Biomedical Systems Biology

Course manual 2017/2018

Course content

In the course Biomedical Systems Biology the teachers will introduce you to a thorough understanding of how molecules interact in cellular systems and thus determine important chemical and cellular processes that occur during health and disease. The recurrent theme is the integrative analysis of stress response in biology where genetic, signal transduction and metabolic reactions form an integrated complex network of spatially and temporally resolved interactions that strive to homeostasis in response to environmental perturbations. The approach reflects the focus on Systems Biology that the course takes and that is in-line with the research done in the masters program as a whole. We offer different biomedical research challenges for the students to work on. These are the development of novel preservative systems to ensure microbial food safety, the development of new antibiotics to cure infection, vaccines against fungal infection, the identification of novel anti HIV-drugs and biomarkers for human mitochondrial disorders. By the end of week 2 key-note lectures provide perspectives of how contemporary biomedical topics are studied with systems biology approaches and a computer practical is taught.
Week 1: Biological systems: from microbes to modelorganisms & man
Week 2: Systems Biology tools & techniques
Week 3: Towards a research proposal
Week 4: Finalizing research proposal and examination

The combination of courses in Biomedical Systems Biology (5234BISB6Y) and is intended to give students a full apprehension of both the theoretical background and practical application of clinically relevant biochemical and molecular biological research.

Study materials

Literature

• Molecular Biology of the Cell, Alberts et al., Taylor & Francis Inc (5th ed.)
• Recommended but not necessary: Biochemistry, Berg et al., Freeman Palgrave Macmillan (7th ed.)

Syllabus

• hand-outs & papers posted on Blackboard.

Software

• Copasi (available at the course)

Objectives

After the course students;

• are able to demonstrate the application of state of the art genomics, genome wide transcript and protein, as well as comprehensive cellular metabolite analysis in the context of Biomedical Systems Biology.
• can apply innovative microscopic analysis in the context of biomedical systems biology.
• are proficient in using microorganisms as well as single and multi-cellular eukaryotic model organisms to study aspects of human health and disease.
• can apply bioinformatics analysis of data obtained and have a basic understanding of network models. A case study is worked at in a tutorial computer practicum.
• are independently able to transform a biomedical query into a scientific biomedical systems biology research proposal.

Teaching methods

• Lectures: 30 hours
• Tutorials: 6 hours
• Assignment: 40 hours (mainly as unsupervised group work)
• Symposium (presentation including preperation): 16 hours
• Selfstudy: ~60 hours
• Question hour: 2 hours
• Exam: 3 hours

Learning activities

Attendance

The programme does not have requirements concerning attendance (OER-B).

Additional requirements for this course:

Assessment

Inspection of assessed work

The date, time and location of the inspection moment are in the DataNose timetable.

Assignments

Assignment

• The Assignment involves a research proposal, an oral presentation and the assessment and discussion of another proposal.

Onderstaande opdrachten komen aan bod in deze cursus:

•    Naam opdracht 1 : beschrijving 2
•    Naam opdracht 2 : beschrijving 1
•    ....

Fraud and plagiarism

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.uva.nl/plagiarism

Course structure

Timetable

The schedule for this course is published on DataNose.

Contact information

Coordinator

• prof. dr. S. Brul