergraduate nursing students. All students were assessed on both the TM and the CM in the pre-test and post-test. After the post-test the students were also assessed while performing the skill on real patients. RESULTS: Differences in the mean scores pre- and post-test were marked in all groups. Training with TM or CM improved student scores substantially but there was no significant difference in mean scores whether students had practiced on TM or CM. Students who practiced on TM performed better on communication with the patient than did students who practiced on CM. Decreasing the ratio of students per TM model helped to increase practice opportunities but did not improve student's mean scores. The result of the assessment on both the TM and the CM had a low correlation with the results of the assessment on real persons. CONCLUSIONS: The TM appears to be an effective alternative to CM for training students on basic IV skills, as students showed similar increases in performance scores after training on models that cost considerably less than commercially available models. These models could be produced using locally available materials in most countries, including those with limited resources to invest in medical education and skills laboratories.
| S-EPMC3533861 | biostudies-other
Project description:Historically, medical trainees were educated in the hospital on real patients. Over the last decade, there has been a shift to practicing skills through simulations with mannequins or patient actors. Virtual reality (VR), and in particular, the use of 360-degree video and audio (cineVR), is the next-generation advancement in medical simulation that has novel applications to augment clinical skill practice, empathy building, and team training. In this paper, we describe methods to design and develop a cineVR medical education curriculum for trauma care training using real patient care scenarios at an urban, safety-net hospital and Level 1 trauma center. The purpose of this publication is to detail the process of finding a cineVR production partner; choosing the camera perspectives; maintaining patient, provider, and staff privacy; ensuring data security; executing the cineVR production process; and building the curriculum.
| S-EPMC7773512 | biostudies-literature
Project description:ObjectiveDespite procedural skills being recognized as an important component of medical school education, medical students are not confident in their ability to carry out a range of medical procedures. We conducted an institutional needs assessment and used the results to inform the creation of a procedure-based preclinical elective for first- and second-year students.MethodsWe surveyed second-, third-, and fourth-year medical students at Alpert Medical School as well as select program directors to guide selection of a list of procedures to be taught in the elective. We then created an extracurricular 10-week procedural skills course for preclerkship medical students utilizing a hands-on, flipped classroom practice model. Volunteer preceptors were recruited from the Department of Emergency Medicine to participate with a student-to-faculty ratio not exceeding 5:1. Knowledge and skill acquisition were assessed using a multiple-choice knowledge exam and 4-station practical exam, respectively. Pre- and post-course online surveys were used to assess self-perceived confidence for all procedures.ResultsWe implemented our procedural skills training course for first- and second-year medical students in the fall of 2015. Forty-four students applied for the first iteration of the course and 15 students were selected to participate. Fourteen students ultimately completed the elective as well as the subsequent course surveys, multiple-choice exam, and practical exam. Students who participated in the elective had increased levels of self-reported confidence at the conclusion of the elective and performed better on a practical exam and multiple-choice exam compared to students who participated in only the standard curriculum.ConclusionA longitudinal preclerkship procedural course early during medical school is a feasible method of teaching procedural skills to a cohort of learners. A number of adjustments could be made to the course in order to scale up and include a larger cohort of students at our own or another institution.
| S-EPMC7771806 | biostudies-literature
Project description:Background:Neurobiological studies suggest that deficits in emotion recognition are common phenomena in alexithymia. Thus, effective treatments for alexithymia often include skills training in the domain of emotion recognition. Given that smartphone-based interventions (SBIs) offering skills training have been shown to be promising adjuncts to psychological treatments, a blended SBI facilitating the training of emotional skills might be effective in reducing alexithymia. Methods:In this pilot trial, N?=?29 individuals reporting elevated alexithymia levels were randomly assigned to a blended SBI including a psychoeducation session and 14?days of training with the mindtastic alexithymia app (MT-ALEX) or a psychoeducation-only control condition. Primary outcome was emotion recognition skills as assessed in a computer-based two-choice task paradigm. Results:On average, participating in the SBI was associated with a significant increase in computer-assessed emotion recognition skills compared to the control condition (d?=?0.97). Conclusions:Study findings provide preliminary evidence that SBIs can improve emotion recognition skills in alexithymic individuals. Research using larger samples and targeting clinical populations is necessary to further evaluate the potential of MT-ALEX.
| S-EPMC6510700 | biostudies-literature
Project description:Spatial neglect is a syndrome due to impaired neural networks critical for spatial attention and related cognitive and motor functions. Affected individuals also have impaired self-awareness of their own neglect symptoms. The present randomized controlled study was the first proof-of-concept pilot examining the multi-context treatment approach using a protocol of spatial exploration strategy training in one brief session (20-30 minutes). The therapist provided supportive feedback and semi-structured guidance to promote strategy learning and self-discovery of omission errors. 40 patients with left-sided neglect after right brain stroke were included. The results showed that the treatment reduced lateralized bias toward the ipsilesional side of space but did not improve overall detection performance. Impaired general self-awareness of daily-life spatial difficulties was found independent of treatment outcome. This implies that judgment regarding responsiveness to treatment should not be made based on an awareness interview or the severity of neglect symptoms. Lastly, the treatment showed the potential of improving online contextual self-awareness of spatial abilities. A collaborative and interactive approach that focuses on helping the patient self-discover, monitor and self-manage their errors, appears to have a potential for decreasing neglect symptoms. Future studies are required to examine additional aspects of the multi-context treatment approach.
| S-EPMC7855016 | biostudies-literature
Project description:Humanistic care in medicine has shown to improve healthcare outcomes. Language barriers are a significant obstacle to humanistic care, and trained medical interpreters have demonstrated to effectively bridge the gap for the vulnerable limited English proficiency (LEP) patient population. One way in which medical schools can train more humanistic physicians and provide language access is through the implementation of programs to train bilingual medical students as medical interpreters. The purpose of this prospective study was to evaluate whether such training had an impact on bilingual medical student's interpretation skills and humanistic traits.Between 2015 and 2017, whole-day (~?8 h) workshops on medical interpretation were offered periodically to 80 bilingual medical students at the Penn State College of Medicine. Students completed a series of questionnaires before and after the training that assessed the program's effectiveness and its overall impact on interpretation skills and humanistic traits. Students also had the opportunity to become certified medical interpreters.The 80 student participants were first- to third- year medical students representing 21 languages. Following training, most students felt more confident interpreting (98%) and more empathetic towards LEP patients (87.5%). Students' scores in the multiple-choice questions about medical interpretation/role of the interpreter were also significantly improved (Chi-Square test, p?<?0.05). All students who decided to take the exam were able to successfully become certified interpreters. Ninety-two percent of participants reported they would recommend the program and would be willing to serve as a future "coaches" for interpreter training workshops delivered to peer students.Our program was successful in increasing self-reported measures of empathy and humanism in medical students. Our data suggests that implementation of medical interpreter training programs can be a successful strategy to develop of humanism in medical students, and aid in the development of sustainable language access for LEP patients.
| S-EPMC6006684 | biostudies-other
Project description:The amendments introduced to the current Veterinary Licensing Ordinance (TAppV) by the Veterinary Licensing Regulation (TAppO) have brought a high degree of skills orientation to fill the gap between academic study and preparing for a wide range of professional skills. In order to improve the veterinary skills of students while conveying fundamental methods in a structured and reproducible way, the University of Veterinary Medicine Hannover, Foundation, has set up the first central veterinary skills lab in Germany. Practical training is provided by means of a three-tier delivery approach. This involves around 40 simulators on an area of approx. 800 m(2) under the guidance of 6-8 staff members, along with supplementary resources such as posters, text instructions and YouTube videos. Since it opened in March 2013, there have been 769 visits to the skills lab and 30,734 hits on YouTube. Initial results show that the skills lab helps to maintain student motivation by teaching them practical skills at an early stage of the basic study-based acquisition of knowledge, whilst reinforcing skills acquisition per se in competence-based teaching. It enables veterinary students to prepare for their first examinations and treatments of live patients in a manner compliant with animal welfare.
| S-EPMC4027805 | biostudies-other
Project description:The article presents the results of the preliminary survey and pilot application of the methodological toolkit for the improvement of certain competencies, which are part of the soft skills of professionals in the long-term care sector in Bulgaria. Based on the survey the authors define 2 target competencies, namely conflict management and empathic interaction. These skills are considered a part of the scope of emotional intelligence and its constituent dimensions and authors use Daniel Goleman's ability-based model as a base for their conceptual frame and theoretical explanations. In order to present their thesis, the authors perform a soft skill analysis of the long-term care sector; define the construct emotional intelligence and justify their choice of a theoretical model for the subsequent survey. On this basis, they develop a training design for the development of these skills and present the results achieved through its pilot application. The study includes 62 participants randomly divided into a test and control groups. The level of targeted skills is measured (before and after) and the authors report a significant increase in those skills (empathic interaction, net effect 1.87; conflict management, net effect 1.75). In conclusion, the authors open a discussion on the importance of emotional management as an essential part of any profession related to health care and underline its importance for the quality of caregiving services.
| S-EPMC7031788 | biostudies-literature
Project description:This pilot randomized controlled trial aimed to determine the feasibility, acceptability, and preliminary efficacy of parental problem-solving skills training (PSST) compared with treatment as usual on improving parental mental health symptoms, physical health and well-being, and parenting behaviors. Effects of parent PSST on child outcomes (pain, emotional, and physical functioning) were also examined. Participants included 61 parents of children aged 10 to 17 years with chronic pain randomized to PSST (n = 31) or treatment as usual (n = 30) groups. Parents receiving PSST participated in 4 to 6 individual sessions of training in problem-solving skills. Outcomes were assessed at pretreatment, immediately after treatment, and at a 3-month follow-up. Feasibility was determined by therapy session attendance, therapist ratings, and parent treatment acceptability ratings. Feasibility of PSST delivery in this population was demonstrated by high compliance with therapy attendance, excellent retention, high therapist ratings of treatment engagement, and high parent ratings of treatment acceptability. PSST was associated with posttreatment improvements in parental depression (d = -0.68), general mental health (d = 0.64), and pain catastrophizing (d = -0.48), as well as in child depression (d = -0.49), child general anxiety (d = -0.56), and child pain-specific anxiety (d = -0.82). Several effects were maintained at the 3-month follow-up. Findings demonstrate that PSST is feasible and acceptable to parents of youths with chronic pain. Treatment outcome analyses show promising but mixed patterns of effects of PSST on parent and child mental health outcomes. Further rigorous trials of PSST are needed to extend these pilot results.
| S-EPMC4935529 | biostudies-literature
Project description:Creating useful software is a major activity of many scientists, including bioinformaticians. Nevertheless, software development in an academic setting is often unsystematic, which can lead to problems associated with maintenance and long-term availibility. Unfortunately, well-documented software development methodology is difficult to adopt, and technical measures that directly improve bioinformatic programming have not been described comprehensively. We have examined 22 software projects and have identified a set of practices for software development in an academic environment. We found them useful to plan a project, support the involvement of experts (e.g. experimentalists), and to promote higher quality and maintainability of the resulting programs. This article describes 12 techniques that facilitate a quick start into software engineering. We describe 3 of the 22 projects in detail and give many examples to illustrate the usage of particular techniques. We expect this toolbox to be useful for many bioinformatics programming projects and to the training of scientific programmers.
| S-EPMC3294241 | biostudies-literature