Unit Guide

BMS2062
Introduction to bioinformatics
Semester 2, 2016

Handbook link:
http://www.monash.edu.au/pubs/2016handbooks/units/index-byfaculty-med.html

Table of contents
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Table of contents
Unit handbook information

Synopsis

Mode of delivery

Workload requirements

Contact Hours

Unit relationships

Prerequisites

Prohibitions

Co-requisites

Chief Examiner(s)

Unit coordinator(s)

Lecturer(s)

Academic overview

Learning outcomes

Teaching approach

Assessment summary

Assessment requirements

10

Participation

11

Assessment tasks

11

Referencing requirements

22

Assignment submission

22

Returning assignments

22

Resubmission of assignments

22

Extensions and penalties

22

Examination material or equipment

Feedback to you

24
24

Unit Schedule

25

Your feedback to us

26

Previous student evaluations of this unit

Learning resources

26
27

Required resources

28

Technological requirements

28

Other information

28

Policies

28

Academic Integrity

28

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Clinical/Fieldwork Placement Procedures and Behaviour Guidelines

28

Honours and Minor Thesis Guidelines

28

Immunisation and Infection Risk

29

Police Checks

29

Working with Children Check Guidelines

29

Graduate Attributes Policy

29

Student Charter

29

Student Services

29

Monash University Library

29

Disability Support Services

29

Other unit information

30

PRACTICAL SYNOPSES

35

Instructions for Practicals

36

General Information on Practicals

36

Computer account access, printing and data storage

36

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Unit handbook information

Synopsis
Bioinformatics unites the major advances in biology, biochemistry and the biomedical sciences
with those in computing, bioinformatics and networking. The unit covers the application of the
internet to biomedical sciences; organisation and uses of scientific databases; use of
computational methods in genomics and proteomics; fundamentals of molecular modelling;
analysis and presentation of biomedical data; and communication of biomedical data using
information technology.

Mode of delivery
Clayton (Day)

Workload requirements
2 Lectures per week, 1 three hour practical session per week.

Contact Hours

5 hrs per week

Unit relationships
Prerequisites
None

Prohibitions
MOL2022.

Co-requisites
Must be enrolled in one of the following:

Bachelor of Biomedical Science (including double degree programs)

Bachelor of Biomedical Science (Scholar Program)

Bachelor of Biomedical Science Advanced with Honours

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Bachelor of Biomedical Science Advanced with Honours

Chief Examiner(s)
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Chief Examiner(s)
Associate Professor Anna Roujeinikova

Unit coordinator(s)
Associate Professor Anna Roujeinikova, Dr Terry Kwok
CONTACT DETAILS

Assoc Prof Anna Roujeinikova (Unit Coordinator)

Phone: 0399029194

Email: [email protected]

Office hours: please email/call to arrange an appointment

Dr Terry Kwok-Schuelein (Small Groups Coordinator and Deputy Convenor)

Phone: 0399029216

Email: [email protected]

Office hours: please email/call to arrange an appointment

Lecturer(s)
Name:ProfessorPhillipBird
Campus:Clayton
Building:Room:
Phone:+61 3 990 29365
Email:[email protected]

Name:DrDieterBulach
Campus:
Building:Room:
Phone:
Email:[email protected]

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Name:DrTerryKwok-Schuelein
Campus:Clayton
Building:76Room:254
Phone:+61 3 990 29216
Email:[email protected]

Name:Associate ProfessorMartinStone
Campus:Clayton
Building:Room:
Phone:+61 3 990 29246
Email:[email protected]

Name:ProfessorMatthewWilce
Campus:Clayton
Building:Room:
Phone:+61 3 990 29244
Email:[email protected]

Name:DrMichelleDunstone
Campus:Clayton
Building:77Room:231
Phone:+61 3 990 29269
Email:[email protected]

Name:Assoc ProfessorAnnaRoujeinikova
Campus:Clayton
Building:Room:
Phone:+61 3 990 29194
Email:[email protected]

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Name:Assoc ProfessorJackieWilce
Campus:Clayton
Building:Room:
Phone:+61 3 990 29226
Email:[email protected]

Name:DrCraigMorton
Campus:
Building:Room:
Phone:
Email:[email protected]

Academic overview
Learning outcomes
Upon successful completion of this unit, students should be able to:
1. Have a basic understanding of the theoretical and practical aspects of information
technology and its wider application to the medical sciences.
2. Develop an understanding of the principles of database searching, using search engines,
sequence alignments, molecular phylogeny, molecular modelling, protein structure and
analysis and medical imaging.
3. Develop their communication and presentation skills and understand the involvement of
information technology in the biomedical sciences.

Teaching approach
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Teaching approach
This Unit is run on Campus. The teaching components of this unit include 2 hours of lectures and 3
hours of practical exercises per week.

Assessment summary
Written examinations (50%) made up of:
Revision quiz (3%)
Mid-semester test (12%)
Final exam (35%) (Hurdle)
Projects and assignments (50%)

A pass in the final exam and mid-semester test must be obtained to pass the unit.
Assessment task

Value

Due date

Practical Exercises

33%

Weeks 2-11

Revision Quiz

3%

Week 2

Disease Protein Assignment

15%

End of Week 4 (Part 1); end of

Week 12 (Part 2)

Professional Development Module 4 (Reflect on and

communicate capability)

2%

End of week 12 (October 21st)

Mid-Semester Test

12%

Week 8

End-of-Semester Exam

35%

End of semester 2 examination

period

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Assessment requirements
Students are required to note the Facultys assessment policy (item 1.2.1) regarding threshold standards at:
http://www.med.monash.edu.au/policies/assessment-policy.html
Students are required to refer to the University Academic Integrity policy and procedure at:
http://www.policy.monash.edu.au/policy-bank/academic/education/conduct/student-academic-integrity-policy.html
The procedures state that:

Proofreading: The process of identifying errors and suggesting corrections to a text. This must not involve rewriting passages of text in
order to clarify meaning; amending the words used by the author (except to identify the correct spelling of the word used); rearranging
passages of text or code, or reformatting other material; contributing additional material to the original; and checking calculations or
formulae.
Academic Integrity and Technology
In line with the Acceptable Use of Information Technology Facilities by Students Procedures, students are not permitted to use
Information and Communications Technology facilities to sell, purchase or offer to write assignments or other assessable work, or to
request help with such work. Furthermore, students are required to take steps to minimise opportunities for others to cheat by, for
example, not saving work to a shared network drive that is accessible by others and not sharing work on social media sites. Failure to
comply with these requirements may result in disciplinary action under Part 7 of the Monash University (Council) Regulations for
collusion or general misconduct, as appropriate in the circumstances.
Students should be aware that the University will monitor and act on information received about the use of cheat sites, paper mills and
other online resources that promote dishonest academic conduct. If a student has been found to have used any of these sources to
breach the Student Academic Integrity Policy, the University will pursue the matter in accordance with Part 7 of the Monash University
(Council) Regulations.

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Participation
To pass BMS2062, students must complete ALL work requirements and participate in ALL the assessment tasks. Practical Results
Sheets must be completed during the assigned session and handed to the demonstrator. Pre-prepared or late Results Sheets will NOT
be marked. Late Project Assignments (Disease & Gene Report, Web Site or Professional Development Module) will attract a 10%
penalty per day and will not be accepted more than 7 days after the due date.
Lateness

Students who arrive more than 10 minutes after the designated start time for a practical session will automatically lose 10% of the
possible marks for the practical exercise. Students who arrive more than 20 minutes after the designated start time for a practical
session will be permitted to submit the practical report for review by the demonstrator but will automatically receive a mark of zero for the
practical exercise.

Absence

If you expect to miss or need to reschedule a practical class due to religious observance or another unavoidable scheduled event you
must contact the small groups coordinator and tutor beforehand and submit an application for special consideration.

If you miss a practical class due to illness without being able to give prior notice you must submit an application for special consideration
within 48 hours. For details, see Special Consideration for In-Semester Assessments section in this manual.

If you are absent from a practical class without receiving special consideration approval, you may complete the exercise(s) in your own
time and ask the demonstrator to correct your answers, but no mark will be provided.

Assessment tasks
Assessment title:Practical Exercises
Alignment with learning outcome(s):Aligns with learning outcomes 1, 2 and 3 of BMS2062
Details of task:There are ten practical exercises (weeks 2-11) that will together contribute 35% of the total mark for the unit. Each
practical is marked out of 100. The assessment criteria, comprising 90% of the mark allocated for each exercise, are specified in the
instructions for that exercise. The other 10% will be given for preparation, attitude, contribution to discussion and application (including

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

instructions for that exercise. The other 10% will be given for preparation, attitude, contribution to discussion and application (including
punctuality):
0 3 Unprepared, poor application or attitude, and/or late arrival. Student hasn't read introduction or instructions; relies on other
students to answer questions; rushes through practical without concentrating; disrupts other students.
4 7 Satisfactory preparation and application; arrives on time. Student works effectively. Asks reasonable questions.
8 10 Well-prepared, good application and attitude; punctual. Student has read and understood introduction and instructions;
works carefully and effectively; asks questions that indicate understanding.
At the beginning of each session there will also be an opportunity to discuss the quiz questions and answers for the previous week's
lectures.

Release date (where applicable):Weeks 2-11

Due date:Weeks 2-11
Word limit:varied
Value:33%
Presentation requirements:As per individual exercise, consult the Practicals Guide and demonstrators.
Estimated return date:varied
Hurdle requirements (where applicable):An aggregate pass mark in the practical/small group sessions/tutorials must be obtained to
pass the unit.
Individual assessment in group tasks (where applicable):These are individual assessments.
Criteria for marking:90% of the mark allocated for each exercise, are specified in the instructions for that exercise. The other 10% will
be given for preparation, attitude, contribution to discussion and application (including punctuality).

Assessment title:Revision Quiz

Alignment with learning outcome(s):Aligns with learning outcomes 1 and 2 of BMS2062
Details of task:BMS2062 builds on the knowledge of molecular biology gained in BMS1062 and the knowledge of protein structure
gained in BMS1011. Therefore it is critical that all students be highly proficient in the central aspects of these topics at the beginning of
this unit.
To help you assess you own level of familiarity with the fundamentals of molecular biology and protein structure, there will be a brief quiz
administered online during the first practical session. This quiz will contribute 3% to the final mark for the unit. The topics to be covered
in this quiz will be briefly summarized during the first lecture of the unit. Students are advised to revise these topics using notes and
textbooks from the previous units.

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Release date (where applicable):Week 2

Due date:Week 2
Word limit:N/A
Value:3%
Presentation requirements:N/A
Estimated return date:N/A
Hurdle requirements (where applicable):Not a hurdle
Individual assessment in group tasks (where applicable):N/A
Criteria for marking:% of the correctly answered MCQs.

Assessment title:Disease Protein Assignment

Alignment with learning outcome(s):Align with Learning Outcomes 1, 2 and 3.
Details of task:Overview
An integral part of the unit is an individual research project on protein dysfunction and disease. Each student will be given a project topic
in week 2 of the practical course. Over the semester you will research the topic. Your written results will be presented in two parts
(Disease & Gene Report and Web Site). The BMS2062 practical course has been designed to teach you the concepts and train you in
the techniques required to carry out the research project. It may be possible to work on your project from time to time during your
practical sessions. Use of the Computing Laboratories outside your scheduled practical sessions is encouraged, as long as they are not
being used for another class.
The Disease Protein Assignment must be completed by you independently of other students. You should take note of the information on
Plagiarism, Cheating and Collusion section of this Unit Guide. Cases of plagiarism, cheating and collusion in this assignment have been
and will be treated very seriously.
THE DISEASE & GENE REPORT AND WEB SITE ARE TOGETHER WORTH 15% OF YOUR FINAL MARK (split between 40% for
Disease & Gene Report and 60% for Web Site). FOR BOTH THE DISEASE & GENE REPORT AND THE WEB SITE, A LATE
PENALTY OF 10% OF POSSIBLE MARKS WILL APPLY FOR EACH OVERDUE DAY. ASSIGNMENTS WILL NOT BE ACCEPTED
MORE THAN 7 DAYS AFTER THE DUE DATE.
Suggested Timeline
Although the assignment will be assessed in only two stages (once around the middle of the semester and once towards the end of the
semester), you are strongly encouraged to complete sections of the assignment throughout the semester, particularly immediately after
the practical sessions covering useful bioinformatics methods. The following suggested timeline is intended to assist you in planning
your work on the project.
Week 2 Receive the name of your protein.

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Week 2 Receive the name of your protein.

Identify the disease related to your protein and write the Disease section of your Disease & Gene Report.
Weeks 3-4 Research the gene encoding your protein; write the Affected Gene section of your Disease & Gene Report and make the
related Figure.
Week 4-5 Write the Overview section of your Disease & Gene Report.
Edit and finalise your Disease & Gene Report.
Submit your Disease & Gene Report through the assignment dropbox on the Unit Moodle site on or before midnight on
Sunday August21st (before week 5).
Week 6 Set up web site template with links to different pages (including those to be completed in following weeks). Incorporate the
information from the Overview, Disease, and Affected Gene sections of your Disease & Gene Report.
Weeks 7-8 Research the protein sequence encoding your protein, its primary structural features and the function of the protein. Write
the relevant sections of the Affected Protein page.
Weeks 9-10 Explore the structure of your protein, identify roles of conserved residues, research relationships between structure,
function and disease-causing mutations; write summaries and prepare graphics for the Affected Protein page.
Week 11 Review of your penultimate Web Site. In your regular practical session you will be required to bring in and present your
nearly finished website (usb stick) and review and discuss the webpages of other students. This may help you to consider aspects of
your own Web Site for improvement before final submission.
Weeks 11-12 Edit and finalise components of your Web Site.
Submit your Web Site via email through the Unit Moodle site on or before midnight on Sunday October 23rd (by the end
of week 12). Instructions for submission of Web Pages will be provided on Moodle.

Release date (where applicable):Week 2

Due date:End of Week 4 (Part 1); end of Week 12 (Part 2)
Word limit:N/A
Value:15%
Presentation requirements:Your written results will be presented in two parts: Disease & Gene Report (Part 1) and Web Site (Part 2).
For Part 1, the Disease & Gene Report should be presented in a Microsoft Word document. For Part 2, you will be asked to presenta
suite of web pages (a Web Site) that describe your findings on a designated topic on protein dysfunction and disease.
Estimated return date:Week 6 (Part 1 - Disease & Gene Report); Week 14 (Part 2-Web Site)

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Estimated return date:Week 6 (Part 1 - Disease & Gene Report); Week 14 (Part 2-Web Site)
Hurdle requirements (where applicable):An aggregate pass mark in the practical/small group sessions/tutorials must be obtained to
pass the unit.
Individual assessment in group tasks (where applicable):These are individual assessments.
Criteria for marking:The following sections provide details about each component of the Disease Protein Assignment.
Disease & Gene Report (40% of assignment marks; 6% of total marks for unit)
On or before midnight on Sunday August21st (before week 5), you must submit a Microsoft Word document containing the following
sections. You will submit your report through the Unit Moodle site (instructions will be provided on Moodle). Page lengths are for Times
New Roman 12 pt font, double-spaced, 2.5 cm margins.
Sections of Disease & Gene Report
Category

Possible Mark

Overview (~0.5 pages)

4 marks

Concise summary of the disease and the mutated gene and protein with links to each other page
The Disease (1-1.5 pages)

16 marks

What is the disease?

What are the major symptoms?

How is the disease currently diagnosed?

How is the disease currently treated?

What is the cellular and molecular basis of the disease?

No figures required

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

The Affected Gene (1-1.5 pages + 1 figure)

20 marks

What is the affected gene?

What is the gene structure (introns/exons, regulatory elements)?

Where is the gene located?

What are the most closely related orthologues and homologues?

What are the most common mutations?

One informative figure required in this section

Formatting, Style and References

Included in above
marks

The marks for each section will take into account the correctness of grammar and punctuation, the clarity
of writing style and the correct use of references. References should be listed on a separate page.

Web Site (60% of assignment marks; 9% of total marks for unit)

On or before midnight on Sunday October 23rd (the end of week 12), you must submit a suite of web pages (a Web Site) that describe
your findings. Note that it must be near completion by your week 11 practical class for a peer review exercise. You will submit your final
project web site via email through the Unit Moodle site; details will be provided at a later date. The Web Site should contain the home
page (Overview) and five additional pages listed below. The content of the Overview, Disease, and Affected Gene pages should be the
same as that submitted for the above Disease & Gene Report (no additional marks will be assigned for the content of these pages).
Marks for the Web Site will be assigned (as listed below) for the content of the Affected Protein, Summary and Future Directions, and
References pages (40 marks for content) and for the design and format of the Web Site (20 marks). Page lengths listed correspond to
text formatted as Times New Roman 12 pt font, double-spaced, 2.5 cm margins; the actual length on the web page will vary depending
on your formatting.
Web Site Content
Category

Possible Mark

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Overview

Content as in previously submitted Disease & Gene Report

The Disease

Content as in previously submitted Disease & Gene Report

The Affected Gene

Content as in previously submitted Disease & Gene Report

The Affected Protein (2-2.5 pages + 2-3 figures)

30 marks

What is the affected protein?

What does the protein normally do?

What are the primary structural properties of the protein (molecular weight, domain structure, post-translational
modifications, etc.)?

Is it part of a protein family? Show relationships (alignment/tree) if relevant.

What is the 3D structure? Show 1-2 structural views and highlight major features.

How does the protein normally function (relationship of structure to function)?

How do mutations affect protein structure and function, i.e. what is the molecular basis of the disease?

2-3 informative figures required in this section.

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Summary and Future Directions (~0.5 pages)

5 marks

Concise and informative summary of the current state of knowledge regarding both the protein and the disease.

Based on our current understanding of the molecular basis of the disease and the protein structure/function,
what are the future prospects for development of new treatments or diagnostics?

No figures required
References (separate page; length as required)

5 marks

Relevant citations listed for peer-reviewed papers and other sites or sources (3).

References are inserted appropriately into text e.g. at end of sentences or paragraphs (2).

Web Site Design

Category

Possible Mark

General

4 marks

Contact person listed with feedback mechanism

Date page last updated included

Spelling and Grammar are correct

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Navigation

3 marks

All internal/external hyperlinks work correctly

Links are easy to recognise and are clearly labeled

Links to all other pages from each page

Consistency

2 marks

Common theme running through all pages of site (same choice of colours, fonts, backgrounds)
Clarity

3 marks

Web pages are not overcrowded

White space, graphic elements and/or alignment are used to effectively organise material

Text is easy to read on chosen background

Concise

4 marks

Information is brief and to the point

Text is broken into paragraphs with an appropriate subheading at the top of each paragraph and main title on
every page

Information mainly fits on single screen (not too much scrolling)

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Compelling

1 mark

Eye catching design/layout (Good choice of colours)

Information is interesting
Graphics

3 marks

Related to purpose of page

Appropriate quality, aspect ratio, and size

Alternative text is offered (Alt tags)

Legends provided for figures

Assessment title:Professional Development Module 4 (Reflect on and communicate capability)

Alignment with learning outcome(s):Aligns with Monash graduate attribute: Monash University prepares its graduates to beresponsible
and effective global citizens.
Details of task:For the three positions of interest, write examples of experiences that match the criteria, using appropriate skill
communication techniques (Situation, Task, Action, Result - STAR) and language
Release date (where applicable):Week 11 (October 10th)
Due date:End of week 12 (October 21st)
Word limit:600 words
Value:2%
Presentation requirements:To be submitted via Mahara
Estimated return date:Week 13 (October 28th)
Hurdle requirements (where applicable):An aggregate pass mark in the practical/small group sessions/tutorials must be obtained to
pass the unit.
Individual assessment in group tasks (where applicable):These are individual assessments.
Criteria for marking:Marks will be assigned for the skills communication for all three jobs (pass (1) / fail (0)); students who pass all three
will get thefull mark.

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Assessment title:Mid-Semester Test

Alignment with learning outcome(s):Aligns with learning outcomes 1 and 2 of BMS2062
Details of task:A mid-semester test (25 multiple choice questions; 40 minutes duration), contributing 12% of the total marks for the unit)
will be held during the scheduled lecture time (1-2 pm) on Monday 12th September (week 8). This will be a multiple choice test covering
all topics discussed in lectures 1-14.
Release date (where applicable):Week 8
Due date:Week 8
Word limit:N/A
Value:12%
Presentation requirements:N/A
Estimated return date:Week 10
Hurdle requirements (where applicable):Combination of the Mid-Semester Test and End-Of-Semester Exam constitutes a hurdle.
Individual assessment in group tasks (where applicable):N/A
Criteria for marking:% of the correctly answered MCQs.

Assessment title:End-of-Semester Exam

Alignment with learning outcome(s):Aligns with learning outcomes 1, 2 and 3 of BMS2062
Details of task:The final exam will be comprehensive, covering all topics discussed in lectures throughout the unit. The exam will
consist of approximately 40-50 multiple choice questions that will test both knowledge and understanding of the material covered in
lectures throughout the unit
THE FINAL EXAMINATION IS WORTH 35% OF THE TOTAL MARKS FOR THE UNIT.

Release date (where applicable):End of semester 2 examination period

Due date:End of semester 2 examination period
Word limit:N/A
Value:35%
Presentation requirements:N/A
Estimated return date:End of semester 2
Hurdle requirements (where applicable):Combination of End-of-Semester Exam and Mid-Sem Test constitutesa HURDLE.Students
must achieve an aggregate pass grade in this hurdlein order to pass the unit.There will be no opportunity for students who do not pass
to retake either the Mid-Sem Test or the final examination.
Individual assessment in group tasks (where applicable):N/A
Criteria for marking:% of correctly answered MCQs

Referencing requirements
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

21

Referencing requirements
To build your skills in citing and referencing, and using different referencing styles, see the online
tutorial Academic Integrity: Demystifying Citing and Referencing at
www.lib.monash.edu/tutorials/citing/
Referencing should be using Harvard (author, date) or Vancouver (numeric) style in text citations
and the references listed alphabetically or numerically respectively.

Assignment submission
Online submission
1) Students are required to submit continuous formative/summative assessment items (where
appropriate) via the Universitys online Learning Management System - Moodle. Assessments
must include a cover sheet. The cover sheet is accessible at: http://www.med.monash.edu.au
/current/student-forms.html.
2)Students must retain a copy of the assessment for their records.
3)No hard copy submissions will be permitted for those assessments requiring online submission.
If the assessment/plagiarism/collusion declaration is being used within Moodle for an assessment
item a separate assignment coversheet is not required.
Please keep a copy of tasks completed for your records.

Hard copy submission: Where hard copy submission is necessary, assignments must includea
cover sheet. The cover sheet is accessible via the Monash portal page located at http://my.
monash.edu under the heading "Learning and Teaching tools". Please keep a copy of tasks
completed for your records.

Returning assignments
Student assignments will be returned by your demonstrator in your practical class or electronically
via Moodle.

Resubmission of assignments
Faculty policyhttp://www.med.monash.edu.au/policies/assessmentr.html
Student assignments cannot be resubmitted.

Extensions and penalties

http://www.med.monash.edu.au/policies/assessmentl.html
Special Consideration
Students should read the Universitys and Facultys Special Consideration Policies at the following

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Students should read the Universitys and Facultys Special Consideration Policies at the following
sites and following the procedures described below.

http://www.monash.edu.au/exams/special-consideration.html

http://www.med.monash.edu.au/policies/assessmentl.html

Special Consideration for In-Semester Assessments

The dates for unit assessments and deadlines are set out in the Unit Guide and Moodle Site. If you
are requesting Special Consideration for any reason that can be reasonably anticipated two weeks
in advance of the assessment task, you must submit an application for special consideration AT
LEAST TWO WEEKS IN ADVANCE. This includes any Special Consideration requests for the
following reasons:

A scheduled medical procedure or ongoing medical condition

Religious observance
Representing the University as an elite athlete
Obligation to military service, jury service, Country Fire Authority or similar

If you miss an assessment task due to an unforeseen emergency such as illness or bereavement,
you must submit an application for special consideration WITHIN TWO DAYS OF THE
ASSESSMENT THAT YOU MISSED.

If you are absent from a practical class for other reasons you may complete the exercise(s) in your
own time and ask the demonstrator to correct your answers, but no mark will be provided.

In-semester special consideration (assignments, practicals, in-semester test/exam)must be

submitted to the School of Biomedical Sciences:
a. Fill inspecial consideration form
b. Attach supporting documentation (i.e. medical certificate)
c. Submit themonlineand select theSchool of Biomedical Sciencesas your faculty, school or
department
d. Contact Monash Connectbylogininto ask.monash for further inquiries.
If you are granted special consideration for a missed Practical Session,you will still need to
complete the corresponding assignment and submit itto your demonstrator no later than 7 days
after the receipt of thisnotice.You are encouraged to contact your demonstratorfor
assistanceregardingthe missed pracand/or the correspondingassignment should itbe

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

assistanceregardingthe missed pracand/or the correspondingassignment should itbe

necessary.

Special Consideration for the Final Exam

If you are unable to attend yourend-of-semester exam, which appears in your exam timetable in
the Web Enrolment System (WES), then you need to apply for special consideration onWES.
For full details on special consideration, please visit the University'sspecial consideration web site.
When on this webpage, please ensure that you refer to the 'When and how to apply' section, to
the tab that outlines the process for 'End-of-semester assessment'.

Students should ensure that supporting documentation is provided. Medical certificates that
do not provide evidence of serious illness will NOT be accepted. For example, the policy
states in part that special consideration will be granted in cases of serious illness or
psychological condition - e.g. hospital admission, serious injury, severe asthma, severe
anxiety or depression.This does not include minor illness such as a mild cold.
Students have 48 hours after their last exam in which to submit an application for special
consideration. However, students should NOT assume that a deferred exam will be granted,
this is the decision of the unit convenor and/or the course convenor.
An exam once deferred cannot be further deferred.

Examination material or equipment

There is no specific material or equipment needed or permitted in the examination room except for
your student ID card and writing materials.

Feedback to you
http://www.med.monash.edu.au/policies/assessmentf.html
Monash aims to provide a learning environment in which students receive a range of ongoing
feedback. For BMS2062, you can enhance your learning experience using the following
mechanisms of communication withlecturers and instructors.

Attend lectures and ask questions afterwards.

Attend practical sessions, ask questionsand discuss topics with your demonstrator during
these sessions.
Email lecturers and/or demonstrators with questions and suggestions.
Provide feedback to your practical group representative for communication to the
convenorand deputy convenor during the end of semester feedback session (or volunteer to
be that representative).
Complete formal evaluations of the unit, lecturers and demonstrators.

24
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Unit Schedule
Wk.
No.

Date

Part I: The Central Dogma of Molecular Biology

Lecture
Monday 9 am CL_20Chn/H2 (repeat)
1 pm CL_16Rnf/S4 (regular time)
Tuesday 8 am CL_16Rnf/S3 (regular time)
4 pm CL_21Rnf/S7 (repeat)

Mon Jul-25

1: Introduction and Review of Biopolymer

Structure/Function (AR/TK)

Tue Jul-26

2: Its Written in Your Genes: The Language of

DNA (PB)

Mon Aug-1

3: Not Just a Messenger: RNA Origami (PB)

Part II: Genes & Genomes: Sequence Variation and Analysis

Tue Aug-2

4: Unlocking an Organism's Genetic Potential

Through Genome Sequencing (DB)

Mon Aug-8

5: Bacterial Antibiotic Resistance and Expression

of Virulence Factors (DB)

Tue Aug-9

6: The Human Genome Project (PB)

Part III: From Genotype to Phenotype

4

Mon Aug-15

7: Avoiding Fools Gold. How Do We Prove that

Virtual Genes Are Real? (PB)

Tue Aug-16

8: Backwards and Forwards: Strategies for

Working Out What Genes Do (PB)

Mon Aug-22

9: What Makes an Individual? Genome

Fingerprinting, Faster Sequencing, & the Route
Towards Personalized Medicine (PB)

Practical
(Mon-Fri, as
allocated)

No Practical

1. Navigating the
Scientific
Literature +
Revision Quiz +
Allocation of
Disease Protein
2. DNA
Databases and
Sequence
Analysis
3. Exploring the
Human Genome
+
Disease &Gene
Report due

4. Web Pages Design and Use

Part IV: Protein Expression and Modification

Tue Aug-23

10: From mRNA to functional protein I (TK)

Mon Aug-29

11: From mRNA to functional protein II (TK)

Tue Aug-30

12: Protein Families: What Can They Teach Us?

(TK)

Mon Sep-5

13: More is Better: One Gene - Many Proteins

(TK)

Tue Sep-6

14: What Do Inflammation, HIV and Malaria have

in Common? (MS)

5. Protein
Families
Finding
Members and
Building Trees
6. Analysis of
Protein
Sequences and
Modifications

25
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Mon Sep-12

15: Mid-Semester Test (venues: Eng Halls EH24, CG63 Histology lab or H1/20Chn - check your
Allocate)

7. Exploring
Protein
Architecture

Part V: Protein Structure and Function

Tue Sep-13

16:
Protein structure and interactions using NMR
spectroscopy (JW)

Mon Sep-19

17: From Structure to Function: Enzymes (AR)

Tue Sep-20

18: Protein binding and recognition (AR)

8. Protein
Structural
Comparisons

Sep 26-Sep
30

Mid-Semester Break

Mon Oct-3

19:
Protein structure determination using Xrays (MW)

Tue Oct-4

20: Protein-membrane interactions (MD)

Mon Oct-10

Professional Development Session (Careers)

Tue Oct-11

21: Protein Machines: (AR)

Mon Oct-17

22: Rational Design of Protein Therapeutics (JW)

Tue Oct-18

23: Rational Design of Small Molecule

Therapeutics (CM)

13

Oct 24-Oct
28

Swot Vac: No formal assessment is undertaken

14-16

Examination period: Link to Assessment Policy:http://www.policy.monash.edu/policybank/academic/education/assessment/assessment-in-coursework-policy.html

10

11

12

9. Protein
Conformational
Changes

10. Web Site

peer review.
No Practical;
Final Web Site
due

Your feedback to us
One of the formal ways students have to provide feedback on teaching and their learning
experience is through the Student Evaluation of Teaching and Units (SETU) survey. The feedback
is anonymous and provides the Faculty with evidence of aspects that students are satisfied with
and areas for improvement.

Previous student evaluations of this unit

In response to the last SETU of this unit, the following changes have been made:
Over the past few years the Faculty of Medicine, Nursing & Health Sciences has made a number
of improvements to its courses as a result of unit evaluation feedback. Some of these benefits
include a more coordinated approach to field placements, clarification of assessment criteria and

26
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

of improvements to its courses as a result of unit evaluation feedback. Some of these benefits
include a more coordinated approach to field placements, clarification of assessment criteria and
consistent assignment submission and return procedures.
Student evaluations of this unit indicate that students would like to see clearer connections
between lecture topics and also more explicit relationships between the lecture and practical
material. As a result of this feedback we have: (1) reorganized the lectures into five sections that
follow the progression of biological information within cells; and (2) modified practical exercises to
emphasise the same concepts that are covered in corresponding lectures. You may wish to use
the open ended questions in the unit evaluation to provide written feedback on your experience of
this and whether it has been helpful to you during this semester.

If you wish to view how previous students rated this unit, please go to
https://emuapps.monash.edu/unitevaluations/index.jsp

Learning resources
Required Resources
Students must be able to transfer electronic data to the computers used in practical classes. It is
recommended that they aquire a usb device for this.

There is no single textbook that covers all aspects of the course. However, the following texts are
recommended and referred to in many lectures.

1. Fundamental Concepts of Bioinformatics by D.E. Krane and M.L. Raymer, (Benjamin

Cummings, 2003). This textbook will be useful for aspects of the unit related to:
Genomics and gene identification
DNA and RNA structure
Protein families and sequence comparisons
Bioinformatics approaches (e.g. those used in many practical exercises)
2. Molecular Biology of the Cell, Alberts et al 5th or 6th Edition (Garland Science, 2007/2015).
This textbook will be useful for aspects of the unit related to:
Gene structure
Mechanisms of transcription and translation
Molecular biology methods
Forward and reverse genetics
Protein modification and degradation
3. Lehninger Principles of Biochemistry, by Nelson & Cox, 5th or6thEdition (W.H. Freeman,
2008/2013). This textbook will be useful for aspects of the unit related to:
Mechanisms of transcription and translation
Post-translational modifications
Protein structure
Protein binding
Enzyme catalysis
Protein machines

Monash Library Unit Reading List (if applicable to the unit)

27
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Monash Library Unit Reading List (if applicable to the unit)

http://readinglists.lib.monash/index.html

Required resources
Students generally must be able to complete the requirements of their course without the
imposition of fees that are additional to the student contribution amount or tuition fees. However,
students may be charged certain incidental fees or be expected to make certain purchases to
support their study. For more information about this, refer to the Higher Education Administrative
Information for Providers, Chapter 18, Incidental Fees at
http://education.gov.au/help-resources-providers

Technological requirements
Students must use Moodle as their definitive Learning Management System. Turnitinis
compulsoryfor student use.
Students must regularly check Moodle for announcements.

Other information
Policies
Monash has educational policies, procedures and guidelines, which are designed to ensure that
staff and students are aware of the University's academic standards, and to provide advice on how
they might uphold them. You can find Monash's Education Policies at:
http://www.policy.monash.edu/policy-bank/academic/education/index.html

Academic Integrity
http://www.med.monash.edu.au/current/plagiarism.html
http://www.policy.monash.edu.au/policy-bank/academic/education/conduct/student-academicintegrity-policy.html
http://www.policy.monash.edu.au/policy-bank/academic/education/conduct/student-academicintegrity-managing-plagiarism-collusion-procedures.html

Clinical/Fieldwork Placement Procedures and Behaviour

Guidelines
http://www.med.monash.edu.au/policies/clinical-fieldwork-placement/index.html

Honours and Minor Thesis Guidelines

http://www.med.monash.edu.au/intranet/education/hon-programs-research-project-minor-thesis-

28
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

http://www.med.monash.edu.au/intranet/education/hon-programs-research-project-minor-thesisguidelines/

Immunisation and Infection Risk

http://www.med.monash.edu.au/current/immunisation/

Police Checks
http://www.med.monash.edu.au/current/police-checks.html

Working with Children Check Guidelines

http://www.med.monash.edu.au/current/wwc-check.html

Graduate Attributes Policy

http://www.policy.monash.edu/policy-bank/academic/education/management/monash-graduateattributes-policy.html

Student Charter
www.monash.edu/students/policies/student-charter.html

Student Services
The University provides many different kinds of services to help you gain the most from your
studies.Contact your tutor if you need advice and see the range of services available at
www.monash.edu/students

Monash University Library

The Monash University Library provides a range of services, resources and programs that enable
you to save time and be more effective in your learning and research.
Go to http://www.monash.edu/libraryor the library tab in my.monash portal for more information.

Disability Support Services

Students who have a disability, ongoing medical or mental health condition are welcome to contact
Disability Support Services.
Disability Support Services also support students who are carers of a person who is aged and frail
or has a disability, medical condition or mental health condition.
Disability Advisers visit all Victorian campuses on a regular basis.

Website:http://monash.edu/disability
Telephone: 03 9905 5704 to book an appointment with an Adviser;
Email:[email protected]

Drop In: Level 1, Western Annexe, 21 Chancellors Walk (Campus Centre) Clayton Campus

29
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Drop In: Level 1, Western Annexe, 21 Chancellors Walk (Campus Centre) Clayton Campus

Other unit information

LECTURE SYNOPSES AND READINGS
PART I: THE CENTRAL DOGMA OF MOLECULAR BIOLOGY
Lecture 1: Introduction and Review of Biopolymer Structure & Function
A/Prof Anna Roujeinikova and Dr Terry Kwok-Schuelein
The central dogma of molecular biology is that DNA sequence gives rise to RNA sequence, which
gives rise to proteins and hence cellular and higher order function (phenotype). We will expand on
this paradigm by discussing the various ways in which DNA, RNA and proteins can be modified or
controlled to regulate their functions and the importance of these regulatory mechanisms in health
and disease. The Disease Protein Assignment is a major activity of this unit that draws upon these
concepts.

Lehninger: Sections 1.3, 4.1-4.3, 26.1, 27.1-27.2

Krane & Raymer: p. 1-19
Lecture 2: Its Written in Your Genes: The Language of DNA
Prof Phil Bird
Over the last half-century, a picture of the biological information contained in DNA has been built
up, allowing bioinformaticians to rapidly scan new DNA sequences looking for patterns that reveal
genes, protein binding sites, viral insertions and structural elements. In this lecture, we will review
the structure, function and organization of DNA. Emphasis will be placed on sequence motifs that
can be found in DNA, and how these contribute to our understanding of DNA function and
information flow in the cell.

Krane and Raymer: Chapter 1, p2 12, p20; Chapter 6, p120 124; p130 -133
Alberts 6th Ed: Chapter 1 p2-5; Chapter 4, p173-179
Lecture 3: Not Just a Messenger: RNA Origami
Prof Phil Bird
In this lecture we will review the structure and function of RNA. Information encoded in DNA flows
to messenger RNA and eventually to proteins. Besides being an information carrier, RNA plays a
pivotal role in the machinery replicating and regulating genes, and driving protein synthesis. The
latter functions of RNA largely depend on its ability to form complex secondary structures and bind
proteins, and predicting these structures de novo remains a challenge for bioinformatics.

Krane and Raymer: Chapter 1, p6 9, p12; Chapter 6, p120 121; p175 -177

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Krane and Raymer: Chapter 1, p6 9, p12; Chapter 6, p120 121; p175 -177
Alberts 6th Ed: Chapter, 1 p2-5; Chapter 6
PART II: GENES & GENOMES: SEQUENCE VARIATION AND ANALYSIS
Lecture 4: Unlocking an Organism's Genetic Potential through Genome Sequencing
Dr Dieter Bulach
The entire genetic potential of an organism is locked within the DNA sequence of its genome.
Therefore, if you can determine the genome sequence of an organism you have the basic
information on how the organism functions at the molecular level. In this lecture we discuss
strategies for determining the sequence of bacterial genomes, including some very recently
developed technologies. We also discuss basic methods for identifying the important information
stored with the genome sequence including the identification of open reading frames,
transcriptional regulatory elements, tRNA and rRNA genes, mobile genetic elements and repetitive
DNA sequences.

Krane and Raymer: Chapter 1, p25-27; Chapter 6, p117-129

D.P. Clark: Molecular Biology (Elsevier, 2010), Chapter 24
Lecture 5: Bacterial Antibiotic Resistance and Expression of Virulence Factors
Dr Dieter Bulach
The comparison of sequenced bacterial genomes can be used to identify genes involved in
specific phenotypic traits of critical importance to bacterial survival. In this lecture we show how
genes involved in antibiotic resistance or virulence can be identified by whole genome sequencing
of highly related bacterial strains. We discuss how genetic differences can be identified and how
putative functions of specific genes can be inferred.

Krane and Raymer: Chapter 1, p25-27; Chapter 6, p117-129

D.P. Clark: Molecular Biology (Elsevier, 2010), Chapter 24
Lecture 6: The Human Genome Project
Prof Phil Bird
Sequencing of the human genome has been completed. Bioinformatics has played a key part in
the Human Genome Project (HGP), and will be central to exploiting the vast amount of data it has
generated. Here we look at the achievements of the HGP and the implications for future
biomedical research. We will consider how protein-coding genes are identified amongst the
background of non-coding and junk DNA.

Krane and Raymer: Chapter 6, p137-141; p148 151

Alberts 6thEd: Chapter 4, p216-233
PART III: FROM GENOTYPE TO PHENOTYPE
Lecture 7: Avoiding Fools Gold. How Do We Prove that Virtual Genes Are Real?

31
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Prof Phil Bird

Although the entire genetic blueprint is present in every nucleated cell, not every gene is switched
on in every cell, and some genes are switched on or off according to developmental or disease
state. Thus full understanding and exploitation of the human genome data requires complementary
methods to determine whether newly-identified (hypothetical) genes are real, and when and where
specific genes are expressed. This is usually done by determining when and where their mRNAs
are produced.

Krane and Raymer: Chapter 1, p23 25; Chapter 6, p129 137; 143 -148
Alberts 6thEd: Chapter 7, p404-407, 413-417,422-430;Chapter 8, p467-484
Lecture 8: Backwards and Forwards: Strategies for Working Out What Genes Do
Prof Phil Bird
Many genes identified by genome sequencing projects are hypothetical, in that there is no
experimental evidence to suggest that they are functional. Other genes encode products whose
biological functions are unknown. We will look at key experimental approaches used to assess
gene function.

Alberts 6thEd: Chapter 8, p485-491,494-506

Lecture 9: What Makes an Individual? Genome Fingerprinting, Faster Sequencing & the Route
towards Personalized Medicine
Prof Phil Bird
No two individuals have exactly the same genomic sequence, and genetic differences between
individuals underpin differing susceptibility to disease, and can influence the response to
treatment. Faster sequencing and array technologies now under development promise a future in
which an individuals genotype can be rapidly and cheaply determined. Single nucleotide
polymorphisms (SNPs) account for most of the differences between individuals, and the analysis
of associations between SNP patterns and disease susceptibility illustrates how such information
might be exploited to personalize medicine.

Recommended reading: Bentley, DR. Genomes for Medicine. Nature 429: 440 (2004)
Alberts 6thEd: Chapter 8, p491-494
Barnes MR. Genetic variation analysis for biomedical researchers: a primer. Methods Mol Biol.
2010;628:1-20. Review.
PART IV: PROTEIN EXPRESSION AND MODIFICATION
Lecture 10 & 11: From mRNA to functional Protein
Dr Terry Kwok-Schuelein
mRNA is translated by the ribosome, a sophisticated molecular assembly consisting of RNA and
protein components. This lecture will discuss the way in which protein sequences are synthesised
and emerge from the ribosome to then adopt their correct three dimensional fold in either a
cytoplasmic or a membrane bound environment. The formation of a functional protein may involve

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

cytoplasmic or a membrane bound environment. The formation of a functional protein may involve
processing, post-translational modification, formation of oligomers or formation of multiprotein
complexes.

Lehninger: Section 4.4

Lecture 12: Protein Families: What Can They Teach Us?
Dr Terry Kwok-Schuelein
The amino acid sequences of proteins dictate their three-dimensional structures and therefore their
biological functions. Therefore, amino acid residues that are important for structure and function
are maintained throughout the course of evolution. By comparing their sequences, it is possible to
identify proteins with similar structures and functions (i.e. protein families) and to identify amino
acid residues with important structural and functional roles.

Lehninger: Section 3.4

Lecture 13: More is Better: One Gene - Many Proteins
Dr. Terry Kwok-Schuelein
The number of proteins produced by an individual is much larger than the number of genes
encoded by that individuals genome. After proteins are produced at the ribosome they can
undergo a wide variety of post-translational modifications, with profound influences on their
functional properties. This lecture: explores several of these modifications and their functional
consequences; examines some of the mechanisms by which the proteome is regulated; and
summarises the major approaches for proteome analysis.

Lehninger: Sections 9.3, 27.2-27.3

Krane & Raymer: Chapter 8
Lecture 14: What Do Inflammation, HIV, and Malaria Have in Common?
A/Prof Martin Stone
A critical aspect of inflammation is the migration of leukocytes (white blood cells) into the
tissues. This migration is regulated by the activation of chemokine receptors in the leukocyte
membranes. However, pathogens such as HIV and malaria can hijack natural chemokine
receptors to gain entry into blood cells. Both the physiological and pathological functions of
chemokine receptors are dependent on specific post-translational modifications of these receptors.
Lecture 15: Mid-Semester Test (note venue)
The mid-semester test will cover any lecture material from parts I to IV of this unit.
PART V: PROTEIN STRUCTURE AND FUNCTION
Lecture 16: Protein Structure and interactions using NMR spectroscopy
A/Prof Jackie Wilce
Protein structure determination can also be undertaken using NMR spectroscopy. This technique
is a complementary method alongside X-ray crystallography for structure determination. It is a
technique that can also be used for measuring and detecting protein interactions with binding

33
BMS2062 Introduction to bioinformatics - Semester 2 - 2016

is a complementary method alongside X-ray crystallography for structure determination. It is a

technique that can also be used for measuring and detecting protein interactions with binding
partners. In this lecture the principles behind this method will be discussed.

Lehninger (4th Ed) Chapter 4 page 137

or Alberts (5th Ed) Chapter 8 page 529
Lecture 17: From Structure to Function: Enzymes
A/Prof Anna Roujeinikova
Enzymes are proteins that catalyse (speed up) biochemical reactions. They carry out this function
by binding to the reaction substrates then binding more strongly to the transitions states of the
reactions. Thus, enzyme interactions with their substrates represent a special case of the
importance of binding interactions.

Lehninger: Chapter 6
Lecture 18: Protein Binding and Recognition
A/Prof Anna Roujeinikova
The biological functions of proteins are typically carried out though transient binding interactions
with each other and with other molecules. This lecture, we will discuss the relationship between
the strength of binding interactions and the structures of the molecules involved. The lecture will
also present methods for observing and measuring these interactions.

Lehninger: Section 5.1

Lecture 19: Structure Determination using X-ray crystallography
Prof Matthew Wilce
Knowledge of the 3D structure of a protein provides an understanding, at the atomic level, of how
a protein functions, or as in the diseased state, how a protein malfunctions. This lecture will review
the principles of protein structure, and give an overview of the use of X-ray crystallography in
structure determination.

Lehninger: pp132-134
Krane & Raymer: pp 191-198
Lecture 20: Protein-membrane interactions
Dr Michelle Dunstone
The role of some proteins is to interact with extra-cellular targets. In this lecture the protein
perforin will be used as an example of a protein that is released from cells to interact with the
membrane of a target cell leading to its destruction. This lecture will illustrate and reinforce many
concepts including: protein 3D structure underlying function, processing of proteins required for
active form, protein oligomerisation, protein-lipid interactions, and protein conformational change.
Lecture 21: Protein Machines: Creations of a Blind Watchmaker
A/Prof Anna Roujeinikova

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Proteins are the molecular machines of our bodies. This lecture will present examples of proteins
as molecular machines and present evidence for the ways they function.

Lehninger: Sections 19.1-19.2

Lecture 23: Rational Design of Protein Therapeutics
A/Prof Jackie Wilce
The advent of biotechnology has made it possible to develop proteins as drugs. However, most
natural proteins are not ideal as therapeutic agents because of properties such as low stability,
aggregation, low bioavailability, or immunogenicity. In this lecture we will discuss cases in which
bioactive proteins have been engineered to enhance their therapeutic properties.

Lehninger: Section 5.2

Lecture 24: Rational Design of Small Molecule Therapeutics
Dr Craig Morton (Guest lecturer)
Traditional drug discovery relies on either serendipity or screening vast libraries of compounds for
the identification of lead molecules. Recent advances in computational biology have allowed the
development of rational drug design. Some of the basic principles of structure-based drug design
will be described.

PRACTICAL SYNOPSES
Practical 1: Navigating the Scientific Literature

Methods to access scientific journals

Use of PubMed to search the scientific literature
Consolidation of concepts relating to translation and the genetic code

Practical 2: DNA Databases and Sequence Analysis

Introduction to NCBI bioinformatics databases and tools

Finding similar DNA sequences (BLASTn)
Retrieving information about a gene
Finding proteins encoded by DNA sequences (BLASTx)
Finding Open Reading Frames (ORFs)
Manipulating a DNA sequence

Practical 3: Exploring the Human Genome

Finding a human gene (OMIM)

Viewing and navigating genome maps
Finding Expressed Sequence Tags (ESTs)
Comparing genomes or humans and model organsims

Practical 4: Web Pages Design and Use

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Retrieve information from web on allocated biomedical topic and on your disease protein
Construct a web site

Practical 5: Protein Families Finding Members and Building Trees

Retrieve sequence information for a protein

Make file of granzymes for multiple alignment
Build simple tree for human granzymes
Look at more complex tree using cytochrome C

Practical 6: Analysis of Protein Sequences and Modifications

Predict the products of proteolytic digests

Identify a protein from the sequences of proteolytic fragments
Predict the masses of mutated or modified protein fragments
Identify protein mutants and modified forms from mass data

Practical 7: Exploring Protein Architecture

Carry out Pymol Tutorial

Examine features of protein structure and stabilizing interactions

Practical 8: Protein Structural Comparisons

Study chymotrypsin structure using Pymol

Load and look at structure of disease protein

Practical 9: Protein Conformational Changes

Compare different structural states of a protein

Define changes in structure

Practical 10: Peer review of Web Sites

Provide and present penultimate Web Site for peer review

Review and feedback of fellow students' work

Instructions for Practicals

General Information on Practicals
Practical sessions in BMS2062 are a series of computer exercises designed to teach students how
to find and use bioinformatics software and interpret the information you obtain. Much of the
software is Web-based but some is installed on the machines in computer labs. Printers are
available in the computer labs, but you must pay for printing using your student account. This
includes the occasional printout of practical results.

Computer account access, printing and data storage

If you have any difficulties with your account please contact the ITS Help Desk.
Local Windows access is available using the username student which has either a blank password

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016

Local Windows access is available using the username student which has either a blank password
in one lab or the password student in the other. Your student Novell account and thus U: drive is
accessible for network printing and data storage. ALWAYS BACK UP YOUR WORK. You are
advised to save files first to the local machine through the desktop (thereby avoiding loss of data
through network glitches), and then copy these files to your network U: drive or to a personal USB
memory stick for safe keeping. Your U: drive will provide adequate space (25Mb) for your all of
your files in this course.
Programs such as PowerPoint, the Web authoring tool Komposer, and PyMol reside locally under
Biochemistry. Web-based utilities such as PubMed and the associated databases are located at
NCBI (ncbi.nlm.nih.gov) in the US. Web-based utilities are available outside Monash and many
programs used in the course are available for free download.

Copyright Monash University 2016. All rights reserved. Except as provided in the Copyright Act 1968, this work may
not be reproducedin any form without the written permission of the host Faculty and School/Department.

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BMS2062 Introduction to bioinformatics - Semester 2 - 2016