The development and application of bioinformatics core competencies to improve bioinformatics training and education

Abstract

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training

“…In recent years, concern about the growing computational skills gap amongst life scientists has prompted the articulation of core bioinformatics competencies, aiming to facilitate development of curricula able to deliver appropriate skills to learners. However, implementing competencies in curricula has proved problematic: this is partly because there are still disparate views on what it means to be a trained bioinformatician, and partly also because competencies are actually complex, multi-dimensional educational end-points, making it difficult to achieve a common understanding of how to deliver requisite training in practice (e.g., [65]; [56]). These problems have led some researchers to suggest refinements to bioinformatics competencies, including the identification of phases of competency, and the provision of guidance on the evidence required to assess whether a given competency has been acquired [20]; others have already revised their competencybased framework to include learning trajectories, charting the progression of individuals' abilities through defined stages via milestones [28].…”

“…It should be stressed that creating any kind of 'framework' to support the development of competencies involves numerous stakeholders and is hugely time-consuming, not least because marrying multiple stakeholder views is hard. For example, the current version of the European e-Competence Framework (e-CF) for ICT skills (http://www.ecompetences.eu) has taken more than 8 years to develop; similarly, the ISCB competencies have been evolving over at least the last 6 years -inevitably, few aspects escape dissent when stakeholders from very different backgrounds, with disparate student populations and different educational goals attempt to achieve consensus [65]. Likewise, formulation of the current version of the MR-Bi has taken more than 2 years, and further refinements are likely to be required with future additional stakeholder input.…”

Blended Bioinformatics Training in Resource-Limited Settings: A case study of challenges and Opportunities for Implementation

“…Especially for bioinformatics, there are huge, urgent, unmet training needs [Attwood et al, 2017] exacerbated by the breadth of the discipline and its rapid evolution [Mulder et al, 2018], notwithstanding difficulty of curricula design to learners of diverse backgrounds [Bishop et al, 2014], and the shortage in experienced qualified trainers [Attwood et al, 2017]. Therefore, various international efforts were exerted to bridge this skills gap, like GOBLET, ELIXIR, BD2K TCC and H3ABioNet.…”

“…The rapid advancements in genomics and molecular biology research and applications necessitates adequate, up-to-date and complimentary training in biology and computer science [Attwood et al, 2017, Mulder et al, 2018.…”

The African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in Africa

“…The article demonstrates how the AGMT initiative adapted the Kern's sixstep model for the development of a medical curriculum. In addition, the Kern's six-step model was modified to incorporate a competency mapping approach developed by the International Society of Computational Bioinformatics (ISCB) (Mulder et al, 2018). Formal medical educational programs have aims and goals that are often not clearly articulated and, in some instances, poorly understood by key constituents inside and outside of the formal education system (Kern and Thomas, 2009).…”