BMB511: Bioinformatica I (5 ECTS)

STADS: 01012601

Level
Bachelor course

Teaching period
The course is offered in the autumn semester.

Teacher responsible
Email: php@bmb.sdu.dk
Email: hjernoe@bmb.sdu.dk

Timetable
Show entire timetable
Show personal time table for this course.

Prerequisites:
None

Academic preconditions:
Students taking the course are expected to:

• Have a basic knowledge of protein chemistry (BMB533/BMB506 or similar is expected to be known)
• Be able to use the Internet and standard computer programs

Course introduction
To give the student an insight in the use of Bioinformatics and the importance of biological databases in modern molecular biology. The student will through practical exercises with direct access to the most important biological databases obtain knowledge of bioinformatics and the associated biology.

The course will take the students behind the software interfaces to see how the software developers use their knowledge on evolution and biology in order to construct alignment and prediction tools. Furthermore the student will be trained to evaluate and comment fellow student replies and to formulate text on bioinformatics concepts. During the course there will be discussions and reflections on the theoretical and practical ethical problems present in the subject and its social function.

Students who attend the course are expected to have knowledge of basic molecular biological concepts and biochemical processes. Among these the central dogma, DNA and protein structure. The course requires active participation. The course will include an extensive use of features of the SDU's e-learning system, including e-tests, self- and peer assessments, wiki and blog. Participation in the course presupposes, therefore, that the student masters these functions and accepts the defined deadlines.

Through the course the students is expected to obtain the following skills:

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

• The ability to find, extract and utilize the information located in the most important biological databases and understand their structure and main characteristics, including understanding the difference between primary and secondary databases.
• Conduct and evaluate homology and motif searches in databases on the Internet and evaluate the results and explain the principles behind.
• Conduct and evaluate binary and multiple alignments of protein sequences and identify homology and further to understand the principles behind the scoring, gap penalties and position specific scoring matrices.
• Construct a phylogenetic tree based on homologous protein sequences and understand the principles behind phylogenetic trees and bootstrap values.
• Be able to pull information about genes and SNPs out of databases using genome browsers.
• To carry out and evaluate secondary structure predictions and understand the principles behind them and behind 3D structure categorization.
• Understand the issues behind working with large data sets e.g. long lists of proteins from proteomics studies and understand the principles behind gene ontology.
• Critically evaluate whether the software works efficiently (i.e., whether the analysis is correct and the results can be interpreted properly)
• Be familiar with the most important resources and software available for bioinformatics on the Internet and the principles behind them.
• Use the above methods for a comprehensive evaluation of sequences and structures.

Subject overview
The following main topics are contained in the course:

• Sequence analysis
• Homology
• Function and identification
• Access to net based databases
• Searching in relevant databases on the World Wide Web
• Multiple sequence alignment and phylogenetic trees
• Genome browser
• GO annotation
• Motif searching
• Structure prediction

Literature

• Selzer, Paul Maria, Marhöfer, Richard, Rohwer, Andreas: Applied Bioinformatics, an introduction.
• Udleverede noter. .

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam

1. Approval of the exercise task sets, pass / fail, internal examination by teacher.

Assessment and marking:

1. Written exam. Internal marking, Danish 7-mark scale. (5 ECTS). (01012602). A closer description of the exam rules will be posted under 'Course Information' on Blackboard.

Reexamination in the same exam period or immediately thereafter.

Expected working hours
The teaching method is based on three phase model.
Intro phase: 14 hours
Skills training phase: 24 hours, hereof:
 - Laboratory exercises: 24 hours

Educational activities

Educational form
Activities during the study phase:

• Wiki
• Self- and peer assessments
• Assignment
• Artikler og bog-materiale
• e-tests

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 at the end of each exercise week and in the weeks following 1-3 peer tasks will be evaluated. 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. It is possible to work with e-tests, however, these are not part of the subject sample.

The lectures (introductory phase), texts (part of the study phase) and exercises during the training phase are intended to complement each other. Each week one or two new topics are added that throughout the course will be linked together.

On the course page in Blackboard 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.

Language
This course is taught in Danish or English, depending on the lecturer. However, if international students participate, the teaching language will always be English.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.