Functionathon

Initial situation

The teaching team works in the field of bioinformatics research. It seeks to predict the functionality of human proteins from publicly available information resulting from large-scale genomics, transcriptomics and proteomics experiments. It is part of an international research consortium (International Human Proteome Organization) and maintains the neXtProt knowledge platform on human proteins. NeXtProt indexes the 20’000 human genes involved in the genesis of proteins. For the majority of these genes, the protein function is known, but there is still a part of the proteins (10%) whose function is not yet known. The research objective is then to investigate these genes and to make hypotheses on the function of the proteins.

The teaching team’s objective was to sensitize its students to bioinformatics research as early as the Bachelor’s degree level. To do so, it used an approach called “CURE” (Course-based Undergraduate Research Experiences) where students are actively involved in research projects. Based on the observation of the success of these schemes and the interest of the research object, the teaching team has set up a similar scheme called Functionathon, which is oriented towards the exploration of human proteins whose functions are not yet known.

The curriculum of the Biomedical Sciences program was developed following extensive consultation within the University and Swiss biomedical companies. In addition to a solid scientific background, autonomy and mastery of written and oral scientific communication are essential skills. Writing a scientific article or report requires a mastery of the scientific subject. It calls for well-defined writing rules, such as the use of short sentences and precise vocabulary, in order to highlight important results. In order to respond to this expectation from the field, the teaching team wished to set up a course format that would allow students to reach the targeted objectives without adding material and theoretical content, and by setting up stimulating and engaging activities.

The teaching must teach students of 1ère year to identify the essential and interesting information of a document, to develop a critical and synthetic spirit, and to master the rules of scientific writing, while taking up the logistic challenge in which it is delivered. Indeed, the teaching in 1ère year is followed in common with the medical students, except for this scientific communication course for which the available time is limited to one afternoon per week (half of this time being devoted to written communication and the other half to oral expression).

The teaching team therefore considered asking students to write MCQ-type questions on imposed subjects as a learning tool. The subjects come from the Basic Medical Sciences (BMS: cell biology, physiology, etc.) taught jointly to students of Human Medicine, Dental Medicine and Biomedical Sciences. This activity has a double interest: it allows students to develop their writing skills while helping them to learn the particularly dense subject matter of BMS.

Project implementation

Practically, the teaching team selects, from the neXtProt database, a few genes (between 3 and 7) coding for proteins whose function is still unknown. The students are then grouped in triads to work on a particular gene. The groups can work on a specific gene or on the same gene depending on the teaching team’s proposal.

The teaching team is composed of 3 tutors who coordinate the groups of students and follow their work throughout the course. The teaching is organized in alternating theoretical classes that provide the basic material necessary for the work required and practical work (TP) where the students advance their research work. After a few theory classes, the rest of the sessions are essentially dedicated to research and exploration.

Each group of students has the mission to collect clues on the function of the protein produced by this gene in different resources. This exploration work carried out by the students allows them to ultimately formulate a research hypothesis on the functionality of the protein being studied. The teaching team provides a roadmap to guide the groups in their work and research methodology and informs them of the tools at their disposal. There are 3 main categories of tools to carry out investigations: literature (reference search engines, e.g., PubMed), databases (more than 2’000 more or less specialized, e.g., Human Protein Atlas) and predictor sites (programs that predict the three-dimensional structure of proteins based on their sequence, for example, or their location in the cell). The groups are helped and guided in their work so that they do not drown in the mass of information available. They are encouraged to keep a critical mind on the tools they discover and to question their limits. The important thing is that they can use a reliable work methodology to obtain the right information by correctly setting up the chosen tools. To transcribe the results of their investigations and write their hypotheses, students work on a shared document with Google Docs (the institutional alternative OneDrive is also suitable).

For the evaluation of the course, in addition to a quiz for the theoretical part (¼ of the grade for the MCQ part), each trinomial must defend during an oral presentation (¾ of the grade for the research part) its hypothesis on the function of the protein it investigated. During this 10-minute presentation, each group of students will have the opportunity to explain to the rest of the class their approach, their choice of tools and possible counterhypotheses. The group will also have to answer questions asked by the teaching team.

The groups’ work is taken up by the teaching team for verification and the content is reinjected into the scientific research community. The hypotheses put forward by the groups can thus be the subject of scientific articles written by the teaching team. Students are strongly encouraged to participate in this process. The published hypotheses can then be taken up and investigated by research teams. If these hypotheses are validated experimentally, the data will be added to the neXtProt platform.

Students are divided into groups of 3-4. Every 15 days, each group is assigned a BMS course that they have previously attended. Each group identifies a part of the course that is suitable for an exam question (e.g., an important molecular mechanism) and composes a MCQ (type A - one correct answer or K’ - multiple correct answers). The writing assignment includes the statement, the answer options, the indication of the correct answer(s), and also the justification of the answers (why the answer options are correct or incorrect). Students must follow the rules of scientific writing: use of strong verbs, present tense, active form, synthetic and precise sentences, specific and relevant vocabulary, definition of context, etc. Students are given an evaluation grid to guide them in the specific points of the essay.

The teaching team corrects the questions composed by the students and ensures that the rules of scientific writing are respected. They ask the SMB teachers to validate the correctness of the answers. Students receive their corrected writing assignments, with comments and an improved question proposal. Submission of assignments and feedback is done on Moodle. Specific courses at regular intervals allow for theoretical reminders and the correction of frequent errors. In addition, workshops offer students the opportunity to compose questions and correct the compositions of their peers. This peer evaluation exercise allows them to develop their critical thinking skills and to validate their knowledge.

The corrected and validated questions are grouped in practice exams. Four times a year, students practice, under real exam conditions, to answer in a limited time the questions composed by their class as well as by previous classes. This exercise forces them to follow a regular revision schedule and trains them to manage time and stress during an exam. Furthermore, the sharing of these practice questionnaires via EduCloud (LMS platform available to students via the EtuMed website) with students in their 1ère Bachelor’s year at the Faculty of Medicine, regardless of their course of study, establishes the 1er interdisciplinary link between the future actors of the medical world.

At the end of the year, the skills developed in the Written Scientific Communication course are evaluated using the same format as the one worked on during the year. Students must write MCQ type questions based on slides from the SMB course. The written questions are evaluated according to a grid.

Thoughts and advice

The course was implemented in 2019 and has been evolving ever since, taking into account student feedback. For example, when the course was first implemented, all the theoretical part of the course was given in blocks at the beginning of the course. The students expressed their interest in being immersed more quickly in practice. The course therefore proposes an alternation of sessions so that the theoretical aspects are given over several sessions and that the students can immediately use the tools presented. This also allows for a better guidance of the students on the practice of the methodology and avoids that they get lost in too abstract considerations.

The teaching team notes the success of the system in terms of student commitment and motivation, which is maintained throughout the course. They point out that it is important to find the right balance between the autonomy of exploration given to the working groups and the methodological framework that is necessary to prevent students from losing sight of their objective. The theory on research methodology and the guidance are therefore very important for maintaining a critical mind and a good orientation towards their research object.

In order to avoid frustrating the students by having to carry out a research in vain, the choice of genes proposed is not random. The teaching team carries out a quick search beforehand and selects “good candidates” for which the elements needed to support the hypotheses are present via the various tools proposed in the course.

The teaching team also notes that it is pleasantly surprised by the quality of the oral presentations delivered by the students on the didactic level and the scientific use of written expression. The students benefit from adapted courses on written and oral scientific communication from the beginning of their studies.

Through this course, Biomedical Sciences students deepen their understanding of the molecular mechanisms, physiology and human biology covered in the BMS courses. They are prepared for the critical analysis of scientific documents and for larger-scale writing projects, develop a critical and synthesizing mind, and show great autonomy in the various group work proposed in the 2e and 3e year Bachelor’s programs.

The concept of this course is simple and easily applicable to other courses, notably the principle of asking students to take the place of teachers to write exam questions. This reversal of the situation, which each teacher can organize on a one-time or regular basis, leads the student to apprehend the subject matter differently and to better appropriate it.

Students are not the only ones who benefit from this work. Some SMB instructors have reported that reading the student-generated questions has given them a fresh perspective on some of their course material. In addition, the student-written questions also add to their pool of potential exam questions. Despite this benefit, the work of correction remains substantial and requires close collaboration between teachers in the same program.

The concept of this course is simple and easily applicable to other courses, notably the principle of asking students to take the place of teachers to write exam questions. Other SMB teachers have already transposed this principle to have their 2e year Bachelor students write exam questions as part of a make-up exam. The questions can be used as exam questions (mock or not) or as quizzes to be given at the beginning of the course to validate the retention of knowledge from previous courses. This reversal of the situation, which each teacher can organize on a one-time or regular basis, leads the learner to apprehend the subject matter differently and to better appropriate it.

Student feedback

“I enjoyed doing research as a group and moving at our own pace.” “Theory and practical courses should overlap” “The teachers were very available and guided us along our research.”

ID 95 - Student Quiz by Priscilla Soulié [04/21] “The group writing questions were very helpful for me to practice writing the questions, discuss with my classmates and be able to present our different points of view and work on the different SMB courses. In fact, through the writing of the questions, it was easier to determine which aspects of the course were mastered and which needed more work.” “I have found these exercises to be very beneficial to the quality of my writing.” “I think it’s great that this course is not only theoretical, but that there are also practical workshops: you learn better!” “The writing classes were good because there were two separate parts: theory and practice (time flies).”