Bioinformatics Course Research Articles

Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students.

We learn more effectively through experience and reflection than through passive reception of information. Bioinformatics offers an excellent opportunity for project-based learning. Molecular data are abundant and accessible in open repositories, and important concepts in biology can be rediscovered by reanalyzing the data. In the manuscript, we report on five hands-on assignments we designed for master's computer science students to train them in bioinformatics for genomics. These assignments are the cornerstones of our introductory bioinformatics course and are centered around the study of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). They assume no prior knowledge of molecular biology but do require programming skills. Through these assignments, students learn about genomes and genes, discover their composition and function, relate SARS-CoV-2 to other viruses, and learn about the body's response to infection. Student evaluation of the assignments confirms their usefulness and value, their appropriate mastery-level difficulty, and their interesting and motivating storyline. The course materials are freely available on GitHub at https://github.com/IB-ULFRI.

Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course.

Computer programming is a fundamental tool for life scientists, allowing them to carry out essential research tasks. However, despite various educational efforts, learning to write code can be a challenging endeavor for students and researchers in life-sciences disciplines. Recent advances in artificial intelligence have made it possible to translate human-language prompts to functional code, raising questions about whether these technologies can aid (or replace) life scientists' efforts to write code. Using 184 programming exercises from an introductory-bioinformatics course, we evaluated the extent to which one such tool-OpenAI's ChatGPT-could successfully complete programming tasks. ChatGPT solved 139 (75.5%) of the exercises on its first attempt. For the remaining exercises, we provided natural-language feedback to the model, prompting it to try different approaches. Within 7 or fewer attempts, ChatGPT solved 179 (97.3%) of the exercises. These findings have implications for life-sciences education and research. Instructors may need to adapt their pedagogical approaches and assessment techniques to account for these new capabilities that are available to the general public. For some programming tasks, researchers may be able to work in collaboration with machine-learning models to produce functional code.

A data science practicum to introduce undergraduate students to bioinformatics for research.

An explosion of data available in the life sciences has shifted the discipline toward genomics and quantitative data science research. Institutions of higher learning have been addressing this shift by modifying undergraduate curriculums resulting in an increasing number of bioinformatics courses and research opportunities for undergraduates. The goal of this study was to explore how a newly designed introductory bioinformatics seminar could leverage the combination of in-class instruction and independent research to build the practical skill sets of undergraduate students beginning their careers in the life sciences. Participants were surveyed to assess learning perceptions toward the dual curriculum. Most students had a neutral or positive interest in these topics before the seminar and reported increased interest after the seminar. Students had increases in confidence level in their bioinformatic proficiency and understanding of ethical principles for data/genomic science. By combining undergraduate research with directed bioinformatics skills, classroom seminars facilitated a connection between student's life sciences knowledge and emerging research tools in computational biology.

Teaching Python programming for bioinformatics with Jupyter notebook in the Post-COVID-19 era.

The COVID-19 pandemic has forced the Bioinformatics course to switch from on-site teaching to remote learning. This shift has prompted a change in teaching methods and laboratory activities. Students need to have a basic understanding of DNA sequences and how to analyze them using custom scripts. To facilitate learning, we have modified the course to use Jupyter Notebook, which offers an alternative approach to writing custom scripts for basic DNA sequence analysis. This approach allows students to acquire the necessary skills while working remotely. It is a versatile and user-friendly platform that can be used to combine explanations, code, and results in a single document. This feature enables students to interact with the code and results, making the learning process more engaging and effective. Jupyter Notebook provides a hybrid approach to learning basic Python scripting and genomics that is effective for remote teaching and learning during the COVID-19 pandemic.

An overview of bioinformatics courses delivered at the academic level in Italy: Reflections and recommendations from BITS.

In Italian universities, bioinformatics courses are increasingly being incorporated into different study paths. However, the content of bioinformatics courses is usually selected by the professor teaching the course, in the absence of national guidelines that identify the minimum indispensable knowledge in bioinformatics that undergraduate students from different scientific fields should achieve. The Training&Teaching group of the Bioinformatics Italian Society (BITS) proposed to university professors a survey aimed at portraying the current situation of bioinformatics courses within undergraduate curricula in Italy (i.e., bioinformatics courses activated within both bachelor's and master's degrees). Furthermore, the Training&Teaching group took a cue from the survey outcomes to develop recommendations for the design and the inclusion of bioinformatics courses in academic curricula. Here, we present the outcomes of the survey, as well as the BITS recommendations, with the hope that they may support BITS members in identifying learning outcomes and selecting content for their bioinformatics courses. As we share our effort with the broader international community involved in teaching bioinformatics at academic level, we seek feedback and thoughts on our proposal and hope to start a fruitful debate on the topic, including how to better fulfill the real bioinformatics knowledge needs of the research and the labor market at both the national and international level.

An integrated microbiome project for charactering microbial diversity in classroom based on virtual simulation experiments.

Microbiome study requires both molecular techniques and bioinformatics skills, which are challenging for biologists to participate in this growing field. To introduce microbiome concepts and skills to students, a 6-week wet-lab and bioinformatics course for undergraduates was implemented through the project-based learning (PBL) approach. In the saliva microbiome project, students collected their saliva samples, performed DNA extraction and PCR amplification, followed by metagenomic analysis to compare the diversity and abundances of microbes among samples. First, students are required to practice molecular techniques and bioinformatics analysis skills in a virtual simulation lab. To our knowledge, our study is the first one to incorporate a virtual lab into microbiome experience. Then, students applied their recently acquired skills to produce and analyze their own 16S amplicon sequencing data and reported their results via a scientific report. The student learning outcomes show that the Virtual lab can improve students' laboratory techniques and research capabilities. Moreover, a simple pipeline to analyze 16S rRNA gene amplicon sequencing data is introduced in a step-by-step manner that helps students to develop analysis skills. This project can be modified as either a virtual course or a module within another course such as microbiology, molecular biology, and bioinformatics. Our study provides evidence on the positive impact of virtual labs on learning outcomes in undergraduate science education.

The impact of gender roles and previous exposure on major choice, perceived competence, and belonging: a qualitative study of students in computer science and bioinformatics classes

ABSTRACT Background and Context While biology has strong female representation, computer science is the least gender equitable of the STEM fields. A better understanding of the barriers that keep women out of computational fields will help overcome those barriers to create a more diverse workforce. Objective We investigated the complexities that influence students’ major choice and their sense of belonging. We were particularly interested in students adjacent to computer science and differences by gender. Method We conducted semi-structured interviews of nineteen students from computer science or bioinformatics courses. We used inductive thematic analysis that included iterative readings of interview transcripts, line-by-line coding, and final theme selection. Findings Most students described pressures stemming from traditional gender roles as they chose their major, but specific pressures differed by gender. Men were more likely to report early exposure to their major field, and women noted feeling behind without those early experiences. This hurt the women’s sense of belonging, as did having few female peers. Implications Increasing early exposure to coding may increase women's representation and sense of belonging in computational fields. Women from contexts with emphasis on traditional gender roles may be drawn to computational fields if they see opportunities for flexible positions.

Study on blended teaching mode and its application based on the ARCS motivational model: Taking bioinformatics course as an example.

With the advent of the “Internet +” era, technologies like big data and artificial intelligence are emerging, and teaching models are constantly being innovated. Blended teaching mode combines the advantages of online teaching and traditional classroom. However, during the process of specific teaching practice, there are many problems such as insufficient use of intelligent platform, insufficient dominant position of students, difficult to maintain a high learning motivation for a long time, and a mere formality of blended teaching. Therefore, this study first uses the Attention, Relevance, Confidence, and Satisfaction motivational model to explore its application in Bioinformatics course blended teaching. The classroom teaching mode was reconstructed from 3 aspects: pre-class guidance, in-class research, and after-class promotion. This model provides new ideas and directions for teaching innovation and curriculum reform in the colleges.

Survey of bioinformatics courses and concentrations in ALA-accredited master's programs.

IntroductionThe interdisciplinary field of bioinformatics is considered an information-based discipline by many. Yet, it is unclear how Master of Library and Information Science (MLIS) degrees prepare librarians to apply their expertise in this unique, often non-textual information environment. The goal of this study is to identify the availability of MLIS-based bioinformatics educational opportunities to provide an update to the current bioinformatics landscape in North American MLIS programs or iSchools.MethodsWe conducted a survey of available bioinformatics courses and program concentrations within 69 ALA-accredited master’s programs. Using course catalogues and program descriptions on department websites, we identified the existence of courses and concentrations specific or related to the field of bioinformatics. We also surveyed the availability of associated certificate programs or degree alternatives.ResultsOnly two library and information science (LIS)-based bioinformatics courses are currently offered to MLIS students in ALA-accredited programs. There are no bioinformatics concentrations offered in the programs surveyed, however two graduate certificates could be applied towards an ALA-accredited master’s degree. Students interested in related fields can pursue degree alternatives, including eight dual degree options.DiscussionThe scarcity of LIS-based bioinformatics courses and program concentrations may suggest that LIS has not adopted bioinformatics into their field nor curricula. As a result, students interested in pursuing careers in bioinformatics and related disciplines must actively seek out opportunities for education and professional development. Bioinformatics degree options within MLIS or iSchools points towards an increased dialogue and acceptance of the connection between bioinformatics and information science, but the lack of ALA -accreditation limits possibilities for emerging librarians.

A phylogenetic study of covid-19 data from Aragon and Catalonia over a year: learning Bioinformatics during a world pandemic

We present here a one year variability analysis of SARS-CoV-2 virus in the Aragon area, comparing it to neighboring Catalonia and focusing on the UK-variant. Research was performed within a Bioinformatics course. Both a detailed assessment on the value of this methodology and novel research conclusions were extracted.

An undergraduate genome research course using "big data".

The ability to analyze large data sets ("Big Data") is an increasingly important skill in modern science. In Biochemistry, the increased volume and velocity of data is particularly evident in the rapid expansion of biological databases. We present a modular bioinformatics course to survey the analysis of genomic data for advanced undergraduates. Research activities include genome scanning for endogenous retroviruses, annotating genomic sequences and a brief exploration of programming in R. A summative poster session was used to disseminate their work. This course is amenable to remote or online instruction. Supplemental materials provided include a schedule and outline. This article reports a session from the virtual international 2021 IUBMB/ASBMB workshop, "Teaching Science on Big Data."

Necessity is the Mother of Invention: A Remote Molecular Bioinformatics Practical Course in the COVID-19 Era.

The COVID-19 pandemic has brought many challenges to human beings, related to not only health and way of life but also teaching because of the interruption of the standard training at universities imposed by lockdowns. Concerning the latter, the academic community had to reinvent itself, in many ways, to carry on with prepandemic education. This article focuses on the use of modern technology and software to create a virtual, highly interactive classroom where a remote but still hands-on course on molecular bioinformatics can be taught, motivating the university students and helping them learn the course contents without significant compromises imposed by successive lockdowns. We implemented such a virtual hands-on molecular bioinformatics course in the second semester of the 2020/2021 academic year. Furthermore, we compared the learning outcomes with those for the earlier editions of the same course in the pre-COVID-19 era, in which the more traditional teaching method was used where all teaching was delivered with physically present lecturers. The virtual classroom proposed here allowed the students to develop skills close to, although slightly below, those obtained with physically present learning.

Exploration on the Teaching Model Reform of ��Bioinformatics�� Course in Agricultural Universities

Exploration on the Teaching Model Reform of ��Bioinformatics�� Course in Agricultural Universities

Interdisciplinary and Transferable Concepts in Bioinformatics Education: Observations and Approaches From a UK MSc Course

Bioinformatics is a highly interdisciplinary subject, with substantial and growing influence in health, environmental science and society, and is utilised by scientists from many diverse academic backgrounds. Education in bioinformatics therefore necessitates effective development of skills in interdisciplinary collaboration, communication, ethics, and critical analysis of research, in addition to practical and technical skills. Insights from bioinformatics training can additionally inform developing education in the tightly aligned and emerging disciplines of data science and artificial intelligence. Here, we describe the design, implementation, and review of a module in a UK MSc-level bioinformatics programme attempting to address these goals for diverse student cohorts. Reflecting the philosophy of the field and programme, the module content was designed either as “diversity-addressing”—working toward a common foundation of knowledge—or “diversity-exploiting”—where different student viewpoints and skills were harnessed to facilitate student research projects “greater than the sum of their parts.” For a universal introduction to technical concepts, we combined a mixed lecture/immediate computational practical approach, facilitated by virtual machines, creating an efficient technical learning environment praised in student feedback for building confidence among cohorts with diverse backgrounds. Interdisciplinary group research projects where diverse students worked on real research questions were supervised in tandem with interactive contact time covering transferable skills in collaboration and communication in diverse teams, research presentation, and ethics. Multi-faceted feedback and assessment provided a constructive alignment with real peer-reviewed bioinformatics research. We believe that the inclusion of these transferable, interdisciplinary, and critical concepts in a bioinformatics course can help produce rounded, experienced graduates, ready for the real world and with many future options in science and society. In addition, we hope to provide some ideas and resources to facilitate such inclusion.

Employing Collaborative Problem-Based Learning for an Immersive Online Experience in an Undergraduate Bioinformatics Course

Employing Collaborative Problem-Based Learning for an Immersive Online Experience in an Undergraduate Bioinformatics Course

An Appraisal of Skill Gaps in Bioinformatics Education

There has been an exponential rise in the field of bioinformatics in the last decade. The specialists of this field need to be well versed in computing, statistics, and mathematics, along with expertise in biological sciences. This review is an attempt to understand the existing skill gaps in the education of bioinformatics globally and to give the policy developers some indicators while designing the curriculum of the bioinformatics course. Authors have found that the pace with which this field is developing is not commensurate with the training and education efforts at the university level globally. But, on a positive note, academia and industry both seem to recognise this lag, therefore, efforts are being made in this direction. This review also summarizes the distinctive features needed to integrate bioinformatics in education for curriculum designing, teaching, and learning methods.

Are We Prepared for Precision Public Health? An Examination of Genomics Content in Graduate Public Health Programs.

With the completion of the Human Genome Project and swift development of genomic technologies, public health practitioners can use these advancements to more precisely target disease interventions to populations at risk. To integrate these innovations into better health outcomes, public health professionals need to have at least a basic understanding of genomics within various disciplines of public health. This descriptive study focused on the current level of genomics content in accredited master of public health (MPH) programs in the United States. We conducted an internet search on all 171 Council on Education for Public Health (CEPH)-accredited MPH programs in the United States for genomics content in required and elective courses using the search terms "genetics," "genomics," and "molecular." Of the 171 CEPH-accredited MPH programs examined, 52 (30.4%) schools and programs in 34 states offered some type of genomics education. Thirty-five (20.5%) schools and programs had a course in genetic epidemiology, 29 (16.9%) had a course in genetic biostatistics or bioinformatics, and 17 (9.9%) had a course in general public health genomics. The remaining 119 offered no course with a focus on genetics or genomics. In addition, some electives or specifically focused courses related to genomics were offered. We found inadequate training in public health genomics for MPH students. To realize the promise of precision public health and to increase the understanding of genomics among the public health workforce, MPH programs need to find ways to integrate genomics education into their curricula.

From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics.

Bioinformatics is a fast-evolving research field, requiring effective educational initiatives to bring computational knowledge to Life Sciences. Since 2017, an organizing committee composed of graduate students and postdoctoral researchers from the Universidade Federal de Minas Gerais (Brazil) promotes a week-long event named Summer Course in Bioinformatics (CVBioinfo). This event aims to diffuse bioinformatic principles, news, and methods mainly focused on audiences of undergraduate students. Furthermore, as the advent of the COVID-19 global pandemic has precluded in-person events, we offered the event in online mode, using free video transmission platforms. Herein, we present and discuss the insights obtained from promoting the Online Workshop in Bioinformatics (WOB) organized in November 2020, comparing it to our experience in previous in-person editions of the same event.

Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education.

MotivationDue to the worldwide COVID-19 pandemic, new strategies had to be adopted to move from classroom-based education to online education, in a very short time. The lack of time to set up these strategies, hindered a proper design of online instructions and delivery of knowledge. Bioinformatics-related training and other onsite practical education, tend to rely on extensive practice, where students and instructors have a face-to-face interaction to improve the learning outcome. For these courses to maintain their high quality when adapted as online courses, different designs need to be tested and the students’ perceptions need to be heard.ResultsThis study focuses on short bioinformatics-related courses for graduate students at the University of Gothenburg, Sweden, which were originally developed for onsite training. Once adapted as online courses, several modifications in their design were tested to obtain the best fitting learning strategy for the students. To improve the online learning experience, we propose a combination of: (i) short synchronized sessions, (ii) extended time for own and group practical work, (iii) recorded live lectures and (iv) increased opportunities for feedback in several formats.Supplementary informationSupplementary data are available at Bioinformatics online.

Development and teaching of a bioinformatics course to biochemistry major students in a Nigerian University during COVID-19 pandemic.

The influence of bioinformatics is pervasive affecting many biological disciplines resulting in changes in biosciences globally but not so in, Nigeria as the course is never taught in any public tertiary institution. This article describes development and teaching of bioinformatics integrated into bachelor's degree programme in biochemistry, during the COVID‐19 pandemic. Resources from the course are available for use by colleagues and students.