BIO9905MERG1 - Bioinformatics for Metagenomic Analyses and Environmental Sequencing
Course content
Metagenomics is the study of genomes recovered directly from environmental samples. This approach is often used to understand the genetic composition and metabolic capacity of microbial communities. Moreover, high throughput sequencing of amplified markers (DNA barcodes) can be used to analyse the taxonomic composition of environmental samples. In this course the students will be introduced to important analytical approaches used for analyzing microbial communities using high throughput sequencing.
Learning outcome
The student will be introduced to high throughput sequencing (methods and concepts) and how the data can be analyzed further to study microbial diversity and metagenomics. Important themes will be (1) filtering and quality assessment of high throughput sequence data, (2) clustering of high throughput sequence data, (3) taxonomic and genetic annotation of high throughput sequence data, (4) microbial diversity analyses, (5) analyses of microbial community composition and change and (6) metabolic reconstruction analyses. The main emphasis will be on the programs/bioinformatics pipelines Qiime and mothur.
Admission
PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.
If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.
PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student within a given deadline.
The examination in this course is not available for external candidates. Only students admitted to the course may sit for the examination.
Prerequisites
Formal prerequisite knowledge
Id does not exist in shared textRecommended previous knowledge
BIO2140 - Molecular biology and Biological Methods, BIO2150 - Biostatistics and Study Design and BIO4200 - Molecular Evolution
Teaching
The course combines lectures (before lunch) and computer labs after lunch each day.
This is an intensive course over five days (March 18-23).
Access to teaching
Id does not exist in shared textExamination
A project report will be compulsory and must be submitted two weeks after the course.
The report will be marked as passed/not passed.
Examination support material
No examination support material is allowed.
Language of examination
Id does not exist in shared textGrading scale
Grades are awarded on a pass/fail scale. Read more about the grading system.
Explanations and appeals
You may request an explanation of your grades, and you may also appeal against your grades or make a complaint about formal examination errors. Read more about explanations and appeals.
Resit an examination
Id does not exist in shared textStudents who fail, will be allowed to deliver a revised report.
Withdrawal from an examination
Id does not exist in shared textSpecial examination arrangements
If you have a disability or a health problem that entails significant inconvenience in an examination situation, you may be considered for special examination arrangements. Mothers who are breastfeeding may apply for extra time to complete the exam.
Evaluation
Feedback from our students is essential to us in our efforts to ensure and further improve the high quality of our programmes and courses. All courses are subject to continuous evaluation. At regular intervals we also ask students on a particular course to participate in a more comprehensive, periodic evaluation of this course.