Syllabus database for doctoral courses

  • Syllabus database for doctoral courses


Swedish title Systembiologi och omik metoderi
English title Systems Biology and the Omics Cascade
Course number 2238
Credits 1.5
Responsible KI department Institutionen för medicinsk biokemi och biofysik
Specific entry requirements
Grading Passed /Not passed
Established by The Board of Postgraduate Education
Established 2008-11-11
Purpose of the course
Intended learning outcomes Following successful completion of the course, the student will acquire a basic level of knowledge regarding systems biology and different omics-related technologies used in the acquistion of large-scale datasets. In addition, students will be updated on recent findings within these fields. Specifically, students will be able to:
Reflect on the utility of omics-related research in terms of hypothesis generation and experimental design.
Relate to principle the appropriate applications of different computer programming languages and algorithms.
Theorize on the future development of omics-related research approaches and systems biology, as well as motivate the answer.
Contents of the course This course will provide students with a broad spectrum overview of the field of systems biology and present the different technologies and methods employed in this type of research approach. Specific aims include the following:
Convey to students the concept and rationale behind systems biology and omics-related research approaches and experimental design.
Provide an overview of available web-based databases, including KEGG, Reactome database, GenBank, PDB, UniProt, EBI, MIPS, and GO.
Explain the strengths and weaknesses behind different computer programming languages and the appropriate applications, including Perl, R, Bioruby, etc.
Educate students on the current state of systems biology and potential future research directions to assist students in applying these methods to their research.
Teaching and learning activities The course will employ a combination of teaching resources including lectures, laboratory exercies and seminars. A significant portion of the course will focus on hands-on learning using computers in the presence of instructuors and IT-personel.
Examination Satisfactory completion of the course will be assessed by written examination consisting of a research report on an aspect of systems biology. This exact subject of the report may be chosen by the student, but must be approved by the course organizer. The final report must be 3 A4 pages or less (12 point font, 2.54 cm margins) including references and must be turned in within 2 weeks of course completion in order to receive course credit (there is no minimum length). The report should make use of the journal articles and concepts discussed during the course, which are expected to generate ideas for the reports. In the event of an unsatisfactory report, as determined by the course organizer, the student will be given one additional week to re-write and resubmit the report.
Literature and other teaching material Given the nature of this type of course, no single textbook will be used. Instead a series of on-line resources will be employed throughout the course. The algorithms lecture will be based on Pavel Pevzner's book, An Introduction to Bioinformatics Algorithms (2004), which is available in Google Books. Some material will be taken from David Mount's textbook Bioinformatics Sequence and Genome Analysis (, which also covers the advantages and disadvantages of the respective algorithms and tools. In addition, topics such as Systems Biology Workbench (, Systems Biology Markup Language (, and the KEGG database suite ( will be presented. Coursework will also be supplemented with appropriate journal articles at the discretion of the instructors.
Compulsory elements Attendance at all laboratory sessions is required. In the case of necessary absence, the student will be required to perform the laboratory exercises outside of class before a grade is issued.
Course responsible Craig Wheelock
Institutionen för medicinsk biokemi och biofysik

Contact person Craig Wheelock
Institutionen för medicinsk biokemi och biofysik