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.
In relation to the competence profile of the degree it is the explicit focus of the course to contribute to the following competences:
- Knowledge of theories and experimental methods within the fields of molecular biology and biochemistry
- Knowledge of the scientific terminology used in the fields of molecular biology and biomedicine
- Knowledge of the importance of biological databases in modern biomedicine and molecular biology
- Understanding of how scientific knowledge is obtained through interplay between theory and experiment
- The ability to acquire new knowledge effectively and independently, and to use that knowledge reflectively
- The understanding that the approach to the topics of the field is independent of national borders
- Be able to apply one or more theories and methods from the fields of biochemistry and molecular biology
- Be able to investigate concrete biochemical and molecular biological phenomena theoretically and or experimentally
- Be able to implement the use of bioinformatics
Expected learning outcome
- Know the most important data formats and concepts, which are used to analyze DNA, RNA, and protein data.
- Find, extract and use the information from the most relevant biological databases (e.g., UniProt.org), 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, including transcriptomics and proteomics.
- Understand the principles behind gene ontology and its use in molecular networks
- Know the concepts of systems biology
- 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
- Bioinformatic image analysis
- Open data and ethics in bioinformatics
Literature
- Lecture presentations
- Handed notes, articles, and assignments.
The study material will be made available on itslearning.
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
Indicative number of lessons
Teaching Method
- Intro phase: 20 hours
- Skills training phase: 22 hours, hereof: Laboratory exercises: 22 hours
- Peer assessments
- Assignment
- Reading papers
The intro phase consists of lectures, which 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 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 articles and 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
| Name | Department | |
|---|---|---|
| Jesper Grud Skat Madsen | jgsm@bmb.sdu.dk | Institut for Biokemi og Molekylær Biologi, ATLAS - Center for Functional Genomics and Tissue Plasticity |
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 |