Project in Algorithms in Molecular Biology
2
Bioinformatics
Advanced studies
Selected algorithm in molecular biology is implemented and experimented on real or/and simulated data. Validation measures and methods to compare the results to other tools are studied.
| Year | Semester | Date | Period | Language | In charge |
|---|---|---|---|---|---|
| 2015 | spring | 04.05-25.05. | 4-4 | English | Leena Salmela |
Lectures
| Time | Room | Lecturer | Date |
|---|---|---|---|
| Mon 12-14 | C222 | Leena Salmela | 04.05.2015-25.05.2015 |
Information for international students
The course will be lectured in English.
General
The course consists of project work involving commonly used bioinformatics tools. The students will develop a pipeline for de novo genome assembly using available tools and implementing one of the stages of the pipeline themselves. The pipeline will be tested on two data sets: One real data set for a known genome and one artificial data set for an artifical genome.
Schedule
- 4 May: Introduction of the project (slides)
- 10 May: DL for returning a plan for the project
- 11 May: Students will shortly present their plan for the project. Discussion of the plans.
- 18 May: Monitoring the progress according to the students' plans. Suggested goals for this DL are either the student's own implementation of an assembly stage or having other tools installed and running. Discussion of problems / issues that have come up.
- 25 May: Students will shortly present the methods used and the results achieved.
- 29 May: DL for returning the project report
Completing the course
Each student is required to
- Submit a plan for the project
- Attend the weekly sessions
- Submit a final report describing the methods used and the results achieved
- Submit the sources of their own implementation of an assembly stage
- Submit the two assembled genomes
Instructions
Instructions for the proejct: amb-project15.pdf
Data: pamb15.zip
Evaluation of the results
The assembled genomes will be evaluated according to widely used measures for the contiguity and length of scaffolds (e.g. N50, number of scaffolds...). The correctness of scaffolds will be evaluated by aligning the scaffolds against the genome.
Grading
The project will be graded as passed/failed. To pass the course a student should complete a project according to the course requirements above. To pass there is no minimum requirement for the evaluation results of the submitted genomes.