Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.
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ABSTRACT:
SUBMITTER: Zhan YA
PROVIDER: S-EPMC6563947 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Developing a position on a socio-scientific issue and defending it using a well-reasoned justification involves complex cognitive skills that are challenging to both teach and assess. Our work centers on instructional strategies for fostering critical thinking skills in high school students using bioethical case studies, decision-making frameworks, and structured analysis tools to scaffold student argumentation. In this study, we examined the effects of our teacher professional development and curricular materials on the ability of high school students to analyze a bioethical case study and develop a strong position. We focused on student ability to identify an ethical question, consider stakeholders and their values, incorporate relevant scientific facts and content, address ethical principles, and consider the strengths and weaknesses of alternate solutions. 431 students and 12 teachers participated in a research study using teacher cohorts for comparison purposes. The first cohort received professional development and used the curriculum with their students; the second did not receive professional development until after their participation in the study and did not use the curriculum. In order to assess the acquisition of higher-order justification skills, students were asked to analyze a case study and develop a well-reasoned written position. We evaluated statements using a scoring rubric and found highly significant differences (p<0.001) between students exposed to the curriculum strategies and those who were not. Students also showed highly significant gains (p<0.001) in self-reported interest in science content, ability to analyze socio-scientific issues, awareness of ethical issues, ability to listen to and discuss viewpoints different from their own, and understanding of the relationship between science and society. Our results demonstrate that incorporating ethical dilemmas into the classroom is one strategy for increasing student motivation and engagement with science content, while promoting reasoning and justification skills that help prepare an informed citizenry.
| S-EPMC3350470 | biostudies-literature
Project description:There is a clear demand for quantitative literacy in the life sciences, necessitating competent instructors in higher education. However, not all instructors are versed in data science skills or research-based teaching practices. We surveyed biological and environmental science instructors (n = 106) about the teaching of data science in higher education, identifying instructor needs and illuminating barriers to instruction. Our results indicate that instructors use, teach, and view data management, analysis, and visualization as important data science skills. Coding, modeling, and reproducibility were less valued by the instructors, although this differed according to institution type and career stage. The greatest barriers were instructor and student background and space in the curriculum. The instructors were most interested in training on how to teach coding and data analysis. Our study provides an important window into how data science is taught in higher education biology programs and how we can best move forward to empower instructors across disciplines.
| S-EPMC8634500 | biostudies-literature
Project description:This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs. Nonetheless the surge of volume and variety of biological and biomedical data has posed new challenges. We discuss how modern cloud computing and big data programming frameworks such as MapReduce and Spark are being used to effectively implement divide-and-conquer in a distributed computing environment. Validation of software is another important issue in big data bioinformatics that is often ignored. Software validation is the process of determining whether the program under test fulfils the task for which it was designed. Determining the correctness of the computational output of big data bioinformatics software is especially difficult due to the large input space and complex algorithms involved. We discuss how state-of-the-art software testing techniques that are based on the idea of multiple executions, such as metamorphic testing, can be used to implement an effective bioinformatics quality assurance strategy. We hope this review will raise awareness of these critical issues in bioinformatics.
| S-EPMC5537105 | biostudies-other
Project description:BackgroundEffective team performance is essential in the delivery of high-quality health-care. Leadership skills therefore are an important part of physicians' everyday clinical life. To date, the development of leadership skills are underrepresented in medical curricula. Appropriate training methods for equipping doctors with these leadership skills are highly desirable.ObjectiveThe review aims to summarize the findings in the current literature regarding training in leadership skills in medicine and tries to integrate the findings to guide future research and training development.MethodThe PubMED, ERIC, and PsycArticles, PsycINFO, PSYNDEX and Academic search complete of EBSCOhost were searched for training of leadership skills in medicine in German and English. Relevant articles were identified and findings were integrated and consolidated regarding the leadership principles, target group of training and number of participants, temporal resources of the training, training content and methods, the evaluation design and trainings effects.ResultsEight studies met all inclusion criteria and no exclusion criteria. The range of training programs is very broad and leadership skill components are diverse. Training designs implied theoretical reflections of leadership phenomena as well as discussions of case studies from practice. The duration of training ranged from several hours to years. Reactions of participants to trainings were positive, yet no behavioral changes through training were examined.ConclusionsMore research is needed to understand the factors critical to success in the development of leadership skills in medical education and to adapt goal-oriented training methods. Requirements analysis might help to gain knowledge about the nature of leadership skills in medicine. The authors propose a stronger focus on behavioral training methods like simulation-based training for leadership skills in medical education.
| S-EPMC3839077 | biostudies-literature
Project description:Rapid research progress in science and technology (S&T) and continuously shifting workforce needs exert pressure on each other and on the educational and training systems that link them. Higher education institutions aim to equip new generations of students with skills and expertise relevant to workforce participation for decades to come, but their offerings sometimes misalign with commercial needs and new techniques forged at the frontiers of research. Here, we analyze and visualize the dynamic skill (mis-)alignment between academic push, industry pull, and educational offerings, paying special attention to the rapidly emerging areas of data science and data engineering (DS/DE). The visualizations and computational models presented here can help key decision makers understand the evolving structure of skills so that they can craft educational programs that serve workforce needs. Our study uses millions of publications, course syllabi, and job advertisements published between 2010 and 2016. We show how courses mediate between research and jobs. We also discover responsiveness in the academic, educational, and industrial system in how skill demands from industry are as likely to drive skill attention in research as the converse. Finally, we reveal the increasing importance of uniquely human skills, such as communication, negotiation, and persuasion. These skills are currently underexamined in research and undersupplied through education for the labor market. In an increasingly data-driven economy, the demand for "soft" social skills, like teamwork and communication, increase with greater demand for "hard" technical skills and tools.
| S-EPMC6294902 | biostudies-other
Project description:Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy. In this paper, we review the challenges of manipulating large-scale next-generation sequencing (NGS) data and diverse clinical data derived from the EHRs for genomic medicine. We introduce possible solutions for different challenges in manipulating, managing, and analyzing genomic and clinical data to implement genomic medicine. Additionally, we also present a practical Big Data toolset for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.
| S-EPMC5343946 | biostudies-literature
Project description:With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources. Notably, the latter can be added on demand, including cloud-based resources, and/or featuring heterogeneous environments. The second goal of making HPCs user-friendly is facilitated by an interactive web interface and a RESTful API, allowing for job monitoring and result retrieval. We used clubber to speed up our pipeline for annotating molecular functionality of metagenomes. Here, we analyzed the Deepwater Horizon oil-spill study data to quantitatively show that the beach sands have not yet entirely recovered. Further, our analysis of the CAMI-challenge data revealed that microbiome taxonomic shifts do not necessarily correlate with functional shifts. These examples (21 metagenomes processed in 172 min) clearly illustrate the importance of clubber in the everyday computational biology environment.
| S-EPMC5929469 | biostudies-literature
Project description:Objective: The objective of this article is a description of the longitudinal communication curriculum in the Model Medicine Curriculum (MSM) at Charité - Universitätsmedizin Berlin. The authors describe the planning and integration of the curriculum into the study program, outline how communicative competence is taught and evaluated in the MSM, and identify which challenges need to be mastered in the process. Project description: Starting with the introduction of the MSM in 2010, students have been spending 102 class hours, spread out over seven semesters, practicing social and communicative competences in the interactive small group format "Communication, Interaction & Teamwork (KIT)". The course contents are closely linked to the topics covered each semester and increase in complexity over the course of their studies. The contents are selected by the KIT planning group whose members continually check the curriculum's timeliness and determine any changes. Students as well as instructors have opportunities for evaluating KIT throughout, and their evaluations are taken into consideration as KIT continues to be updated. Instructors from different disciplines teach KIT courses. They participate in mandatory didactic trainings that prepare them to teach KIT. During their 4th and 9th semesters, respectively, students take summative exams that test their communicative competence. Results: According to the semester evaluations by students and instructors, students participating in KIT improved their conversation management skills (students: M=2.2, SD=1.1, instructors: M=1.9, SD=0.7, on a scale of 1-5). In addition, students and graduates rate KIT to be (very) relevant, consider the degree to which it is taught in the MSM to be (very) high, and consider KIT to be a meaningful part of the curriculum. Students taking the summative exams in their 4th and 9th semesters achieve a mean score of 75.9%, respectively 76.9%, in the purely communicative stations and 82.6%, respectively 83.3%, in the global evaluation of communicative competence in clinical-practical stations. Discussion: Survey and exam results alike indicate that the communication training is well accepted by students and instructors and that the training led to an improvement in general and specific communicative skills. Due to a lack of control groups or a pre-post design, it has thus far not been possible to unequivocally demonstrate a causal relationship between communicative competence trainings and good test results. Quality control measures, such as trainings for instructors and regular course evaluations, have been designed to address any challenges in the implementation of the communication curriculum at the faculty level. Conclusion: Building on the experience with the Charité's Reformed Medical Curriculum, a longitudinal, competence-based communication curriculum was integrated into the MSM's overall curriculum. This measure remedied a gap in the medical training that many graduates of regular study programs had previously bemoaned (Jansen 2010 [1]).
| S-EPMC7994867 | biostudies-literature
Project description:BackgroundThe further development of research capacity in low- and middle-income countries is critical to the delivery of evidence-based healthcare, the design of sound health policy and effective resource allocation. Research capacity is also critical for the retention of highly skilled faculty and staff and for institutional internationalization.ObjectivesWe summarize the accomplishments, challenges and legacy of a five-year program to train biomedical researchers entitled "Enhanced Advanced Biomedical Research Training for Mozambique (EABRTM)".MethodsA program conducted from 2015-2021 built upon the Medical Education Partnership Initiative to develop research capacity at Eduardo Mondlane University (UEM) and allied institutions. The project included design and implementation of postgraduate training programs and bolstered physical and human research infrastructure.FindingsThe program supported development and implementation of UEM's first doctoral (Bioscience and Public Health) and master (Biosciences) programs with 31 and 23 students enrolled to date, respectively. Three master programs were established at Lúrio University from which 176/202 (87.1%) and 107/202 (53.0%) students obtained a Postgraduate Diploma or master's degree, respectively. Scholarships were awarded to 39 biomedical researchers; 13 completed master degrees, one completed a PhD and five remain in doctoral studies. Thirteen administrative staff and four biomedical researchers were trained in research administration and in biostatistics, respectively. A total of 119 courses and seminars benefited 2,142 participants. Thirty-five manuscripts have been published to date in peer-reviewed international journals of which 77% are first-authored by Mozambicans and 44% last-authored by Africans. Sustainability was achieved through 59 research projects awarded by international agencies, totaling $16,363,656.42 and funds ($ 7,319,366.11) secured through 2025.ConclusionsThe EABRTM program substantially increased research and mentorship capacity and trained a new generation of biostatisticians and research administrators. These programmatic outcomes significantly increased the confidence of early stage Mozambican researchers in their ability to successfully pursue their career goals.
| S-EPMC9354555 | biostudies-literature
Project description:BackgroundThree-dimensional (3D) visual displays have been suggested to aid laparoscopic skills training by providing the depth cues not present in traditional two-dimensional (2D) displays. However, few studies have robustly investigated the impact of viewing mode (2D vs. 3D) on learning outcomes.PurposeTo examine how viewing mode (2D vs. 3D) impacts the acquisition and transferability of basic laparoscopic skills by comparing performance between transfer and control groups on a complete proficiency-based training program.MethodA counterbalanced between-subjects design was employed. Each participant was randomly allocated to one of four groups, comprising two transfer groups (trained in one viewing mode and tested in the alternate mode: the 2D → 3D and 3D → 2D groups) and two control groups (trained and tested in one viewing mode: the 2D → 2D and 3D → 3D groups). Participants completed proficiency-based training in six laparoscopic training tasks. Testing included two further repetitions of all tasks under test conditions. Objective performance measures included the total number of repetitions to reach proficiency, and total performance scores (i.e. time + error penalties across all repetitions) in training and testing.ResultsThe groups trained in 3D demonstrated superior training performance (i.e. less time + errors) and took fewer repetitions to reach proficiency than the groups trained in 2D. The groups tested in 3D also demonstrated superior test performance compared to those tested in 2D. However, training mode did not yield significant test differences between the groups tested in 2D (i.e. 2D → 2D vs. 3D → 2D), or between the groups tested in 3D (i.e. 3D → 3D vs. 2D → 3D).ConclusionNovices demonstrate superior performance in laparoscopic skills training using a 3D viewing mode compared to 2D. However, this does not necessarily translate to superior performance in subsequent testing or enhanced learning overall. Rather, test performance appears to be dictated by the viewing mode used during testing, not that of prior training.
| S-EPMC8263422 | biostudies-literature