Making authentic science accessible-the benefits and challenges of integrating bioinformatics into a high-school science curriculum

Learning and STEM identity gains from an online module on sequencing-based surveillance of antimicrobial resistance in the environment: An analysis of the PARE-Seq curriculum

COVID-19 necessitated the rapid transition to online learning, challenging the ability of Science, Technology, Engineering, and Math (STEM) professors to offer laboratory experiences to their students. As a result, many instructors sought online alternatives. In addition, recent literature supports the capacity of online curricula to empower students of historically underrepresented identities in STEM fields. Here, we present PARE-Seq, a virtual bioinformatics activity highlighting approaches to antimicrobial resistance (AMR) research. Following curricular development and assessment tool validation, pre- and post-assessments of 101 undergraduates from 4 institutions revealed that students experienced both significant learning gains and increases in STEM identity, but with small effect sizes. Learning gains were marginally modified by gender, race/ethnicity, and number of extracurricular work hours per week. Students with more extracurricular work hours had significantly lower increase in STEM identity score after course completion. Female-identifying students saw greater learning gains than male-identifying, and though not statistically significant, students identifying as an underrepresented minority reported larger increases in STEM identity score. These findings demonstrate that even short course-based interventions have potential to yield learning gains and improve STEM identity. Online curricula like PARE-Seq can equip STEM instructors to utilize research-driven resources that improve outcomes for all students, but support must be prioritized for students working outside of school.

Conceptualizing learning about proteins with a molecular viewer in high school based on the integration of two theoretical frameworks

The use of a molecular viewer to visualize proteins has become more prevalent in high schools in recent years. We relied on the foundations of two theoretical frameworks to analyze questions in two learning tasks designed for 10th- to 12th-grade biotechnology majors that make use of Jmol. The two theoretical frameworks were: (i) classification of scientific knowledge into content, procedural, and epistemic knowledge; and (ii) evaluation of the cognitive skills central to visual literacy in biochemistry. During the analysis, two sub-elements of procedural knowledge emerged from the data: (i) the visualization of molecular models, and (ii) the use of Jmol software features. Based on the theoretical frameworks and data analysis, we suggest a conceptualization of learning about proteins using a molecular viewer, where the scientific knowledge elements are integrated with the eight cognitive skills central to visual literacy in biochemistry. In addition, a model presenting a hierarchy for the knowledge elements and sub-elements is suggested. In this model, content knowledge is a basic requirement; without it, the other knowledge elements cannot be used. Moreover, the use of epistemic knowledge or Jmol software features is not possible without visualization of the molecular models, which requires content knowledge. This conceptualization is expected to facilitate the development of learning tasks, decrease the complexity of knowledge acquisition for students; it may also assist the teacher during the teaching process.

Integrating Biomedical Informatics Training into Existing High School Curricula

Growing demand for biomedical informaticists and expertise in areas related to this discipline has accentuated the need to integrate biomedical informatics training into high school curricula. The K-12 Bioinformatics professional development project educates high school teachers about data analysis, biomedical informatics and mobile learning, and partners with them to expose high school students to health and environment-related issues using biomedical informatics knowledge and current technologies. We designed low-cost pollution sensors and created interactive web applications that teachers from six Philadelphia public high schools used during the 2019-2020 school year to successfully implement a problem-based mobile learning unit that included collecting and interpreting air pollution data, as well as relating this data to asthma. Through this project, we sought to improve data and health literacy among the students and teachers, while inspiring student engagement by demonstrating how biomedical informatics can help address problems relevant to communities where students live.

Bioinformatics-Based Activities in High School: Fostering Students' Literacy, Interest, and Attitudes on Gene Regulation, Genomics, and Evolution

The key role of bioinformatics in explaining biological phenomena calls for the need to rethink didactic approaches at high school aligned with a new scientific reality. Despite several initiatives to introduce bioinformatics in the classroom, there is still a lack of knowledge on their impact on students' learning gains, engagement, and motivation. In this study, we detail the effects of four bioinformatics laboratories tailored for high school biology classes named "Mining the Genome: Using Bioinformatics Tools in the Classroom to Support Student Discovery of Genes" on literacy, interest, and attitudes on 387 high school students. By exploring these laboratories, students get acquainted with bioinformatics and acknowledge that many bioinformatics tools can be intuitive for beginners. Furthermore, introducing comparative genomics in their learning practices contributed for a better understanding of curricular contents regarding the identification of genes, their regulation, and how to make evolutionary assumptions. Following the intervention, students were able to pinpoint bioinformatics tools required to identify genes in a genomics sequence, and most importantly, they were able to solve genomics-related misconceptions. Overall, students revealed a positive attitude regarding the integration of bioinformatics-based approaches in their learning practices, reinforcing their added value in educational approaches.

MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration

BACKGROUND

The complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts. This complexity creates a barrier to wider implementation of experiential genomics education, even in settings with substantial computational resources and expertise. Reducing the need for specialized software tools will increase access to hands-on genomics pedagogy.

RESULTS

MySeq is a React.js single-page web application for privacy-protecting interactive personal genome analysis. All analyses are performed entirely in the user's web browser eliminating the need to install and use specialized software tools or to upload sensitive data to an external web service. MySeq leverages Tabix-indexing to efficiently query whole genome-scale variant call format (VCF) files stored locally or available remotely via HTTP(s) without loading the entire file. MySeq currently implements variant querying and annotation, physical trait prediction, pharmacogenomic, polygenic disease risk and ancestry analyses to provide representative pedagogical examples; and can be readily extended with new analysis or visualization components.

CONCLUSIONS

MySeq supports multiple pedagogical approaches including independent exploration and interactive online tutorials. MySeq has been successfully employed in an undergraduate human genome analysis course where it reduced the barriers-to-entry for hands-on human genome analysis.

Teaching a difficult topic using a problem-based concept resembling a computer game: development and evaluation of an e-learning application for medical molecular genetics

BACKGROUND

Genetic testing rapidly penetrates into all medical specialties and medical students must acquire skills in this area. However, many of them consider it difficult. Furthermore, many find these topics less appealing and not connected to their future specialization in different fields of clinical medicine. Student-centred strategies such as problem-based learning, gamification and the use of real data can increase the appeal of a difficult topic such as genetic testing, a field at the crossroads of genetics, molecular biology and bioinformatics.

METHODS

We designed an electronic teaching application which students registered in the undergraduate Medical Biology course can access online. A study was carried out to assess the influence of implementation of the new method. We performed pretest/posttest evaluation and analyzed the results using the sign test with median values. We also collected students' personal comments.

RESULTS

The newly developed interactive application simulates the process of molecular genetic diagnostics of a hereditary disorder in a family. Thirteen tasks guide students through clinical and laboratory steps needed to reach the final diagnosis. Genetics and genomics are fields strongly dependent on electronic databases and computer-based data analysis tools. The tasks employ publicly available internet bioinformatic resources used routinely in medical genetics departments worldwide. Authenticity is assured by the use of modified and de-identified clinical and laboratory data from real families analyzed in our previous research projects. Each task contains links to databases and data processing tools needed to solve the task, and an answer box. If the entered answer is correct, the system allows the user to proceed to the next task. The solving of consecutive tasks arranged into a single narrative resembles a computer game, making the concept appealing. There was a statistically significant improvement of knowledge and skills after the practical class, and most comments on the application were positive. A demo version is available at https://medbio.lf2.cuni.cz/demo_m/ . Full version is available on request from the authors.

CONCLUSIONS

Our concept proved to be appealing to the students and effective in teaching medical molecular genetics. It can be modified for training in the use of electronic information resources in other medical specialties.

Harnessing robotic automation and web-based technologies to modernize scientific outreach

Technological breakthroughs in the past two decades have ushered in a new era of biomedical research, turning it into an information-rich and technology-driven science. This scientific revolution, though evident to the research community, remains opaque to nonacademic audiences. Such knowledge gaps are likely to persist without revised strategies for science education and public outreach. To address this challenge, we developed a unique outreach program to actively engage over 100 high-school students in the investigation of multidrug-resistant bacteria. Our program uses robotic automation and interactive web-based tools to bridge geographical distances, scale up the number of participants, and reduce overall cost. Students and teachers demonstrated high engagement and interest throughout the project and valued its unique approach. This educational model can be leveraged to advance the massive open online courses movement that is already transforming science education.

This Community Page article describes the use of robotic automation and web-based tools to allow high-school students around the world to run empirical experiments remotely and to collaboratively investigate the emergence of multidrug resistance during bacterial evolution.

Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching

We present here an interdisciplinary workshop on the subject of biomolecules offered to undergraduate and high school students with the aim of boosting their interest toward all areas of science contributing to the study of life. The workshop involves mathematics, physics, chemistry, computer science and biology. Based on our own areas of research, molecular modelling is chosen as the central axis as it involves all disciplines. To provide a strong biological motivation for the study of the dynamics of biomolecules, the theme of the workshop is the origin of life. All sessions are built around active pedagogy, including games, and a final poster presentation.