Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

Welch, Lonnie R.; Brooksbank, Cath; Schwartz, Russell; Morgan, Sarah; Gaëta, Bruno; Kilpatrick, Alastair M.; Mietchen, Daniel; Moore, Benjamin L.; Mulder, Nicola; Pauley, Mark A.; Pearson, William R.; Radivojac, Predrag; Rosenberg, Naomi; Rosenwald, Anne G.; Rustici, Gabriella; Warnow, Tandy

doi:10.1371/journal.pcbi.1004943

Cited by 22 publications

(29 citation statements)

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“…The increased availability of microbiome and other “big data” data sets has coincided with calls for life science undergraduates to have bioinformatics “minimum skill sets” or “core competencies” in order to meet the growing demand to analyze that data ( Tan et al, 2009 ; Welch et al, 2016 ; Mulder et al, 2018 ; Sayres et al, 2018 ). PUMAA has been in use in the Research Immersion in Microbiology undergraduate laboratories at UCLA for a number of years, resulting in the development of a suite of instructional materials and tutorials to train students in many of the bioinformatics skills necessary to meet this demand.…”

Section: Discussionmentioning

confidence: 99%

“…In practice, the instructional staff runs the PUMAA program and provides students with files ready for use in Excel, ranacapa, STAMP, and other tools. One limitation of this approach is that students do not get direct experience with command-line bioinformatics, which is one of the core competencies for undergraduate life sciences education described by several different bioinformatics curriculum committees ( Tan et al, 2009 ; Welch et al, 2016 ; Mulder et al, 2018 ; Sayres et al, 2018 ). However, the International Society for Computational Biology’s Curriculum Task Force has refined their core competencies and designated different user profiles requiring different levels of competency ( Mulder et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

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PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

et al. 2020

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Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

et al. 2020

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“…In order to gain a broader appreciation of which competencies the bioinformatics community considers relevant for different bioinformatics user profiles, the ISCB Curriculum Task Force has run several competency workshops (discussion sessions for defining the competencies and their applications) both at ISCB conferences and at other bioinformatics education venues such as the GOBLET (Global Organisation for Bioinformatics Learning, Education and Training) Annual General Meeting. Each iteration of a competency workshop has greatly enhanced not only the competencies themselves but also the definitions of the user profiles [ 1 ] and the competency-use case scoring mechanism.…”

Section: Development Of Core Competencies For Bioinformaticsmentioning

confidence: 99%

“…By contrast, a bioinformatics user (which we define as someone making use of bioinformatics resources in an applied context, such as in medical practice) would need a basic level of understanding of the methods and a stronger focus on the interpretation of the outputs. In a recent publication [ 1 ], the ISCB Education Committee’s Curriculum Task Force described the potential for refinement and application of bioinformatics core competencies for different user groups. Here, we describe the further refinement of these competencies and provide a series of use cases illustrating their applications to different bioinformatics education and training programs globally.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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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.

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“…Bioinformatics is an interdisciplinary area that requires a depth knowledge in computational, statistical/mathematical and life sciences subjects. In 2016, the ISCB Education Committee's Curriculum Task Force described needs for bioinformatics education and competencies of bioinformatics engineers who actively develops algorithms and computational systems, as well as of bioinformatics users that explore computational infrastructures and softwares in specific contexts to work on data analysis of different sorts, such as population genetics, phylogeny, medical genetics (Mulder et al, 2018;Welch et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

From bioinformatics user to bioinformatics engineer: a report

Araújo

2020

Preprint

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Teaching computer programming is not a simple task and it is challenging to introduce the concepts of programming in graduate programs of other fields. Little efforts have been made on engaging students in computational development after programming trainings. An emerging need is to establish subjects of bioinformatics and programming languages in genetics and molecular biology graduate programs, when students in these degree programs are immersed in a sea of genomic and transcriptomic data, which demands proficient computational treatment. I report an empirical guideline to introduce programming languages and recommend Python as first language for graduate programs in which students were from genetics and molecular biology backgrounds. Including the development of programming solutions related to graduate students' research activities may improve programming skills and better engagement. These results suggest that the applied approach leads to enhanced learning of introductory to autonomy in highly advanced programming concepts by graduate students. This guide should be extended for other research programs.

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Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

Cited by 22 publications

References 10 publications

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

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

From bioinformatics user to bioinformatics engineer: a report

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