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BINF2010

Introduction to Bioinformatics

Sara Ballouz, PhD


CSE, UNSW
K17 401A
Welcome! Course convener: Sara Ballouz
School of Computer Science and
Engineering

Room: K17-401A

About me:
- Studied at UNSW!
- BEng/BSc
Bioinformatics/Genetics
- PhD Bioinformatics
- Postdoctoral fellow at CSHL in
the US
- Group leader at the Garvan
- Now Senior Lecturer and Director
of Studies for Bioinformatics
Team Tutors:

Sasha Barisic

Vinayak Kuanr
Focus of the course
• Introduction to the various sub-fields of bioinformatics from
both biological and computational points of view
• Illustrated series of case studies by guest lecturers working in
the field
• Complemented by computer labs demonstrating the use of a
common bioinformatics applications and websites
• Assignment on a bioinformatics script
• Introductory tutorials on R and Python
Assumed knowledge
• Basic molecular biology
• Basic statistics
Course delivery
• In-person lectures, labs and tutorials
• Live lectures also offered
• Lecture recordings will be available
• MS teams
• Moodle
• Assignment
• Labs and quizzes
Lectures
• Lectures are every Monday (9-11am) and Tuesdays (4-5pm)
• They will be in-person.
• Monday at Old Main Building G31(K-K15-G31), and Tuesdays at
Ainsworth G02 (K-J17-G02) and streamed live (echo360).
• All lectures will be recorded
Labs
• Both lab-sessions on offer are in-person
• Wednesday 1-3pm (Brass) and Thursday 10am-12pm (Brass)
• Brass Lab J17 305 (K-J17-305)
• Bring your questions to the lab session
• Labs are available through Moodle, and will be released one week before
• Attempt the lab beforehand
• Lab quiz is due one week after the lab session
• Ok to work in pairs
• Some labs use UNIX command line and programs running on CSE
computers
• Resources on Moodle on how to access the CSE computers remotely
• First lab is not assessed but provides an introduction to using UNIX (more on quizzes
later)
Tutorials
• Weekly, in-person
• Both tutorials are on Tuesdays 5-6pm
• Ainsworth 101 (K-J17-101)
• Civil Engineering G6 (K-H20-G6)
• No marked assessments, but weekly self-tests
• Available on github, with solutions released week after
• Introduction to R and Python
• Data visualization and data wrangling
• Python tutorials will help you on the assignment
Course learning outcomes
1. Define bioinformatics and provide examples of common uses in analysing genome, protein
and expression data and in modelling biological systems
2. Describe some common application areas of bioinformatics and the techniques used therein
(genome annotation, rational drug design, medical genomics etc) and describe and explain
some common bioinformatics algorithms and common data types used in these applications
3. Apply common bioinformatics procedures using commonly available software and websites,
including: retrieving relevant sequences and structures from databases; identifying ORFs in a
DNA sequence; identifying the function of an unknown sequence by similarity searching;
identifying the function of an unknown sequence by pattern searches or based on
physicochemical properties; creating a multiple sequence alignment and a phylogenetic tree;
4. Construct simple shell scripts in UNIX to perform file management tasks and launch programs.
5. Explain the impact of bioinformatics on modern biology and relevant ethical and social issues
6. Discuss some common challenges in the engineering of computer systems for bioinformatics
7. Use R to visualise complex data and analyse transcriptomics data
Assessments
Item Description Weight Due date CLOs

Labs Labs with quiz 25% Weekly 3,4,7

Midterm On material from weeks 1 – 4 15% Week 5 1,2,5

Scripting bioinformatics
Assignment 15% Week 9 3,4
pipeline

On whole course but During exam


Final exam 40% 1,2,6
emphasis on weeks 5 – 10 time
Lab quizzes (25%)
• Weekly labs with quiz at the end of the lab
• Quizzes are due a week after the lab, but you can submit any
time before that
• Quizzes are a few questions around the lab material, and you will
need to work through the lab to answer them
• Most weeks will have a lab quiz except when noted e.g., for
week 1 and week 5
Midterm (15%)
• Scheduled for week 5
• Time: 1 hour 15 minutes (students with ELPs have extra time as
required)
• Around 5 short answer essay questions (on alignment,
database similarity searching, genome annotation, phylogeny
and structural bioinformatics), and 4 questions are problem-
type questions asking you to apply algorithms discussed in the
lectures
• Practice mid-term will be released in week 4
Assignment (15%)
• Example of APIs common in bioinformatics, where a
script/software calls a number of other programs and passes
data between them
• Spec will be released in week 5
• 2 versions depending on your programming expertise, both to be
written in python but with slightly different requirements
• Regular version for students with no scripting experience
• Advanced version for students who have done COMP2041
• Students who are doing or have done COMP2041 but choose to do the
simpler version will have their mark capped at 65%.
Final exam (40%)
• During the exam period and will be centrally timetabled.
• Length is ~2 hours except if you have ELPs and will be online
through inspera. You should get the link to the exam closer to
the date.
• There will be two kinds of questions, multiple choice questions
covering the entire course since week 1, and short essay
questions covering the main sections that were not covered in
the midterm. I.e., one on each of: transcriptomics, proteomics,
and experimental design.
• A practice exam will be released near the end of term
Content
Week Lecture Tutorial Lab
Introduction to bioinformatics.
Setting up your Introduction to UNIX
1 Sequence data, evolution and alignment
environment(s) command line
Sequence databases, RESTful APIs
Sequence alignment by dynamic programming Basic sequence analysis
2 Introduction to Python
Database searching and multiple sequence alignment using EMBOSS
Genome informatics: applications and assembly
3 algorithms, annotation and genome databases Data viz with Python Phylogeny and UPGMA
Phylogeny inference and UPGMA algorithm
Structural bioinformatics &
Functions and data
4 Case study: characterising a new protein (Bruno Structural bioinformatics
wrangling
Gaeta)
NO MONDAY LECTURE - PUBLIC HOLIDAY Biopython basics
5 Midterm exam
Midterm exam Assignment info session
Content
Week Lecture Tutorial Lab

6
FLEXIBILITY WEEK

7
Transcriptomics Biopython Advanced UNIX and shell scripting

8 Experimental design (Peter Humburg)


Introduction to R Transcriptome analysis using R
Distributed and application-specific hardware
in bioinformatics (Hasindu Gamaarachchi)
9
Proteomics (Marc Wilkins) Data viz with R Proteomics

10 Case Study: Genomics (Eleni Giannoulatou)


Case study: medical application of human
Recap Workflow management using Galaxy
genomics and transcriptomics (Fabio
Luciani)
Additional content
• Due to the public holiday and scheduling issues, you will be
missing some content.
• In your own time, you will be expected to watch two extra
lectures:
• Bio-image analysis (A/Prof Yang Song)
• Drug design (Dr Yunki Yau)
• One or two MCQs from each of these lectures will be in the
final exam
Changes to the course based on
feedback
• Tutorials were not useful
• Updated some parts and removed some of the R tutorials and including more
Python related to the assignment. These were introduced new last year, so
still tweaking to optimise these. Feedback appreciated!
• “Assignment was confusing and had lots of mistakes. “
• Main errors fixed (I hope!). This was also a new assignment since students
hated the previous ones. Some more tutorials will hopefully help.
• Lecture slides had mistakes.
• Corrected most that I could catch. But keeping an eye out for them is good for
all of us!
Still room for improvement, so please fill in the mid-term feedback
survey (on moodle) and myExperience survey (end of term)!

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