BMB511: Bioinformatica I
Comment
Entry requirements
Academic preconditions
Students taking the course are expected to:
- Have a basic knowledge of concepts in molecular biology and biochemical processes. This includes the central dogma, nucleic acid and protein structure.
- Have a basic knowledge of protein chemistry (BMB533 or similar is expected to be known)
- Be able to use the Internet and standard computer programs
Course introduction
To give the student insight into the use of bioinformatics and biological data science, and the significance and background of biological databases and programs in biology and biomedicine. Through practical exercises, the student will obtain knowledge of bioinformatics and the underlying biological phenomena and learn to relate to the analysis and results.
The course will take the student behind the software to see, how researchers use their knowledge of biology to construct bioinformatic tools. In addition the student will be trained in analyzing experimental data qualitatively as well as quantitatively. Furthermore, the student will be trained in evaluating and commenting the work of other students, and to formulate texts on bioinformatical concepts. In the course, theoretical and practical ethical problems within the subject as well as the function of the subject in society, will be discussed and reflected upon.
Students who follow this course are expected to have basic knowledge of concepts in molecular biology and biochemical processes. This includes the central dogma, nucleic acid and protein structure.
The course requires active participation. The functions of the SDU e-learning system, such as e-tests and self- and peer assessment, will be used extensively in the course, and thus the student is required to master these functions and accept the associated deadlines.
Through the course the students is expected to obtain the following competencies:
- Be able to use the relevant course tools, formulate a critical assessment of the results obtained, relate them to each other and explain the principles behind the tools used. That is, they must be able to apply bioinformatics in practice.
- Be able to demonstrate knowledge of the course topics, so that they are able to identify issues in which these topics are relevant and explain how the tools they have used in the course, can be used in these new issues. That is, they must be able to apply this knowledge reflectively.
- Be able to describe and explain relevant concepts on the subject and explain the biological phenomena and evolutionary forces that relate to the concepts.
- Acquired knowledge of methods for analyzing biomedical image data
- Develop and formulate constructive criticism of peer’s responses.
- Acquired knowledge about the importance of biological databases in modern molecular biology
- Understand ethical dilemmas in the use of e.g. national gene databases
- Understand how scientific knowledge is achieved by an interplay between theory and experiment
Expected learning outcome
- Have an overall understanding of Bioinformatics, and know the biomolecules which are typically analyzed using bioinformatics
- Find, extract and use the information from the most relevant biological databases, and understand the structure and most important characteristics of these.
- Know and use bioinformatics tools to characterize and compare nucleic acid sequences
- Know and use bioinformatics tools to investigate and compare protein sequence, structure and function.
- Understand the key concepts in analyzing and visualizing quantitative data from omics experiments
- Understand the principles behind gene ontology and its use in molecular networks
- Know the concepts of systems biology
- Critically evaluate if software and data analysis is functioning effectively (i.e. is the analysis correct and can the results be read clearly)
- Know the possibilities of using machine learning and statistical analysis to answer biological questions on the basis of large datasets
- Understand the importance of open source code and open data policies and the accompanying ethical considerations
- Analyze digital images obtained by optical spectroscopy of biological samples, and extract information about the cellular processes from the images.
Content
The following main topics are contained in the course:
- Bioinformatics data and databases
- Qualitative analysis of biomolecules
- Quantitative analysis of biomolecules
- Visualization and interpretation of data
- Systems biology
- Image analysis
- Machine learning in biology and biomedicine
- Ethics in bioinformatics
Literature
- “Introduction to Bioinformatics” (5th edition) af Arthur M. Lesk.
- Handed notes.
See itslearning for syllabus lists and additional literature references.
Examination regulations
Prerequisites for participating in the exam a)
Timing
Tests
Approval of the exercise task sets
EKA
Assessment
Grading
Identification
Language
Examination aids
ECTS value
Additional information
Exam element a)
Timing
Prerequisites
| Type | Prerequisite name | Prerequisite course |
|---|---|---|
| Examination part | Prerequisites for participating in the exam a) | N200005101, BMB511: Bioinformatica I |
Tests
Written exam
EKA
Assessment
Grading
Identification
Language
Duration
Examination aids
ECTS value
Additional information
Indicative number of lessons
Teaching Method
- Intro phase: 20 hours
- Skills training phase: 22 hours, hereof: Laboratory exercises: 22 hours
- Self- and peer assessments
- Assignment
- Reading papers and book
The intro phase consists of lectures, encouraging a dialogue of questions from both teacher and student, and through small, simple and relevant tasks handed out at the lectures. The lectures will introduce the course topics and supplement the content of the relevant texts with additional knowledge and perspectives. This means that lectures includes learning that may not necessarily be found in the texts, but which can be found in the lecture slides/notes.
During the training phase the work is independent, mainly with the use of various subject-related tools complemented with theoretical questions and exercises to describe evaluate and explain the results obtained. The students have in the training phase access to a dialogue with the instructor and / or teacher and fellow students. The students are trained in the goal descriptions as described in the course description above. The training phase includes self- and peer assessments, which are submitted and evaluated regularly during the course. These are included in the prerequisite test.
In the study phase, students are expected to work independently with the textbook and the articles selected by the teacher. Additionally they are expected to work with various tasks.
The lectures (introductory phase), texts (part of the study phase) and exercises during the training phase are intended to complement each other.
On the course page on the SDU e-learning platform detailed information about the deadline for prerequisite sample elements and possible options for re-evaluation will be presented. All elements must be handed in, ie including peer reviews.
Teacher responsible
Additional teachers
| Name | Department | City | |
|---|---|---|---|
| Daniel Wüstner | wuestner@bmb.sdu.dk | Institut for Biokemi og Molekylær Biologi | |
| Ole Nørregaard Jensen | jenseno@bmb.sdu.dk | Institut for Biokemi og Molekylær Biologi | |
| Veit Schwämmle | veits@bmb.sdu.dk | Institut for Biokemi og Molekylær Biologi |