Know-how of holding a Bioinformatics competition: Structure, model, overview, and perspectives.

The article presents a framework for a Bioinformatics competition that focuses on 4 key aspects: structure, model, overview, and perspectives. Structure represents the organizational framework employed to coordinate the main tasks involved in the competition. Model showcases the competition design, which encompasses 3 phases. Overview presents our case study, the League of Brazilian Bioinformatics (LBB) 2nd Edition. Finally, the section on perspectives provides a brief discussion of the LBB 2nd Edition, along with insights and feedback from participants. LBB is a biannual team competition launched in 2019 to promote the ongoing training of human resources in Bioinformatics and Computational Biology in Brazil. LBB aims to stimulate ongoing training in Bioinformatics by encouraging participation in competitions, promoting the organization of future Bioinformatics competitions, and fostering the integration of the Bioinformatics and Computational Biology community in the country, as well as collaboration among participants. The LBB 2nd Edition was launched in 2021 and featured 251 competitors forming 91 teams. Knowledge competitions promote learning, collaboration, and innovation, which are crucial for advancing scientific knowledge and solving real-world problems. In summary, this article serves as a valuable resource for individuals and organizations interested in developing knowledge competitions, offering a model based on our experience with LBB to benefit all levels of Bioinformatics trainees.

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.

Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources.

Stand-alone life science training events and e-learning solutions are among the most sought-after modes of training because they address both point-of-need learning and the limited timeframes available for "upskilling." Yet, finding relevant life sciences training courses and materials is challenging because such resources are not marked up for internet searches in a consistent way. This absence of markup standards to facilitate discovery, re-use, and aggregation of training resources limits their usefulness and knowledge translation potential. Through a joint effort between the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), the Bioschemas Training community, and the ELIXIR FAIR Training Focus Group, a set of Bioschemas Training profiles has been developed, published, and implemented for life sciences training courses and materials. Here, we describe our development approach and methods, which were based on the Bioschemas model, and present the results for the 3 Bioschemas Training profiles: TrainingMaterial, Course, and CourseInstance. Several implementation challenges were encountered, which we discuss alongside potential solutions. Over time, continued implementation of these Bioschemas Training profiles by training providers will obviate the barriers to skill development, facilitating both the discovery of relevant training events to meet individuals' learning needs, and the discovery and re-use of training and instructional materials.

1st ASCS: Expanding the ISCB Student Council Symposia to Asia.

Since 2004, the ISCB Student Council (ISCB-SC) has successfully organized Student Council Symposia across several continents, including North America, Latin America, Europe, and Africa, as well as local events led by more than 25 Regional Student Groups (RSG) across the world. The ISCB-SC Symposia provide students and early career researchers the chance to showcase their work at an international venue in a format that includes keynote talks, round table discussions, workshops, and more. After several efforts spanning several years to build enough critical mass in the region, we have successfully organized the first Asian Student Council Symposium (1st ASCS). This article discusses the organizational details of this unprecedented event, the challenges faced, and the lessons learned.

A course-based undergraduate research experience for bioinformatics education in undergraduate students.

With rapid development of sequencing technology and the continuous accumulation of biological big data, people who are capable of using bioinformatic skills to analyze omics data and work out biological problems are urgently needed in the workforce, which highlights the importance of developing bioinformatics skills early in the undergraduate curriculum. Meanwhile, course-based undergraduate research experience (CURE) courses have been proved to be an effective teaching format that have many advantages over traditional labs and lectures. Here we introduced an implementation of CURE course of bioinformatics data analysis and visualization for undergraduate students in major of bioinformatics and evaluated the learning outcomes. We were able to address 10 out of 15 core competencies identified by Network for Integrating Bioinformatics into Life Sciences Education. Besides, results evaluated by Laboratory Course Assessment Survey demonstrated the goals of collaboration, discovery and relevance, and iteration were accomplished in our course. Meanwhile, a significant increase in scores of final examinations and a long-term improvement on students' research ability on bioinformatics data analysis and visualization were also observed. In summary, this CURE course is useful for undergraduate students learning related knowledge and participate in authentic research in the field of bioinformatics.

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.

Ten simple rules for running a summer research program.

To continue to advance the field of computational biology and fill the constantly growing need for new trainees who are well positioned for success, immersive summer research experiences have proven to be effective in preparing students to navigate the challenges that lay ahead in becoming future computational biologists. Here, we describe 10 simple rules for planning, offering, running, and improving a summer research program in computational biology that supports students in honing technical competencies for success in research and developing skills to become successful scientific professionals.

Highlights of the 1st Ecuadorian-Venezuelan Symposium of Young Researchers in Bioinformatics (1SEVJIB).

The COVID-19 pandemic profoundly changed how scientific conferences are organized, fostering virtual meetings. These online events have allowed students and researchers to overcome geographical, administrative and economic barriers to attend and organize high-quality international symposiums. Moreover, these virtual conferences have contributed to the creation of inclusive activities that strengthen scientific communities. Here, we summarize the main activities and learnings from the 1st Ecuadorian-Venezuelan Symposium of Young Bioinformatics Researchers (1SEVJIB), organized by the Ecuadorian and Venezuelan ISCB-SC Regional Student Groups (RSGs). This symposium aimed to provide an opportunity for undergraduate and postgraduate students from Ecuador, Venezuela, and other Latin American countries to share their Bioinformatics research. The 1SEVJIB was the first bi-national conference organized by two RSGs from Latin America (LatAm). This symposium was a two-day virtual meeting with five activities: 1) oral student presentations, 2) poster session, 3) keynote lectures, 4) workshop, and 5) round table. This conference promoted the scientific exchange and cooperation networks between young Bioinformatics researchers and students from Ecuador, Venezuela, and LatAm, giving them opportunities to boost their scientific careers.

Integrating experience with databases, bioinformatics, and wet lab exercises for students in an introductory genetics course.

Students often have no exposure to the incredible amount of genomic and proteomic data that is freely and easily accessible online. Becoming familiar with these resources, and seeing how they could be applied to a specific research question, is a prerequisite for students to apply them to their own scientific development. Many students have to "see it" and "do it" before they "get it." This paper describes a teaching laboratory for undergraduate Genetics students that combines exploration of several publicly available databases with some simple bioinformatic exercises and "'real" live experience in a wet lab exercise. The goal is to teach skills in applying genomic data to a real scientific question. In this exercise, students identify a target protein after exploring several protein and signal transduction databases, such as the Kyoto Encyclopedia of Genes and Genomes database. They then search for the encoding RNA in a newly available sea star mature egg transcriptome database and for the DNA in an existing sea star genome database. The students design primers against specific regions or domains in their target RNA and amplify these by reverse transcription PCR against RNA purified from fresh sea star eggs. The PCR reactions are analyzed by agarose gel electrophoresis. It is hoped that the combination of the computational biology exercises with the real lab work will excite the students and stimulate them to explore this exciting new biology further.

Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey.

The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology and bioinformatics fields by providing opportunities for improving their academic and technical skills in the field. Over the last ten years, we have built a well-known student-driven academic society in Turkey that organizes numerous events every year and continues to grow with over 650 current members. Celebrating the 10th anniversary of RSG-Turkey, in this communication, we share our experiences, five main lessons we learned, and the steps to establish a long-standing academic community: having a clear mission, building a robust structure, effective communication, turning challenges into opportunities, and building collaborations. We believe that our experiences can help students and academics establish long-standing communities in fast-developing areas like bioinformatics.

The Biomedical Informatics Short Course at Woods Hole/Georgia: Training to Support Institutional Change.

The U.S. National Library of Medicine's Biomedical Informatics Short Course ran from 1992 to 2017, most of that time at the Marine Biological Laboratory in Woods Hole, Massachusetts. Its intention was to provide physicians, medical librarians and others engaged in health care with a basic understanding of the major topics in informatics so that they could return to their home institutions as "change agents". Over the years, the course provided week-long, intense, morning-to-night experiences for some 1,350 students, consisting of lectures and hands-on project development, taught by many luminaries in the field, not the least of which was Donald A.B. Lindberg M.D., who spoke on topics ranging from bioinformatics to national policy.

Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students.

Artificial Intelligence (AI) has the power to improve our lives through a wide variety of applications, many of which fall into the healthcare space; however, a lack of diversity is contributing to limitations in how broadly AI can help people. The UCSF AI4ALL program was established in 2019 to address this issue by targeting high school students from underrepresented backgrounds in AI, giving them a chance to learn about AI with a focus on biomedicine, and promoting diversity and inclusion. In 2020, the UCSF AI4ALL three-week program was held entirely online due to the COVID-19 pandemic. Thus, students participated virtually to gain experience with AI, interact with diverse role models in AI, and learn about advancing health through AI. Specifically, they attended lectures in coding and AI, received an in-depth research experience through hands-on projects exploring COVID-19, and engaged in mentoring and personal development sessions with faculty, researchers, industry professionals, and undergraduate and graduate students, many of whom were women and from underrepresented racial and ethnic backgrounds. At the conclusion of the program, the students presented the results of their research projects at the final symposium. Comparison of pre- and post-program survey responses from students demonstrated that after the program, significantly more students were familiar with how to work with data and to evaluate and apply machine learning algorithms. There were also nominally significant increases in the students' knowing people in AI from historically underrepresented groups, feeling confident in discussing AI, and being aware of careers in AI. We found that we were able to engage young students in AI via our online training program and nurture greater diversity in AI. This work can guide AI training programs aspiring to engage and educate students entirely online, and motivate people in AI to strive towards increasing diversity and inclusion in this field.

Bringing bioinformatics to schools with the 4273pi project.

Over the last few decades, the nature of life sciences research has changed enormously, generating a need for a workforce with a variety of computational skills such as those required to store, manage, and analyse the large biological datasets produced by next-generation sequencing. Those with such expertise are increasingly in demand for employment in both research and industry. Despite this, bioinformatics education has failed to keep pace with advances in research. At secondary school level, computing is often taught in isolation from other sciences, and its importance in biological research is not fully realised, leaving pupils unprepared for the computational component of Higher Education and, subsequently, research in the life sciences. The 4273pi Bioinformatics at School project (https://4273pi.org) aims to address this issue by designing and delivering curriculum-linked, hands-on bioinformatics workshops for secondary school biology pupils, with an emphasis on equitable access. So far, we have reached over 180 schools across Scotland through visits or teacher events, and our open education resources are used internationally. Here, we describe our project, our aims and motivations, and the practical lessons we have learned from implementing a successful bioinformatics education project over the last 5 years.

The European Bioinformatics Institute (EMBL-EBI) in 2021.

The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive range of freely available and up-to-date molecular data resources, which includes over 40 resources covering every major data type in the life sciences. This year's service update for EMBL-EBI includes new resources, PGS Catalog and AlphaFold DB, and updates on existing resources, including the COVID-19 Data Platform, trRosetta and RoseTTAfold models introduced in Pfam and InterPro, and the launch of Genome Integrations with Function and Sequence by UniProt and Ensembl. Furthermore, we highlight projects through which EMBL-EBI has contributed to the development of community-driven data standards and guidelines, including the Recommended Metadata for Biological Images (REMBI), and the BioModels Reproducibility Scorecard. Training is one of EMBL-EBI's core missions and a key component of the provision of bioinformatics services to users: this year's update includes many of the improvements that have been developed to EMBL-EBI's online training offering.

Bioinformatics mentorship in a resource limited setting.

BACKGROUND: The two recent simultaneous developments of high-throughput sequencing and increased computational power have brought bioinformatics to the forefront as an important tool for effective and efficient biomedical research. Consequently, there have been multiple approaches to developing bioinformatics skills. In resource rich environments, it has been possible to develop and implement formal fully accredited graduate degree training programs in bioinformatics. In resource limited settings with a paucity of expert bioinformaticians, infrastructure and financial resources, the task has been approached by delivering short courses on bioinformatics-lasting only a few days to a couple of weeks. Alternatively, courses are offered online, usually over a period of a few months. These approaches are limited by both the lack of sustained in-person trainer-trainee interactions, which is a key part of quality mentorships and short durations which constrain the amount of learning that can be achieved. METHODS: Here, we pioneered and tested a bioinformatics training/mentorship model that effectively uses the available expertise and computational infrastructure to deliver an in-person hands-on skills training experience. This is done through a few physical lecture hours each week, guided personal coursework over the rest of the week, group discussions and continuous close mentorship and assessment of trainees over a period of 1 year. RESULTS: This model has now completed its third iteration at Makerere University and has successfully mentored trainees, who have progressed to a variety of viable career paths. CONCLUSIONS: One-year (intermediate) skills based in-person bioinformatics training and mentorships are viable, effective and particularly appropriate for resource limited settings.