PHVIT9560 Bioinformatics with emphasis on analysis of high throughput sequencing data Course description

Target Group

The target group is PhD candidates / students who plan to conduct Action Research projects and want to learn more about epistemology, methodology and ethics related to their own work

Admission requirements

The admission requirement is a five-year master’s degree (three years + two years) or equivalent qualifications in teacher education, other pedagogical education, educational science, development studies, or other education on equivalent level in subjects relevant for teacher education.

In case of a large number of applicants, PhD-students enrolled in the PhD programme in Educational Sciences for Teacher Education will be prioritized, then students in other PhD-programmes, then academic employees at the Faculty of Teacher Education and International Studies.

Applicants that are not enrolled on the PhD-programme at the Faculty of Education and International Studies at OsloMet must send a summary in English of maximum one A4 sheet with relevant information about their own project / area of interest, containing topic, methodology, theoretical approach, and why this course might be relevant for their project.

Admission requirements

This course is primarily aimed at PhD candidates admitted to the PhD programme in Health Sciences and PhD students from Memorial University, Newfoundland. General terms for admission to the course is a completed master's degree in molecular biology or equivalent qualification (e.g. completed MABIO4400). Priority will be given to PhD candidates from OsloMet and Memorial University, Newfoundland.

Note that all students must have a laptop not more than 2 years old (windows 7 or more recent or mac with OS X). The laptop must be able to connect to wireless network.

On completion of the course, the PhD candidate has achieved the following learning outcomes, defined in terms of knowledge, skills, and general competence:

Knowledge

The PhD candidate

• is able to conduct bioinformatics analysis projects in agreement with best practice (transparency and reproducibility) in the field of bioinformatic science's philosophy
• is in the forefront of knowledge about the current high throughput sequencing (HTS) technologies and understands the differences, benefits and drawbacks of these HTS technologies
• can evaluate and make sound decisions on which platform and bioinformatic approach to use for different HTS projects.
• Can contribute to development of new knowledge and interpret results from various HTS applications

Skills

The PhD candidate can

• Plan a HTS research project and choose optimal sequencing platform
• Carry out the relevant bioinformatic analyses both on the command-line (unix) and R-studio, and utilize web-based resources like Galaxy server and Genbank E-utilities.
• Interpret the results of bioinformatics analysis of HTS (e.g. reliability, sensitivity and specificity) and judge their value for answering biological questions
• Disseminate the results of HTS based research

General competence

The PhD candidate can

• argue in favour of particular HTS technologies or bioinformatic approaches on the basis of current knowledge
• argue in favour of the kind of materials and the number of samples to select/include in different kinds of HTS projects
• can participate in discussions on HTS methodology

The course consists of three weeks consecutive work that includes the following teaching methods: self-study including exercises/questionaries related to background theory (one week), lectures and seminars (one week), and practical exercises in the use of different software programmes for analysis of HTS data (one week). The outcomes of the practical exercises in last week are discussed in plenary sessions.

It is required that students complete all the obligatory practical exercises .

All obligatory exercises must be completed to take the final exam. The final exam is a written examination with invigilation, 4 hours. One internal and one external examiner will assess the answer papers submitted by all candidates.

Grades are awarded on the basis of pass or fail.

One internal and one external examiner will assess the answer papers submitted by all candidates.