Releasing the ‘GENI': Integrating Research into the Classroom through GENI-ACT

Background: The integration of genomics research into the undergraduate biology curriculum provides students with the opportunity to become familiar with bioinformatics tools and answer original research questions. By annotating predicted genes students can connect genes to proteins and predict their cellular functions. Our purpose with this project was to upscale the research experience through integration with classroom experience giving underprepared students access to research projects and to assess learning outcomes. Methods: In order to carry out the study we utilized the Genomics National Initiative - Annotation Collaboration Toolkit (GENI-ACT) developed by the Joint Genome Institute. A variety of assessments were carried out to determine if the project engaged students, generated interest in scientific research and improved student research aptitude. Students were asked to take a pre-course/post course test consisting of 9 questions. The questions included a multi-part problem-solving question as well as some basic questions. The results were analyzed using t-tests. Genome annotation results were graded according to a simple rubric and given a score out of 140 for each annotation. Finally, students were also administered a post-course survey consisting of 18 questions and a comment section at the end. The subject matter of the questions were placed in 5 different categories: Annotation Instruction, Research Skills and Research Aptitude, Genome annotation satisfaction, Communication of Results, Research Career and Independent Research. Results: As part of the program students annotated 60 predicted genes of Methanothermobacter thermautotrophicus and Methanobacterium sp. SWAN-1. We found from the pre/post course tests that students exhibited a tremendous gain in knowledge of genome annotation over the semester. The class average on the pre-test was 15.2% ± 4%. 0% of students met or exceeded the criterion of success for the pre-test, however, 93.9% of students met or exceeded the criterion of success for the post-test. These results suggest that there has been a tremendous gain in knowledge over the semester. Student annotation grades also indicated that the majority of the students had mastered genome annotation. The average grade for the class was 95.75% suggesting that most of the students had mastered the technique. Furthermore, the post-course student survey indicated that students gained research skills and acknowledged that genome annotation was a positive experience. Conclusions: Our study demonstrates that under prepared students can successfully master genomics research. Importantly, students experienced a tremendous gain in knowledge over the semester, were engaged while annotating genes, gained confidence & research skills and overall it was a positive experience for them.