6 EC
Semester 1, period 2
5224BEDI6Y
Sensing and integration of environmental signals takes place in all biological systems, which requires a certain level of decision-making by the involved organisms. To exemplify such research on signal integration, this course will cover biological processes taking place in the belowground environment surrounding plant root systems. This includes the regulation of root development and function on a molecular level and how roots adjust to climate change, abiotic stress, and colonization by micro-organisms. The relevance of the interaction with the soil microbiota on a community-level and underlying dynamics will be discussed in the context of sustainable agriculture. A major focus will be the employment of bioinformatic methods and machine-learning approaches in describing, analyzing, and interpreting gene expression and microbiome data, which will be practically explored in computer tutorials. The topics of the lectures and tutorials revolve around ongoing research at the UvA:
Biological context
Bioinformatic tools
Scientific articles will be provided as PDFs on Canvas.
Instructions and protocols for the tutorials and assignments will be provided on Canvas.
Lecture slides will be provided on Canvas.
The lectures will convey knowledge about the biological processes regarding plant root development and root microbiome interactions, and about bioinformatic tools for omics data analysis. In computer tutorials, the students practice the analysis of published data related to the biological processes that they learned about. In additional biology tutorials, students study a scientific topic on their own in small groups and explain the outcome to their peers in a flipchart presentation. The teachers guide them throughout these assignments.
Activity | Hours | |
Hoorcollege | 24 | |
Tentamen | 3 | |
Vragenuur | 2 | |
Werkcollege | 46 | |
Self study | 93 | |
Total | 168 | (6 EC x 28 uur) |
Additional requirements for this course:
Attendance at lectures is strongly recommended, as lecture content will be part of the exam. Attendance at tutorials is compulsory. The reviewing of relevant literature and preparation for the exam will be done by the students as a self-study.
| Item and weight | Details |
|
Final grade | |
|
0.5 (50%) Tentamen | Must be ≥ 5 |
|
0.3 (30%) Computer assignments | Must be ≥ 5.5 |
|
0.2 (20%) Biology tutorials | Must be ≥ 5.5 |
The exam is not digital, is weighted 50% of the final grade, and the cut-off score is >=5.0. The exam is an "Open Book"type of exam. The PDFs of the lectures and the papers used in the assignments can be brought with you to the exam. You will have 6 questions to answers that will test your knowledge and insight in the study matters. Each of the two computer assignments will be weighted 15% of the final grade, and each of them individually has a cut-off of 5.5. The two biology tutorials are 10% each of the final grade, cut-off is 5.5. To pass the course, the final grade needs to be >=5.5. The weighting of exam and assignments will remain the same for the retakes. The scheduling of assignment and tutorial retakes will be announced on Canvas.
Within 20 working days after the announcement of the results of a written examination, the student can, on request, inspect their assessed work, the questions and assignments set, and the standards applied for grading. The date and time for this inspection will be communicated to the student on Canvas.
In the computer tutorials, the students individually analyze data sets and can ask for guidance by the teacher. The teacher assesses the assignments based on placement in the right scientific content, accuracy of analysis, and interpretation of results. In the biology tutorials, the students research a scientific question in small groups based on reviewing scientific literature. They summarize the topic, explain the findings, and give suggestions for future research directions, in the format of a flipchart presentation. This is assessed based on scientific content, clarity of thought, and presentation style. Feedback on all tutorials is given at the latest one week afterwards. The information taught in the lectures will be assessed in a written exam with open questions. The exam is graded. Computer assignments, tutorials and the exam need to be passed to pass the course.
The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl
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