AGRIS9Z03 - Bioinformatics

Module Details

Module Code: AGRIS9Z03
Full Title: Bioinformatics
Valid From: Semester 1 - 2019/20 ( June 2019 )
Language of Instruction:English
Duration: 1 Semester
Credits: 7.5
Module Owner:: Sergio Moreira
Departments: Unknown
Module Description: This module aims to provide students with knowledge and competence in the use of computational biology in the analysis of molecular data. This course has emphasis on bioinformatics related to High-Throughput Sequencing (HTS) processing, analysis and interpretation of output of genomics data using bioinformatical tools.
 
Module Learning Outcome
On successful completion of this module the learner will be able to:
# Module Learning Outcome Description
MLO1 Discuss the omics technologies and the impacts of bioinformatics in the agricultural sector
MLO2 Demonstrate a mastery of advanced theoretical knowledge and skills relating to high-throughput sequencing applications
MLO3 Critically assess, interpret and manipulate raw sequencing data
MLO4 Evaluate the impact of high-throughput sequencing in the agricultural sector
Pre-requisite learning
Module Recommendations
This is prior learning (or a practical skill) that is strongly recommended before enrolment in this module. You may enrol in this module if you have not acquired the recommended learning but you will have considerable difficulty in passing (i.e. achieving the learning outcomes of) the module. While the prior learning is expressed as named DkIT module(s) it also allows for learning (in another module or modules) which is equivalent to the learning specified in the named module(s).
No recommendations listed
 
Module Indicative Content
Bioinformatics and its Applications
High-Throughput Sequencing workflow, denovo genome assembly and annotation, transcriptomics using RNA-seq, 16S metagenomics, epigenomics
Bioinformatics Workstation
Working on a Unix system, filesystem basics, commands for working with directories and files, issuing commands on a Unix system, viewing and editing files
Tools for Bioinformatics
n/a
Sequence analysis, pairwise alignment and database searching
Using search engines, NCBI, BLAST, Ensembl, UniprotKB, Pfam, Global and local pairwise alignment, pairwise sequencing comparison using specialised software (e.g. splign), prediction of protein structure and function, multiple sequence alignment
High-Throughput Sequencing
Genome assembly, interpretation and quality check of raw sequencing data, align HTS data against a reference genome, annotating and analysing whole genome sequencing
Practical Exercises
Practicals will be delivered through computer based sessions. Computer-based practicals will allow the Student to become familiar with different types of genetic data sets and the use of various open source software for sequence/genome analyses. By completing these practicals, students will strengthen their understanding of basic bioinformatics applications in an agricultural context.
Learning and Teaching Resources
n/a
Students will receive feedback in the following ways:
- Discussions with the lecturer will provide feedback throughout the module - Academic feedback will be provided on continuous assessment - Feedback on final examination will be given in line with the Institute’s policy
Students will be supported in their learning in the following ways:
- Formal lectures - IT based tutorials - Small group investigation - MOODLE site with tutor directed materials (e.g. links to literature, e-learning materials and contemporary scientific related topics) - Independent study
Module Assessment
Assessment Breakdown%
Project60.00%
Practical40.00%
Module Special Regulation
 

Assessments

Full Time

No Course Work
Project
Assessment Type Project % of Total Mark 60
Marks Out Of 0 Pass Mark 0
Timing n/a Learning Outcome 1,2,4
Duration in minutes 0
Assessment Description
Students will conduct research in a current omics related project. During this project, students will analyse and evaluate the used of omics technologies relating to the agricultural sector.
Practical
Assessment Type Practical/Skills Evaluation % of Total Mark 40
Marks Out Of 0 Pass Mark 0
Timing n/a Learning Outcome 2,3
Duration in minutes 0
Assessment Description
Students will participate in weekly computer-based practicals. During practical sessions, students will evaluate and appraise different bioinformatical tools pertinent to sequence/genome analysis. The students will use specialised techniques, skills and modern computer-based tools necessary for genome assembly and annotation.
No Final Examination
Reassessment Requirement
A repeat examination
Reassessment of this module will consist of a repeat examination. It is possible that there will also be a requirement to be reassessed in a coursework element.

DKIT reserves the right to alter the nature and timings of assessment

 

Module Workload

Workload: Full Time
Workload Type Contact Type Workload Description Frequency Average Weekly Learner Workload Hours
Lecture Contact No Description Every Week 1.00 1
Practical Contact No Description Every Week 2.00 2
Directed Reading Non Contact No Description Every Week 3.00 3
Independent Study Non Contact No Description Every Week 5.00 5
Online Learning (non contact) Non Contact No Description Every Week 1.00 1
Total Weekly Learner Workload 12.00
Total Weekly Contact Hours 3.00
This module has no Part Time workload.
 
Module Resources
Recommended Book Resources
  • Andreas D. Baxevanis, B. F. Francis Ouellette. (2004), Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd. Wiley-Blackwell, p.560.
  • Shui Qing Ye. (2007), Bioinformatics: A Practical Approach, Chapman and Hall/CRC, p.648.
Recommended Article/Paper Resources
Supplementary Article/Paper Resources
Other Resources