BCHM459-22S2 (C) Semester Two 2022

Genomics

15 points

Details:
Start Date: Monday, 18 July 2022
End Date: Sunday, 13 November 2022
Withdrawal Dates
Last Day to withdraw from this course:
  • Without financial penalty (full fee refund): Sunday, 31 July 2022
  • Without academic penalty (including no fee refund): Sunday, 2 October 2022

Description

Students taking this course will develop a deep knowledge in a current area of genome biology and evolution. Students will get to grips with the latest research in this fast moving field, read deeply on a chosen topic, and develop strong critical thinking, writing and debating skills.

Genomics is an integrally important part of biology. Through the sequencing, characterisation, and study of DNA, it is now possible to decode the complete genetic complement of any organism. Genome science is revolutionising almost all fields of biological enquiry. In this course we will look at the genomic technologies that are transforming biology, the biological and evolutionary insights arising from genome research, and the process of genome sequencing, from start to finish.

You will learn about genome sequencing, annotation and the analysis of genomes using various types of genomic data and bioinformatics tools: the course will be based around the analysis and interpretation of genomic (bacterial genome), gene amplicon sequencing and gene expression data.

Tutorials will be structured around the discussion of assigned papers and practical investigation of genomic data. Seminars will cover topics such as advanced genome annotation and analysis, metabarcoding pipelines and differential gene expression analysis. The course will be project-based and will involve some group work.

Recommended preparatory course(s): Any of BIOL313, 333, 334, 335 or 300-level BCHM.

Learning Outcomes

  • As a student in this course, I will develop:
  • An up-to-the-minute knowledge of methods in genomics (assessment task: Projects 1, 2, and 3)
    Related graduate attributes: GP1, GP2, GP5
  • An understanding of genomics as a tool for answering biological questions (as opposed to a means of generating data for the sake of it) (assessment task: Projects 1, 2, and 3)
    Related graduate attributes: GP1, GP2, GP5
  • Reading skills required to navigate, understand and question scientific literature (assessment task: Projects 1, 2, and 3)
    Related graduate attributes: GP1, GP2, GP5
  • Experience in writing in the style of project proposals and scientific papers (assessment task: Projects 1, 2, and 3)
    Related graduate attributes: GP1, GP2, GP5
  • Experience in scientific collaboration involving data analysis, interpretation and presentation of results (assessment task: Projects 1, 2, and 3)
    Related graduate attributes: GP1, GP2, GP5

    Transferable Skills / Pūkenga Ngaio
    As a student in this course, I will develop the following skills:
  • Understand genomic methods and results presented in research papers and technical reports.  The ability to critically evaluate and interpret genomic information is essential in higher level courses and in research
    Related graduate attributes: GP1, GP2, GP5
  • Have the ability to apply advanced genomic analysis concepts.  This is important for distinguishing different types of genetic variation and their potential functional impacts and is broadly applicable to multiple research fields
    Related graduate attributes: GP1, GP2, GP5
  • Basic knowledge of how samples and data are collected for generation of genomic information.  This is broadly applicable across multiple research fields
    Related graduate attributes: GP1, GP2, GP5
  • Knowledge of statistical analysis of genome data, essential for higher level courses and across research and employment sectors
    Related graduate attributes: GP1, GP2, GP5
  • The ability to know which method to apply to which dataset, which is essential in further research in all areas of genomics
    Related graduate attributes: GP1, GP2, GP5
  • Communication skills – the ability to describe what results mean in the context of the problem, and being able to explain the results to someone else is essential for any professional career
    Related graduate attributes: GP1, GP2, GP5

Restrictions

BIOL430/BCHM406/BIOL459

Equivalent Courses

Timetable 2022

Students must attend one activity from each section.

Tutorial A
Activity Day Time Location Weeks
01 Thursday 09:00 - 11:00 Ernest Rutherford 464 Computer Lab (21/7, 18/8, 15/9, 29/9, 13/10)
E12 (4/8)
18 Jul - 24 Jul
1 Aug - 7 Aug
15 Aug - 21 Aug
12 Sep - 18 Sep
26 Sep - 2 Oct
10 Oct - 16 Oct

Course Coordinator / Lecturer

Amy Osborne

Lecturers

Matthew Stott and Sarah Flanagan

Assessment

Assessment Due Date Percentage  Description
Participation 10% Participation and contribution
Assignment 1 03 Aug 2022 10% Intro to practical computing for biologists
Assignment 2 17 Aug 2022 20% How to use regular expressions in biological computing
Assignment 3 26 Aug 2022 15% Whole genome sequencing introduction and pipeline demonstration
Assignment 4 28 Sep 2022 15% Whole genome sequencing
Assignment 5 29 Oct 2022 30% Transcriptomics


There are THREE project-based assessment items for BIOL459, each comprising 30% of your final grade.  10% of your final grade is reserved for participation and contribution.  There is NO final exam for BIOL459, so it is important that you engage and contribute. You will be provided with guidelines regarding the scope and depth of your written report for each of the three assessments. You are expected to work in self-assembled teams to produce your outputs for each assessment, however each student will need to produce their own final assessment for each of the three projects.  

For each of the three written assessments, each student will be required to submit a statement of who they worked with to produce the outputs for their project.  You will need to convey precisely what YOU contributed to the project, and others, and weight everyone’s contribution by percentages.  You will be given guidelines around how this will work during the first tutorial.  The course coordinators reserve the right to adjust individual student marks to mitigate any disproportionate effects resulting from the self- and peer-assessment of performance.

NOTE: All items of assessment, whether individual or group, are marked by at least two members of the teaching staff.

Class material on Learn (Ako) & use of Turnitin Resources used or referred to will be available on-line on the course link in Learn.  Please also note that we will be requesting that you submit written work in both hard copy (for grading) and in electronic form (for assessment of originality using “Turnitin”). Instructions will be given on how you do this via Learn.   Guidelines for successful group work The majority of the course will involve you engaging with research your chosen group and working in your group to analyze the data and prepare your findings to present in your written report.   To complete the course successfully, you will need to organise regular work-group meetings: no-one else will do this for you. Your learning and group work will be supported by tutor advice.  The group work and problem based aspects of this course make it unusual, and this may be your first experience with one or more of these situations. Therefore , your expectations of yourself and others need to be adjusted accordingly in an effort to keep them realistic (and reduce stress!). Clear communication (within and between all parties) is obviously a key factor here. We will discuss expectations in class. You must play a full part in your group, or you will attract the attention of the course coordinator. Your expectations of your group, and theirs of you, are also important. Each group should work with the guidance of the allocated staff member. Having learning is student said that, the approach to centred, with you using the skills you have developed in preceding courses and taking responsibility for your own learning. This means that you as a group will work to clarify your research focus, you will decide (with guidance) how it will best be researched, and then how best to report the results. 4

Indicative Fees

Domestic fee $1,084.00

* All fees are inclusive of NZ GST or any equivalent overseas tax, and do not include any programme level discount or additional course-related expenses.

For further information see School of Biological Sciences .

All BCHM459 Occurrences

  • BCHM459-22S2 (C) Semester Two 2022