INF5380 – High Performance Computing in Bioinformatics
Course description
Course content
This course focuses on the application of high performance computing (HPC) to bioinformatics analysis. The main target is to provide a background on how to effectively use HPC clusters for running computationally or data intensive bioinformatics applications. The course will mainly include teaching students selected bioinformatics tools and workflows, and how to use HPC platforms to speed up and maximize the overall throughput of intensive bioinformatics analysis. This would include, e.g. how to optimize the use of available compute nodes, and how to adapt the application to the available resources on each compute node.The course will cover both how to efficiently use parallelism when writing your own programs, as well as how to adapt and wrap existing tools in manner that efficiently exploits resources available on parallel architectures.
Learning outcome
After finishing the course the students should know:
- Resource intensive bioinformatics tools for, e.g. assembly, mapping/alignment, and multiple alignment. This would include the use of commandline tools and portal based tools, e.g. Galaxy.
- How those tools work, how this would influence the runtime, and the possibility of parallelizing the computation.
- When to use parallelization and distribution.
- The basic structure of HPC clusters, and how to run jobs on a cluster
- How to evaluate the use of resources on a cluster, and how to optimize the use of memory and CPUs
- How to adapt or write wrappers around existing tools to process large datasets efficiently using parallellisation
Admission to the course
Only taught even years (i.e. Spring 2020, Spring 2022, etc).
This course is only avaliable if the PhD version has capacity.
Recommended previous knowledge
Basic unix competence and basic knowledge of bioinformatics applications is required. Basic programming skills, preferably in Python.
Overlapping courses
- 5 credits overlap with INF9380 – High Performance Computing in Bioinformatics (discontinued).
Teaching
This as an intensive two weeks course with lectures and hands on exercises 7 hours a day, Monday to Friday. About half the time with lectures and the other half with exercises. In total lectures and exercises are estimated to 70 hours. Selfstudy/reading of curriculum is estimated to 30 hours. Preparation time for written report (home exam) is estimated to 40 hours. The total workload for the course is estimated to 140 hours.
Examination
Practical student project (home exam) with hand-in of written report.
It will also be counted as one of?your three?attempts to sit the exam for this course, if you sit the exam for one of the following courses: INF9380 – High Performance Computing in Bioinformatics (discontinued)
Grading scale
Grades are awarded on a scale from A to F, where A is the best grade and F?is a fail. Read more about?the grading system.
Resit an examination
More about examinations at UiO
- Use of sources and citations
- Special exam arrangements due to individual needs
- Withdrawal from an exam
- Illness at exams / postponed exams
- Explanation of grades and appeals
- Resitting an exam
- Cheating/attempted cheating
You will find further guides and resources at the web page on examinations at UiO.