Bridge the gaps in handeling big data
In response to the job market requests, the project team aims to equip future biologists with first-hand experiences in big data skills. However, while facing the rapidly upgrading biotechnology world, the current biology curricula suffer from several gaps in handling big data. These gaps are:
- Traditional analysis methods and modern computationally-intensive data handling.
- The young and older generation’s learning styles.
- School laboratory facility and big data creation requirement.
In order to bridge these three gaps, the primary goal of this project was to use a novel DNA detection method as an entry point in building a generic curricula upgrading scheme. A side-by-side learning strategy was designed to guarantee effective knowledge transfer. Students, teachers and teaching assistants would learn to generate and analyze big DNA datasets together. By creating and implementing such a system, the project team aims to build a sustainable method to effectively merge technological updates into education.
Developing and implimentation in three rounds
This project ran in three rounds with three interactive work packages: the so-called wet-lab, the dry-lab and the dissemination teams. In each of these rounds of implementation, the project team used a novel side-by-side learning model. In this model, a teacher, a teaching assistant and two to four students teamed up to learn the subject together. The project team also used the train-the-trainer model to boost teacher’s skills in the subject.
To carry out the innovation, the novel portable DNA detection device Oxford Nanopore MinION© was used to create big DNA data. Also, the open-source data handling platform Galaxy was used to carry out data analysis education.
The development and implementation process was timely reported by the department newsletter. The project team created several course catalogs in GitHub, BrightSpace, Teams and SharePoint. The training scheme was announced periodically via group meetings, Teams notifications and emails. Most of the Galaxy tutorials were made open-source and announced via the international Galaxy training network.
The biggest challenge during this project was the COVID-19 pandemic impact. The project team had to switch most of the learning activities online. Due to the 1.5-meter regulation, lab usage was limited and so the project team had to stretch many subjects on both time and space aspects in order to guarantee the effect of learning.
Evaluation and results
One of the three work packages was the dissemination team. This team focused on education quality, student competence building and scientific research qualities, respectively.
The dissemination team was composed by the academy educationalists, members of the examination committee and the scientific experts from the Centre of Expertise. The scientific experts judged the scientific quality of the student reports. The examination committee evaluated whether the students had experienced an upward learning curve by comparing their lab performance and report quality to their previous study records. And the educationalists helped in designing a detailed questionnaire to collect feedbacks from the participants.
Individual interviews were done with selected participants in order to have more detailed feedbacks. After dissemination, improvement points were timely reflected to the project leaders. The dissemination was carried out by (online) meetings and online questionnaires (Microsoft Forms) at each round of the activities. The project produced important results:
- Most of the participants reflected that their knowledge and skills in big data creation/handling exceeded the novice level.
- The side-by-side learning model was highly appraised.
- The project team received an evaluation score of 4.2 out of 5 for the train-the-trainer events.
- The project team summarized an effective scheme which can help to embrace other technique upgrades in the future.
The COVID-19 pandemic caused many difficulties. Participants reflected that online learning decreased their concentration and confidence. To monitor the learning process, the project team used the Galaxy Tiaas system, but still direct interaction was missed.
To replicate this project, one must bear in mind that scheduling ahead is essential for side-by-side learning scheme in order to guarantee the availability of the multidisciplinary participants in a learning group.
Project impact and future development
This project has brought a great impact to both inside and outside of the school of life sciences and environmental technology (ALST), Avans University of Applied Sciences.
As a continuation of the project, the project leader adapted the project scheme and created the ‘ATGM BootCamp of Data skills (ABCDs)’. In ABCDs, all teachers of ALST will participate in series of data skill workshops. The infrastructure, network and dissemination experiences resulted from the project will benefit greatly to the ABCDs project.
By integrating the tutorials and protocols created from this Comenius project, the project team formed a big data creation and analysis learning module for second year biology students. The first round of trail gained an evaluation of 4.3 out of 5 from the students.
The project team centralized their big data Galaxy protocols and implemented them in a ‘see it, use it, teach it’ train-the-trainer course. Both the ABCDs project and the Galaxy course are open to all teachers from universities of applied science.
Literature
- Donovan, S. (2008). Big data: teaching must evolve to keep up with advances. Nature, 455(7212), 461-461.
- Afgan, E., Baker, D., Batut, B., Van Den Beek, M., Bouvier, D., Čech, M., ... & Blankenberg, D. (2018). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic acids research, 46(W1), W537-W544.
- Juul, S., Izquierdo, F., Hurst, A., Dai, X., Wright, A., Kulesha, E., ... & Turner, D. J. (2015). What’s in my pot? Real-time species identification on the MinION™. BioRxiv, 030742.
- National Academies of Sciences, Engineering, and Medicine. (2017). Preparing for future products of biotechnology. National Academies Press.
- Bulte, C., Betts, A., Garner, K., & Durning, S. (2007). Student teaching: views of student near-peer teachers and learners. Medical teacher, 29(6), 583-590.
Products and presentations
From below two links to the Galaxy based big DNA data analysis protocols that the project team created. They are suited for two- and third-year biology students as (open access) teaching materials.
Comenius Teaching Fellow 2019
