36 results
Search Results
2. Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.
- Author
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Bonham, Kevin S. and Stefan, Melanie I.
- Subjects
STEM education ,COMPUTATIONAL biology ,BIBLIOMETRICS ,SCIENCE publishing ,SCIENCE & state - Abstract
While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
3. Ten simple rules for developing good reading habits during graduate school and beyond.
- Author
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Méndez, Marcos
- Subjects
READING ,HABIT formation ,COMPREHENSION ,HISTORY ,PERIODICALS ,BIBLIOGRAPHICAL citations - Abstract
The author talks about several rules that a person can follow to develop good reading habits in graduate school and beyond. Topics discussed include the importance of developing the habit of reading on a daily basis; the need to develop comprehension skills; and the need to study the history of one's discipline. Also mentioned are the importance of creating a list of relevant journals, the need to read books, and the benefits of using a reference manager.
- Published
- 2018
- Full Text
- View/download PDF
4. Ten Simple Rules for a Bioinformatics Journal Club.
- Author
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Lonsdale, Andrew, Sietsma Penington, Jocelyn, Rice, Timothy, Walker, Michael, and Dashnow, Harriet
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BIOINFORMATICS ,INFORMATION science ,COMPUTATIONAL biology ,CLUBS ,SCIENTIFIC literature ,SOCIETIES - Abstract
The article outlines the rules for a bioinformatics journal club which, according to the authors, is a great way to take in the scientific literature, keep up with developments in their field, and hone their communication and analytical skills. The rules include holding a journal club at eight in the morning, finding good articles for discussion, and expanding the roster of leaders as people join the journal club.
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- 2016
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5. The life history of learning: Demographic structure changes cultural outcomes.
- Author
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Fogarty, Laurel, Creanza, Nicole, and Feldman, Marcus W.
- Subjects
LEARNING ,CULTURAL pluralism ,POPULATION ,DEMOGRAPHIC characteristics ,SOCIAL evolution - Abstract
Human populations show rich cultural diversity. Underpinning this diversity of tools, rituals, and cultural norms are complex interactions between cultural evolutionary and demographic processes. Most models of cultural change assume that individuals use the same learning modes and methods throughout their lives. However, empirical data on ‘learning life histories’—the balance of dominant modes of learning (for example, learning from parents, peers, or unrelated elders) throughout an individual’s lifetime—suggest that age structure may play a crucial role in determining learning modes and cultural evolutionary trajectories. Thus, studied in isolation, demographic and cultural evolutionary models show only part of the picture. This paper describes a mathematical and computational framework that combines demographic and cultural evolutionary methods. Using this general framework, we examine interactions between the ways in which culture is spread throughout an individual’s lifetime and cultural change across generations. We show that including demographic structure alongside cultural dynamics can help to explain domain-specific patterns of cultural evolution that are a persistent feature of cultural data, and can shed new light on rare but significant demographic events. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
6. Ten simple rules for drawing scientific comics.
- Author
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McDermott, Jason E., Partridge, Matthew, and Bromberg, Yana
- Subjects
COMIC books, strips, etc. ,SCIENTIFIC terminology ,SCIENTIFIC communication ,SCIENCE journalism ,SCIENTIFIC community - Abstract
The article presents guidelines for drawing scientific comics for efficient communication of difficult ideas. Suggestions mentioned include finding the right shapes for use in conveying the appropriate message one is trying to make, making one's comics simple to convey a complicated idea easier to understand, and taking time to ensure that the details in one's comics are right.
- Published
- 2018
- Full Text
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7. Ten simple rules for successfully completing a graduate degree in Latin America.
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Ruelas Inzunza, Ernesto, Salazar-Rivera, Gabriela I., Láinez, Magdiel, Ruiz-Gómez, María Guadalupe, Domínguez-Eusebio, Carlo A., Cristóbal-Sánchez, Griselda, Teodosio Faustino, Issaac A., Pérez-López, Edel, Campbell, Meagan L., Merfa, Marcus Vinicius, Latorre Beltrán, Ivonne Tatiana, Armas, Fernanda, and Mota-Vargas, Claudio
- Subjects
GRADUATE education ,LIFE science education ,LIFE sciences ,SCHOLARSHIPS ,EDUCATION - Abstract
This article offers tips for students to complete a graduate degree in biological sciences in Latin America. Topics discussed include the features that underlie the performance of graduate programs around the world, the importance of investigating the graduate program and the adviser, scholarship programs for graduate students, and the need to follow administrative procedures from admission to graduation.
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- 2017
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8. Ten simple rules for providing optimal administrative support to research teams.
- Author
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Garrido, Romina, Trowbridge, Casandra A., and Tamura, Nana
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RESEARCH teams ,ADMINISTRATIVE assistants ,SOCIAL learning ,PROFESSIONAL relationships ,SCIENTIFIC community ,CULTURAL pluralism ,HEBBIAN memory ,BUSINESS communication - Abstract
You can help your principal investigator on the oversight of grant rules and procedures, keeping protocols up to date, writing reports, and fulfilling requests from the Institutional Review Board (IRB). Regardless, what is important is for the administrator to be curious about science and make the effort to get a basic familiarity with the scientific discipline and academic working environment they are supporting. Although human resources, principal investigators, and lab managers are a large part of the onboarding process for a new employee, administrative staff are typically involved in the process as well. [Extracted from the article]
- Published
- 2019
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9. Fast and near-optimal monitoring for healthcare acquired infection outbreaks.
- Author
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Adhikari, Bijaya, Lewis, Bryan, Vullikanti, Anil, Jiménez, José Mauricio, and Prakash, B. Aditya
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MEDICAL personnel ,INFECTION ,PREVENTIVE medicine ,HOSPITAL patients - Abstract
According to the Centers for Disease Control and Prevention (CDC), one in twenty five hospital patients are infected with at least one healthcare acquired infection (HAI) on any given day. Early detection of possible HAI outbreaks help practitioners implement countermeasures before the infection spreads extensively. Here, we develop an efficient data and model driven method to detect outbreaks with high accuracy. We leverage mechanistic modeling of C. difficile infection, a major HAI disease, to simulate its spread in a hospital wing and design efficient near-optimal algorithms to select people and locations to monitor using an optimization formulation. Results show that our strategy detects up to 95% of “future” C. difficile outbreaks. We design our method by incorporating specific hospital practices (like swabbing for infections) as well. As a result, our method outperforms state-of-the-art algorithms for outbreak detection. Finally, a qualitative study of our result shows that the people and locations we select to monitor as sensors are intuitive and meaningful. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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10. Think: Theory for Africa.
- Author
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Currin, Christopher B., Khoza, Phumlani N., Antrobus, Alexander D., Latham, Peter E., Vogels, Tim P., and Raimondo, Joseph V.
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SCIENTIFIC knowledge ,SOCIAL sciences education ,TECHNOLOGY ,COMPUTATIONAL neuroscience ,SCIENCE & state - Abstract
The article offers information on the challenging scientific problems faced by humanity. Topics discussed include information on the efforts to empower Africans to join the global neuroscience community; discussions on the BRAIN initiative in the U.S. and the Human Brain Project in Europe; and the information on the limiting factor for computational neuroscience development in Africa.
- Published
- 2019
- Full Text
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11. Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?
- Author
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Davies, Angela C., Harris, Diane, Banks-Gatenby, Amanda, and Brass, Andy
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PROBLEM-based learning ,FACE-to-face communication ,COMMUNITIES of practice ,CLINICAL education ,COURSEWARE ,SEMI-structured interviews ,VIRTUAL communities - Abstract
We have now reached the genomics era within medicine; genomics is being used to personalise treatment, make diagnoses, prognoses, and predict adverse outcomes resulting from treatment with certain drugs. Genomic data is now abundant in healthcare, and the newly created profession of clinical bioinformaticians are responsible for its analysis. In the United Kingdom, clinical bioinformaticians are trained within a 3-year programme, integrating a work-based placement with a part-time Master’s degree. As this profession is still developing, trainees can feel isolated from their peers whom are located in other hospitals and can find it difficult to gain the mentorship that they require to complete their training. Building strong networks or communities of practice (CoPs) and allowing sharing of knowledge and experiences is one solution to addressing this isolation. Within the Master’s delivered at the University of Manchester, we have integrated group-centred problem-based learning (PBL) using real clinical case studies worked on during each course unit. This approach is combined with a flipped style of teaching providing access to online content in our Virtual Learning Environment before the course. The face-to-face teaching is used to focus on the application of the students’ knowledge to clinical case studies. In this study, we conducted semistructured interviews with 8 students, spanning 3 cohorts of students. We evaluated the effectiveness of this style of teaching and whether it had contributed to the formation of CoPs between our students. Our findings demonstrated that this style of teaching was preferred by our students to a more traditional lecture-based format and that the problem-based learning approach enabled the formation of CoPs within these cohorts. These CoPs are valuable in the development of this new profession and assist with the production of new guidelines and policies that are helping to professionalise this new group of healthcare scientists. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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12. From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training.
- Author
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McGrath, Annette, Champ, Katherine, Shang, Catherine A., van Dam, Ellen, Brooksbank, Cath, and Morgan, Sarah L.
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LEAD ,TRAINING planes ,TRAINING of scientists ,MOLECULAR biology ,INDUSTRIAL research ,BIOINFORMATICS - Abstract
Demand for training life scientists in bioinformatics skills led to the development of a train-the-trainer collaboration between the European Molecular Biology Laboratory–European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-the-trainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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13. Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.
- Author
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Zhan, Yingqian Ada, Wray, Charles Gregory, Namburi, Sandeep, Glantz, Spencer T., Laubenbacher, Reinhard, and Chuang, Jeffrey H.
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LIFE science education ,UNIVERSITIES & colleges ,BIG data ,COMPUTATIONAL biology ,ART colleges - Abstract
Bioinformatics has become an indispensable part of life science over the past 2 decades. However, bioinformatics education is not well integrated at the undergraduate level, especially in liberal arts colleges and regional universities in the United States. One significant obstacle pointed out by the Network for Integrating Bioinformatics into Life Sciences Education is the lack of faculty in the bioinformatics area. Most current life science professors did not acquire bioinformatics analysis skills during their own training. Consequently, a great number of undergraduate and graduate students do not get the chance to learn bioinformatics or computational biology skills within a structured curriculum during their education. To address this gap, we developed a module-based, week-long short course to train small college and regional university professors with essential bioinformatics skills. The bioinformatics modules were built to be adapted by the professor-trainees afterward and used in their own classes. All the course materials can be accessed at . [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
14. Establishing a computational biology flipped classroom.
- Author
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Compeau, Phillip
- Subjects
FLIPPED classrooms ,COMPUTATIONAL biology ,STUDENT-centered learning ,EFFECTIVE teaching ,BIOINFORMATICS - Abstract
In a flipped classroom, students complete automated modules to replace a traditional lecture, allowing the time devoted for the lecture to be devoted to constructive tasks reinforcing student knowledge. Yet although the flipped classroom offers a compelling approach for fostering a constructivist, student-centric learning environment, research on the efficacy of flipped classes has been mixed. For that matter, is it possible to successfully flip a classroom in an advanced, heavily specialized course like a bioinformatics algorithms course? Over the past several years, the author has implemented a flipped version of such a course and will discuss some of the successes and pitfalls encountered. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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15. Ten simple rules for providing a meaningful research experience to high school students.
- Author
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Lescak, Emily A., O’Neill, Kate M., Collu, Giovanna M., and Das, Subhamoy
- Subjects
RESEARCH ,HIGH school students ,MENTORING ,STEM education ,STEM occupations - Abstract
An editorial is presented on rules for providing a meaningful research experience to high school students. Topics discussed include ten rules for becoming an effective research mentor for high school students and their training, research opportunities as undergraduates and career consideration in science, technology, engineering, and mathematics and bridging the gap between scientists and the general public on scientific research.
- Published
- 2019
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16. Ten simple rules for organizing a webinar series.
- Author
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Fadlelmola, Faisal M., Panji, Sumir, Ahmed, Azza E., Ghouila, Amel, Akurugu, Wisdom A., Entfellner, Jean-Baka Domelevo, Souiai, Oussema, Mulder, Nicola, and null, null
- Subjects
WEBINARS ,COMMUNITIES ,AUDIENCES ,EMAIL ,SOCIAL media - Abstract
The article presents ten simple rules for hosting a regular webinar series with particular emphasis on resource-constrained communities like many in Africa. Topics include aligning a webinar theme to the expectations of the audience; settling on a convenient and user friendly webinar platform; and announcing webinars through mailing lists and social media platform.
- Published
- 2019
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17. Strategies and opportunities for promoting bioinformatics in Zimbabwe.
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Shoko, Ryman, Manasa, Justen, Maphosa, Mcebisi, Mbanga, Joshua, Mudziwapasi, Reagan, Nembaware, Victoria, Sanyika, Walter T., Tinago, Tawanda, Chikwambi, Zedias, Mawere, Cephas, Matimba, Alice, Mugumbate, Grace, Mufandaedza, Jonathan, Mulder, Nicola, and Patterton, Hugh
- Subjects
BIOINFORMATICS ,LIFE sciences ,HIV infections ,AIDS ,TUBERCULOSIS - Abstract
The article reviews progress made by scientists in bioinformatics and propose strategies for boosting bioinformatics capacity. It mentions information on Eastern Africa Network for Bioinformatics Training (EANBiT), which aims at developing practitioners who can develop and use bioinformatics approaches to biosciences. It presents use of biosciences in treating infectious diseases such as the human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), and tuberculosis (TB).
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- 2018
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18. Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015.
- Author
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Marziano, Valentina, Poletti, Piero, Béraud, Guillaume, Boëlle, Pierre-Yves, Merler, Stefano, and Colizza, Vittoria
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CHICKENPOX ,INFECTIOUS disease transmission ,VARICELLA-zoster virus ,PATHOGENIC microorganisms ,EPIDEMIOLOGY - Abstract
Annual incidence rates of varicella infection in the general population in France have been rather stable since 1991 when clinical surveillance started. Rates however show a statistically significant increase over time in children aged 0–3 years, and a decline in older individuals. A significant increase in day-care enrolment and structures’ capacity in France was also observed in the last decade. In this work we investigate the potential interplay between an increase of contacts of young children possibly caused by earlier socialization in the community and varicella transmission dynamics. To this aim, we develop an age-structured mathematical model, informed with historical demographic data and contact matrix estimates in the country, accounting for longitudinal linear increase of early childhood contacts. While the reported overall varicella incidence is well reproduced independently of mixing variations, age-specific empirical trends are better captured by accounting for an increase in contacts among pre-school children in the last decades. We found that the varicella data are consistent with a 30% increase in the number of contacts at day-care facilities, which would imply a 50% growth in the contribution of 0-3y old children to overall yearly infections in 1991–2015. Our findings suggest that an earlier exposure to pathogens due to changes in day-care contact patterns, represents a plausible explanation for the epidemiological patterns observed in France. Obtained results suggest that considering temporal changes in social factors in addition to demographic ones is critical to correctly interpret varicella transmission dynamics. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
19. Submit a Topic Page to PLOS Computational Biology and Wikipedia.
- Author
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Mietchen, Daniel, Wodak, Shoshana, Wasik, Szymon, Szostak, Natalia, and Dessimoz, Christophe
- Subjects
COMPUTATIONAL biology ,AUTHORS ,READERSHIP ,ORIGIN of life - Abstract
The article offers information on the periodical's `Topic Pages' project as a way to help fill important gaps in Wikipedia's coverage of computational biology content and to credit authors for their contributions. It mentions that hypercycle theory is now more accessible not only for advanced readers, but also for ordinary people who seek knowledge on the computational aspects of the origins of life.
- Published
- 2018
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20. Eleven quick tips for running an interdisciplinary short course for new graduate students.
- Author
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Saunders, Timothy E., He, Cynthia Y., Koehl, Patrice, Ong, L. L. Sharon, and So, Peter T. C.
- Subjects
INTERDISCIPLINARY education ,GRADUATE students ,REASONING ,LIFE science education - Abstract
Quantitative reasoning and techniques are increasingly ubiquitous across the life sciences. However, new graduate researchers with a biology background are often not equipped with the skills that are required to utilize such techniques correctly and efficiently. In parallel, there are increasing numbers of engineers, mathematicians, and physical scientists interested in studying problems in biology with only basic knowledge of this field. Students from such varied backgrounds can struggle to engage proactively together to tackle problems in biology. There is therefore a need to establish bridges between those disciplines. It is our proposal that the beginning of graduate school is the appropriate time to initiate those bridges through an interdisciplinary short course. We have instigated an intensive 10-day course that brought together new graduate students in the life sciences from across departments within the National University of Singapore. The course aimed at introducing biological problems as well as some of the quantitative approaches commonly used when tackling those problems. We have run the course for three years with over 100 students attending. Building on this experience, we share 11 quick tips on how to run such an effective, interdisciplinary short course for new graduate students in the biosciences. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
21. Meet-U: Educating through research immersion.
- Author
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Abdollahi, Nika, Albani, Alexandre, Anthony, Eric, Baud, Agnes, Cardon, Mélissa, Clerc, Robert, Czernecki, Dariusz, Conte, Romain, David, Laurent, Delaune, Agathe, Djerroud, Samia, Fourgoux, Pauline, Guiglielmoni, Nadège, Laurentie, Jeanne, Lehmann, Nathalie, Lochard, Camille, Montagne, Rémi, Myrodia, Vasiliki, Opuu, Vaitea, and Parey, Elise
- Subjects
COMPUTATIONAL biology ,CLOUD computing ,RESEARCH methodology ,BIOLOGY students ,SCIENTISTS - Abstract
We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, with protein–protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at . [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
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22. Ten simple rules to create a serious game, illustrated with examples from structural biology.
- Author
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Baaden, Marc, Delalande, Olivier, Ferey, Nicolas, Pasquali, Samuela, Waldispühl, Jérôme, and Taly, Antoine
- Subjects
VIDEO games ,SCIENCE ,RULES ,TEACHING ,GAMES - Abstract
The article presents simple rules for developing serious scientific videogames. One rule is that the goal of the game should be defined in a clear way in terms of science and teaching. Another rule is that equilibrium has to be created between scientific accuracy and player accessibility. Another rule is that one should let the players interact with scientific data.
- Published
- 2018
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23. Ten simple rules for collaborative lesson development.
- Author
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Devenyi, Gabriel A., Emonet, Rémi, Harris, Rayna M., Hertweck, Kate L., Irving, Damien, Milligan, Ian, and Wilson, Greg
- Subjects
CURRICULUM planning ,LESSON planning - Abstract
The article offers tips on how to develop collaborative lessons.
- Published
- 2018
- Full Text
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24. Projecting social contact matrices in 152 countries using contact surveys and demographic data.
- Author
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Prem, Kiesha, Cook, Alex R., and Jit, Mark
- Subjects
SOCIAL contact ,SURVEYING (Engineering) ,DEMOGRAPHIC databases ,DYNAMIC models ,MARKOV processes - Abstract
Heterogeneities in contact networks have a major effect in determining whether a pathogen can become epidemic or persist at endemic levels. Epidemic models that determine which interventions can successfully prevent an outbreak need to account for social structure and mixing patterns. Contact patterns vary across age and locations (e.g. home, work, and school), and including them as predictors in transmission dynamic models of pathogens that spread socially will improve the models’ realism. Data from population-based contact diaries in eight European countries from the POLYMOD study were projected to 144 other countries using a Bayesian hierarchical model that estimated the proclivity of age-and-location-specific contact patterns for the countries, using Markov chain Monte Carlo simulation. Household level data from the Demographic and Health Surveys for nine lower-income countries and socio-demographic factors from several on-line databases for 152 countries were used to quantify similarity of countries to estimate contact patterns in the home, work, school and other locations for countries for which no contact data are available, accounting for demographic structure, household structure where known, and a variety of metrics including workforce participation and school enrolment. Contacts are highly assortative with age across all countries considered, but pronounced regional differences in the age-specific contacts at home were noticeable, with more inter-generational contacts in Asian countries than in other settings. Moreover, there were variations in contact patterns by location, with work-place contacts being least assortative. These variations led to differences in the effect of social distancing measures in an age structured epidemic model. Contacts have an important role in transmission dynamic models that use contact rates to characterize the spread of contact-transmissible diseases. This study provides estimates of mixing patterns for societies for which contact data such as POLYMOD are not yet available. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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25. The application of project-based learning in bioinformatics training.
- Author
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Emery, Laura R. and Morgan, Sarah L.
- Subjects
BIOINFORMATICS ,CORE competencies ,LIFE scientists ,SEQUENCE alignment ,PHYLOGENY ,EDUCATION - Abstract
The article focuses on the application of project-based learning in bioinformatics training and to foster collaboration and develop interpersonal competencies. It mentions overcome the challenge of composing a training course that could develop the competencies with increasingly heterogeneous audience of life scientists. It also mentions topics of the course which include sequence alignment, phylogenetics, and networks and pathways.
- Published
- 2017
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26. Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions.
- Author
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Dorratoltaj, Nargesalsadat, Marathe, Achla, Lewis, Bryan L., Swarup, Samarth, Eubank, Stephen G., and Abbas, Kaja M.
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INFLUENZA treatment ,H1N1 influenza ,VACCINES ,PANDEMICS ,EPIDEMIOLOGY ,PUBLIC health - Abstract
The study objective is to estimate the epidemiological and economic impact of vaccine interventions during influenza pandemics in Chicago, and assist in vaccine intervention priorities. Scenarios of delay in vaccine introduction with limited vaccine efficacy and limited supplies are not unlikely in future influenza pandemics, as in the 2009 H1N1 influenza pandemic. We simulated influenza pandemics in Chicago using agent-based transmission dynamic modeling. Population was distributed among high-risk and non-high risk among 0–19, 20–64 and 65+ years subpopulations. Different attack rate scenarios for catastrophic (30.15%), strong (21.96%), and moderate (11.73%) influenza pandemics were compared against vaccine intervention scenarios, at 40% coverage, 40% efficacy, and unit cost of $28.62. Sensitivity analysis for vaccine compliance, vaccine efficacy and vaccine start date was also conducted. Vaccine prioritization criteria include risk of death, total deaths, net benefits, and return on investment. The risk of death is the highest among the high-risk 65+ years subpopulation in the catastrophic influenza pandemic, and highest among the high-risk 0–19 years subpopulation in the strong and moderate influenza pandemics. The proportion of total deaths and net benefits are the highest among the high-risk 20–64 years subpopulation in the catastrophic, strong and moderate influenza pandemics. The return on investment is the highest in the high-risk 0–19 years subpopulation in the catastrophic, strong and moderate influenza pandemics. Based on risk of death and return on investment, high-risk groups of the three age group subpopulations can be prioritized for vaccination, and the vaccine interventions are cost saving for all age and risk groups. The attack rates among the children are higher than among the adults and seniors in the catastrophic, strong, and moderate influenza pandemic scenarios, due to their larger social contact network and homophilous interactions in school. Based on return on investment and higher attack rates among children, we recommend prioritizing children (0–19 years) and seniors (65+ years) after high-risk groups for influenza vaccination during times of limited vaccine supplies. Based on risk of death, we recommend prioritizing seniors (65+ years) after high-risk groups for influenza vaccination during times of limited vaccine supplies. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
27. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.
- Author
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Jongeneel, C. Victor, Achinike-Oduaran, Ovokeraye, Adebiyi, Ezekiel, Adebiyi, Marion, Adeyemi, Seun, Akanle, Bola, Aron, Shaun, Ashano, Efejiro, Bendou, Hocine, Botha, Gerrit, Chimusa, Emile, Choudhury, Ananyo, Donthu, Ravikiran, Drnevich, Jenny, Falola, Oluwadamila, Fields, Christopher J., Hazelhurst, Scott, Hendry, Liesl, Isewon, Itunuoluwa, and Khetani, Radhika S.
- Subjects
GENOMICS ,GENETIC databases ,BIOINFORMATICS ,INFORMATION science ,PUBLIC health - Abstract
The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises to gauge the ability of its participating research and service groups to analyze typical genome-wide datasets being generated by H3Africa research groups. We describe a framework for the assessment of computational genomics analysis skills, which includes standard operating procedures, training and test datasets, and a process for administering the exercise. We present the experiences of 3 research groups that have taken the exercise and the impact on their ability to manage complex projects. Finally, we discuss the reasons why many H3ABioNet nodes have declined so far to participate and potential strategies to encourage them to do so. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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28. Ten simple rules to make the most out of your undergraduate research career.
- Author
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Yu, Megan and Kuo, Yu-Min
- Subjects
RESEARCH ,UNDERGRADUATES ,CAREER development ,MASSIVE open online courses ,RESEARCH personnel - Abstract
The article discusses several rules for undergraduates to help them intellectually enrich their research experiences, in view of benefits of research in undergraduate education, and their struggle in understanding purpose of work. Topics include need for undergraduates to start early to explore research interests and goals for career; having a background knowledge in the research area using resources like Massive Open Online Courses; and having positive relationships with research colleagues.
- Published
- 2017
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29. Ten simple rules for short and swift presentations.
- Author
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Lortie, Christopher J.
- Subjects
SCIENTIFIC communication ,SLIDES (Photography) ,GRAPHIC design ,SCIENCE ,COMMUNICATION - Abstract
The article offers tips on preparing short and swift scientific presentations. Since immediacy is important, preparing one primary message for the audience is suggested. Slides can be used to present a clear story by discussing one major point per slide. Using simple visuals is recommended. The style, graphical design, language and imagery of the presentation should be consistent.
- Published
- 2017
- Full Text
- View/download PDF
30. Ten simple rules for responsible big data research.
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Zook, Matthew, Barocas, Solon, boyd, danah, Crawford, Kate, Keller, Emily, Gangadharan, Seeta Peña, Goodman, Alyssa, Hollander, Rachelle, Koenig, Barbara A., Metcalf, Jacob, Narayanan, Arvind, Nelson, Alondra, and Pasquale, Frank
- Subjects
RESEARCH ethics ,BIG data ,DATA security failures ,RESEARCH methodology ,PREVENTION - Abstract
The article discusses the results of a two-year project which aimed to provide guidance to the National Science Foundation (NSF) on how to best encourage ethical practices in scientific and engineering research involving the use of big data research methods and infrastructures. The assumption that most data represent or impact people should be used to guide one's analysis. Researchers are also encouraged to situate and contextualize data to anticipate privacy breaches and minimize harm.
- Published
- 2017
- Full Text
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31. The Virtuous Cycle of a Data Ecosystem.
- Author
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Voytek, Bradley
- Subjects
INFORMATION sharing ,BIG data ,DATA mining ,AGGREGATION (Statistics) ,META-analysis - Abstract
The article discusses the virtuous cycle of a data ecosystem. Topics include the increasing creation of digital data of all types, the benefits of data sharing which include data remixing and combining, bias minimization and meta-analysis, and the growth of data collection techniques along with data aggregation and mining algorithms.
- Published
- 2016
- Full Text
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32. Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries
- Author
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Patricia Carvajal-López, Piraveen Gopalasingam, Amel Ghouila, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Paballo Abel Chauke, Alice Matimba, Alejandro Reyes, Selene L. Fernandez-Valverde, Nicola Mulder, Marco Cristancho, Javier De Las Rivas, Fatma Z. Guerfali, Victoria Dominguez Del Angel, Benjamin Moore, Wellcome Trust, National Institutes of Health (US), Biotechnology and Biological Sciences Research Council (UK), Global Challenges Research Fund, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), Universidad de Salamanca, and Instituto Nacional de Bioinformática (España)
- Subjects
Budgets ,Financial Management ,Economics ,Computer science ,Social Sciences ,Economic Geography ,Database and Informatics Methods ,Learning and Memory ,0302 clinical medicine ,Sociology ,Simple (abstract algebra) ,Psychology ,Biology (General) ,0303 health sciences ,Geography ,Ecology ,4. Education ,Software Engineering ,ComputingMilieux_GENERAL ,Professions ,Interdisciplinary Placement ,Editorial ,Computational Theory and Mathematics ,Modeling and Simulation ,Low and Middle Income Countries ,Educational Status ,Engineering and Technology ,Workshops ,Curriculum ,Human learning ,Computer and Information Sciences ,Coronavirus disease 2019 (COVID-19) ,Bioinformatics ,QH301-705.5 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Training course ,MEDLINE ,Research and Analysis Methods ,Education ,Computer Software ,Human Learning ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Genetics ,Learning ,Animals ,Humans ,Molecular Biology ,Developing Countries ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Cognitive Psychology ,Sustainability science ,Biology and Life Sciences ,Computational Biology ,Data science ,Trainees ,Low and middle income countries ,Instructors ,People and Places ,Earth Sciences ,Cognitive Science ,Population Groupings ,Finance ,030217 neurology & neurosurgery ,Neuroscience - Abstract
© 2021 Moore et al., Bioinformatics training is required at every stage of a scientist’s research career. Continual bioinformatics training allows exposure to an ever-changing and growing repertoire of techniques and databases, and so biologists, computational scientists, and healthcare practitioners are all seeking learning opportunities in the use of computational resources and tools designed for data storage, retrieval, and analysis. There are abundant opportunities for accessing bioinformatics training for scientists in high-income countries (HICs), with well-equipped facilities and participants and trainers requiring minimal travel and financial costs alongside a range of general advice for developing short bioinformatics training courses [1–3]. However, regionally targeted bioinformatics training in low- and middle-income countries (LMICs) often requires more extensive local and external support, organization, and travel. Due to the limited expertise in bioinformatics in LMICs in general, most bioinformatics training requires a fair amount of collaboration with experts beyond the local community, country, or region. A common model of training, used as the basis of this article, includes a local host collaborating with local, regional, and international experts gathering to train local or regional participants. Recently, there has been a growth of capacity strengthening initiatives in LMICs, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABioNet) Initiative [4–6], the Capacity Building for Bioinformatics in Latin America (CABANA) Project [7], the Asia Pacific BioInformatics Network (APBioNet) [8], and the Wellcome Connecting Science Courses and Conferences program [9]. One of the important strands of these initiatives is a drive to organize and deliver valuable bioinformatics training, but organizing and delivering short bioinformatics training workshops in an LMIC present a unique set of challenges. This paper attempts to build upon the sage advice for organizing bioinformatics workshops with specific guidance for organizing and delivering them in LMICs. It describes the processes to follow in organizing courses taking into consideration the low-resource setting. We should also note that LMICs are not a monolithic group and that setting, context, temporality, and specific location matters. LMICs are a complex regional grouping [10] and should be treated as such; however, we will present some common lessons that we hope will help organizers and trainers of bioinformatics training events in LMICs to navigate the often different, challenging, and rewarding experience., The authors who contributed to this manuscript are funded as follows: BM receives salary support from Wellcome Trust grants [WT108749/Z/15/Z, WT108749/Z/15/A], PC, VR, NM, AG’s salaries are funded in whole, or in part, by the NIH Common Fund H3ABioNet grant [U24HG006941], MC, SLFV, AR, PG, PCL’s salaries were partly funded by the UKRI-BBSRC ‘Capacity building for bioinformatics in Latin America’ (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1], JDLR is funded by ISCiii AES [ref. PI18/00591] at the CSIC/USAL (Spain) and by CYTED, RIABIO (Red Iberoamericana 521RT0118), AM’s salary is funded by [WT206194/Z/17/Z], GO is funded by the CABANA grant and SM is funded by the EMBL-EBI.
- Published
- 2021
33. The Development of Audio-Visual Integration for Temporal Judgements.
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Adams, Wendy J.
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SENSORIMOTOR integration ,PERCEPTUAL-motor processes ,SENSORY processing disorder ,SENSES - Abstract
Adults combine information from different sensory modalities to estimate object properties such as size or location. This process is optimal in that (i) sensory information is weighted according to relative reliability: more reliable estimates have more influence on the combined estimate and (ii) the combined estimate is more reliable than the component uni-modal estimates. Previous studies suggest that optimal sensory integration does not emerge until around 10 years of age. Younger children rely on a single modality or combine information using inappropriate sensory weights. Children aged 4–11 and adults completed a simple audio-visual task in which they reported either the number of beeps or the number of flashes in uni-modal and bi-modal conditions. In bi-modal trials, beeps and flashes differed in number by 0, 1 or 2. Mutual interactions between the sensory signals were evident at all ages: the reported number of flashes was influenced by the number of simultaneously presented beeps and vice versa. Furthermore, for all ages, the relative strength of these interactions was predicted by the relative reliabilities of the two modalities, in other words, all observers weighted the signals appropriately. The degree of cross-modal interaction decreased with age: the youngest observers could not ignore the task-irrelevant modality—they fully combined vision and audition such that they perceived equal numbers of flashes and beeps for bi-modal stimuli. Older observers showed much smaller effects of the task-irrelevant modality. Do these interactions reflect optimal integration? Full or partial cross-modal integration predicts improved reliability in bi-modal conditions. In contrast, switching between modalities reduces reliability. Model comparison suggests that older observers employed partial integration, whereas younger observers (up to around 8 years) did not integrate, but followed a sub-optimal switching strategy, responding according to either visual or auditory information on each trial. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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34. Ten simple rules for partnering with K-12 teachers to support broader impact goals
- Author
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Louise S. Mead, Kristin M. Bass, Alexa Warwick, Frieda Reichsman, and Angela Kolonich
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0301 basic medicine ,Evolutionary Genetics ,Science and Technology Workforce ,Biomedical Research ,Social Sciences ,Careers in Research ,Science education ,0302 clinical medicine ,Learning and Memory ,Sociology ,ComputingMilieux_COMPUTERSANDEDUCATION ,Psychology ,Cooperative Behavior ,Biology (General) ,Grade level ,Simple (philosophy) ,Schools ,Ecology ,Professional development ,Research Personnel ,Professions ,Science research ,Editorial ,Computational Theory and Mathematics ,Modeling and Simulation ,Physical Sciences ,Educational Status ,Engineering ethics ,Human learning ,Science Policy ,QH301-705.5 ,Science ,Materials Science ,Schoolchildren ,Biology ,Education ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Human Learning ,Genetics ,Humans ,Learning ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Cognitive Psychology ,Biology and Life Sciences ,Teachers ,030104 developmental biology ,Science Education ,People and Places ,Cognitive Science ,Scientists ,Population Groupings ,School Teachers ,030217 neurology & neurosurgery ,Professional expertise ,Neuroscience - Abstract
Contributing to broader impacts is an important aspect of scientific research. Engaging practicing K-12 teachers as part of a research project can be an effective approach for addressing broader impacts requirements of grants, while also advancing researcher and teacher professional growth. Our focus is on leveraging teachers' professional expertise to develop science education materials grounded in emerging scientific research. In this paper, we describe ten simple rules for planning, implementing, and evaluating teacher engagement to support the broader impact goals of your research project. These collaborations can lead to the development of instructional materials or activities for students in the classroom or provide science research opportunities for teachers. We share our successes and lessons learned while collaborating with high school biology teachers to create technology-based, instructional materials developed from basic biological research. The rules we describe are applicable across teacher partnerships at any grade level in that they emphasize eliciting and respecting teachers' professionalism and expertise.
- Published
- 2020
35. Ten quick tips for delivering programming lessons
- Author
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Greg Wilson
- Subjects
0301 basic medicine ,Computer and Information Sciences ,QH301-705.5 ,Computer science ,Social Sciences ,computer.software_genre ,Education ,Craft ,Computer Software ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Human Learning ,0302 clinical medicine ,Learning and Memory ,Cognition ,Sociology ,Memory ,Computer software ,Genetics ,Learning ,Psychology ,Humans ,Biology (General) ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Language ,Ecology ,Recall ,Multimedia ,Teaching ,Cognitive Psychology ,Biology and Life Sciences ,Teachers ,Professions ,030104 developmental biology ,Computational Theory and Mathematics ,Modeling and Simulation ,Instructors ,People and Places ,Memory Recall ,Cognitive Science ,Population Groupings ,Workshops ,computer ,Value (mathematics) ,030217 neurology & neurosurgery ,Human learning ,Neuroscience - Abstract
Teaching well is a craft like any other, and success often comes from an accumulation of small improvements rather than from any single large change. This paper describes 10 practices you can use when teaching programming (and other subjects). All are easy to adopt and have proven their value in institutional classrooms, intensive workshops, and other settings.
- Published
- 2019
36. Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience.
- Author
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Gurwitz, Kim T., Aron, Shaun, Panji, Sumir, Maslamoney, Suresh, Fernandes, Pedro L., Judge, David P., Ghouila, Amel, Domelevo Entfellner, Jean-Baka, Guerfali, Fatma Z., Saunders, Colleen, Mansour Alzohairy, Ahmed, Salifu, Samson P., Ahmed, Rehab, Cloete, Ruben, Kayondo, Jonathan, Ssemwanga, Deogratius, Mulder, Nicola, and Null, Null
- Subjects
BIOINFORMATICS ,ONLINE education ,DISTANCE education ,EDUCATION - Abstract
Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge “Introduction to Bioinformatics” course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery–mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online “question and discussion” forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
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