BIOL430-14W (C) Whole Year 2014

Genomics

30 points

Details:
Start Date: Monday, 24 February 2014
End Date: Sunday, 16 November 2014
Withdrawal Dates
Last Day to withdraw from this course:
  • Without financial penalty (full fee refund): Friday, 7 March 2014
  • Without academic penalty (including no fee refund): Friday, 5 September 2014

Description

This course covers the principles of genome analysis (genomics) drawing upon the wealth of information being generated by genome mapping and sequencing projects. Seminar topics will examine how the application of modern molecular genetic techniques, coupled with comparative evolutionary analyses, are improving our understanding of biological systems.

Genomics is a new and 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, and in the course we will look at examples from fields as diverse as medicine, microbiology, molecular genetics, ecology and evolution.

The course is taught as 12 two-hour sessions, that will comprise a mixture of discussion, presentation and computer-based tutorials. It is divided into four broad modules: genome technologies and bioinformatics, functional genomics, comparative genomics and genome biology and evolution.

We will cover emerging experimental technologies in genomics and functional genomics, with a focus on human health and genetics. You will apply these to developing your own genome sequencing proposal.

A key component of the course is hands-on genome sequence analysis, where you will learn how to annotate and analyse genomes using bioinformatics and comparative genomics tools. For this part of the course, you will work as teams and write a draft paper based on unpublished sequence data given to your group during the course.

In addition, we will examine the biology of genomes, examining how genomes evolve and how population genetics and modes of reproduction impact the architecture and make-up of genomes.

Learning Outcomes

  • An up-to-the-minute knowledge of methods in genome sequencing and functional genomics methodologies.
  • An understanding of genomics as a tool for answering biological questions (as opposed to a means of generating data for the sake of it).
  • Reading skills required to navigate, understand and question scientific literature.
  • Practical bioinformatics skills in genome annotation and data analysis.
  • A broad understanding of how genomes evolve.
  • Experience in writing grant proposals, short reports and scientific papers.
  • Experience in scientific collaboration involving data analysis, interpretation and presentation of results.
  • Oral presentation skills

Prerequisites

Subject to approval of the Head of School.

Restrictions

Equivalent Courses

Timetable Note

The course will take the form of twelve 2-hour sessions, which will comprise a combination of formal lectures, discussion and tutorial sessions. Articles drawn from the scientific literature will form the basis of the readings, and students are expected to have read the relevant papers prior to each session. Detailed information about each session, together with reading lists and other resources, will be available on Learn.

Course Coordinator / Lecturer

Anthony Poole

Lecturers

Chris Glover , Paul Gardner and Stinus Lindgreen

Guest Lecturers

Dr Martin Kennedy (Department of Pathology, University of Otago) and Dr Anna Pilbrow (Department of Medicine, University of Otago)

Textbooks / Resources

Recommended Reading

Brown, T. A; Genomes 3 ; 3rd ed; Garland Science Pub, 2007 (See chapters 2-9 and 18-19).

There will also be some material and exercises aimed at helping you get started if you have not taken BIOL330 or an equivalent course.

Additional Course Outline Information

Academic integrity

It is essential that you are aware that plagiarism is considered a very serious offence by the Academic community, the University and the School of Biological Sciences. Plagiarism is defined as taking content from another work or author and presenting it, without attribution, as if it is your own work. Content here includes text (sentences or major parts of sentences), display items (graphs and tables), and overall structure (the detailed sequence of ideas). Plagiarism includes:
• re-use of previous assignments (even if each individual sentence has been rephrased to say the same thing in different words, if the overall structure is re-used)  
• copying of another student’s work (with or without their consent)
• the unreferenced use of published material or material from the internet e.g. cutting and pasting of paragraphs or pages into an essay.
For most pieces of in-term assessment you will be given information concerning the use of direct and indirect quotes from previously published work. If you are in any doubt about appropriate use of published material, please speak with a member of academic staff. If you are still unsure what plagiarism is, then seek advice.

It is a School policy that courses may request you submit work electronically for subsequent analysis of originality using Turnitin. Students agree that by taking courses in BIOL, required papers may be subject to submission for textual similarity review to Turnitin.com for the detection of plagiarism.  All submitted papers will be included as source documents in the Turnitin.com reference database solely for the purpose of detecting plagiarism of such papers.  Use of the Turnitin.com service is subject to the Terms and Conditions of Use posted on the Turnitin.com site.

Assessment and grading system

SBS Grading
(A+ 90% or above
A 85 – 90
A- 80 – 84
B+ 75 – 79
B 70 – 74
B- 65 – 69
C+ 60 – 64
C 55 – 59
C- 50 – 54

A restricted pass (R) may be awarded to those who are close to a pass (i.e. an overall score of 48-49.9%) AND who have achieved at least a 40% overall score in both in-course assessment and tests/exams. If an R grade is awarded you gain credit for the course but cannot continue into papers that require this course as a pre-requisite. NB. The R grade is only available at 100 and 200 level - it cannot be awarded for third year papers.

Failing grades: D     40-48 ; E     0–39

Requests for extensions

What if I can’t get it finished in time?
Reports and assignments should be handed in on time. Extensions may be granted if you have a valid reason. If you require an extension, you should request one from the course co-ordinator (or the lecturer responsible for marking the work), with as much notice as possible.  Please do this BEFORE the deadline for the assignment. If you have been given an extension you should hand the work DIRECTLY to the course coordinator (do not put it in the drop box as it may not be cleared after the due date).
If an extension has not been granted:
• work must be handed in by the due date to gain full credit
• work handed in up to 7 days after the deadline will be marked, but the marks will be discounted 25% before they are recorded to the student's credit
• any work handed in more than 7 days after the deadline date will not be marked or earn credit.

What do I do if I’m sick?

If you feel that illness, injury, bereavement or other critical circumstances have prevented you from completing an item of assessment worth 10% or more of total course assessment or have affected your performance in a test or exam, you should visit a doctor within 24 hours and submit the application form to Erskine 235 within 7 days. The application form is available on-line or from the Student Health and Counselling Service. You should also notify the course co-ordinator.  For further details on aegrotat applications, please refer to the University’s website - http://www.canterbury.ac.nz/exams/aegrotats.shtml). The aegrotat provisions are intended to assist students who have covered the work of a course but have been prevented by illness or other critical circumstances from demonstrating their mastery of the material or skills at the time of assessment – they do not excuse you from doing the assessment. If the examiner cannot assess your aegrotat application because of lack of other evidence, you may be asked to sit a special assessment if you miss a final exam. You should also expect to be required to submit additional work if you miss a major assignment (e.g. a field trip for which a major write-up is required). Please note: acceptance of the grounds for an aegrotat application does not simply excuse you from completing items of assessment if you are requested to do so. You will be given reasonable time to complete any such work.

What do I do if I have to miss something?

In rare cases you may not be able to sit a test or exam, or attend a field trip, because of involvement in international or national representative sport or cultural groups. In such cases see the course co-ordinator, and a course of action (usually the sitting of an equivalent test or exam at a different time, or submitting an equivalent piece of written assessment) will be arranged. This should be done well in advance of the set date for a missed exam/test/assignment. Please note – holiday trips, weddings, birthday parties etc. are not given special status in the University policy, so please do not ask for special consideration in these circumstances.

What if I fail part of the course?

In BIOL, we require a satisfactory level of achievement in both the theoretical aspects of the discipline and in practical activities. This means you must attend all class activities and submit all items of assessment unless you have a very good reason not to (e.g. medical reasons). A student must attain a score of at least 40% for in-course assessment and at least 40% in the course exam/test, AND score at least 50% overall for the course, to be awarded a passing grade.

What’s the best way to give feedback?

We welcome constructive feedback at all times – help us to make this a valuable course for you.  We endeavour to remain approachable at all times.  If you would rather give feedback anonymously, please use the ERAU survey or talk to lab demonstrators, or your class rep. who will all report back to the staff-student liaison committee that includes a representative from each of the undergraduate classes. Class representatives will be selected from each class at the start of course.

Indicative Fees

Domestic fee $1,818.00

* 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 BIOL430 Occurrences

  • BIOL430-14W (C) Whole Year 2014