BMB511: Bioinformatica I

Study Board of Science

Teaching language: Danish or English depending on the teacher, but English if international students are enrolled
EKA: N200005112, N200005102
Assessment: Second examiner: None, Second examiner: Internal
Grading: Pass/Fail, 7-point grading scale
Offered in: Odense
Offered in: Autumn
Level: Bachelor

STADS ID (UVA): N200005101
ECTS value: 5

Date of Approval: 12-04-2023


Duration: 1 semester

Version: Archive

Comment


Entry requirements

None

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, including having a basic understanding of using R.

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 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

When the course is over, the students are expected to be able to:

  • 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

Autumn

Tests

Mandatory assignments

EKA

N200005112

Assessment

Second examiner: None

Grading

Pass/Fail

Identification

Full name and SDU username

Language

Normally, the same as teaching language

Examination aids

To be announced during the course

ECTS value

0

Additional information

Examination consists of approval of the exercise task sets.
The prerequisite examination is a prerequisite for participation in exam element a)

Exam element a)

Timing

January

Prerequisites

Type Prerequisite name Prerequisite course
Examination part Prerequisites for participating in the exam a) N200005101, BMB511: Bioinformatica I

Tests

Written exam

EKA

N200005102

Assessment

Second examiner: Internal

Grading

7-point grading scale

Identification

Student Identification Card

Language

Normally, the same as teaching language

Duration

3 hours

Examination aids

All common aids are allowed e.g. books, notes, computer programmes which do not use internet etc. 

Internet is not allowed during the exam. However, you may visit the course site in itslearning to fill in the MCQ test. If you wish to use course materials from itslearning, you must download the materials to your computer the day before the exam. During the exam you cannot be sure that all course materials is accessible in itslearning.    

ECTS value

5

Additional information

The re-examination is changed to a oral examination if nine or fewer students have registered. The oral exam is without aids and preparation time. Duration: 20 minutes. Including. Assessment. The student draws a topic and then starts to tell them what they know about the topic. The questions to the student will be based on this topic, but will only be delimited by the syllabus.

Indicative number of lessons

42 hours per semester

Teaching Method

The teaching method is based on three phase model.
  • Intro phase: 20 hours
  • Skills training phase: 22 hours, hereof: Laboratory exercises: 22 hours
Activities during the study phase:
  • Assignments
  • 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.

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.

Teacher responsible

Name E-mail Department
Jesper Grud Skat Madsen jgsm@bmb.sdu.dk Data Science

Additional teachers

Name E-mail 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
Thøger Jensen Krogh thjk@bmb.sdu.dk Administration og Service
Veit Schwämmle veits@bmb.sdu.dk Institut for Biokemi og Molekylær Biologi

Timetable

Administrative Unit

Biokemi og Molekylær Biologi

Team at Educational Law & Registration

NAT

Offered in

Odense

Recommended course of study

Transition rules

Transitional arrangements describe how a course replaces another course when changes are made to the course of study. 
If a transitional arrangement has been made for a course, it will be stated in the list. 
See transitional arrangements for all courses at the Faculty of Science.