Faculty of Computer Science & Engineering

CS474 - BIOINFORMATICS
Introduction
Dr. Raja Hashim Ali
27 Aug 2019
 Faculty of Computer Science & Engineering

Instructor, TA, Class timings, Office hours

• Instructor
• Name: Dr. Raja Hashim Ali (teaching 1st time)
• Email: Hashim.ali@giki.edu.pk (Add “CS474” to the subject)
• Office: G13 – Main lobby, FCSE.
• Office hours: Tues 08.00-09.00, Wed,Thurs,Fri 8.00-10.00 & by appointment.
• Teaching Assistant
• Name: Engr. Muhammad Faizan Khan (assisting 1st time)
• Email: gcs1864@giki.edu.pk
• Office: G36 – Graduate lab, Ground floor, FCSE.
• Office hours: Mon, Wed 09.00-13.00, Tues 09.00-12.20, Thurs 14.30-17.00
• Class Hours (all lectures in MLH 2 FCSE)
• Tues 09:00-09:50.
• Wed 10:30-11:20.
• Thurs 10:30-11:20.

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Class webpage, email

• GIKI Content Management System - GIKI CMS

• Check the page carefully and regularly!
• Get attendance record and keep a tab on your presence.

• Google drive – CS474 page

• Check the page carefully and regularly!
• Get assignments, lectures, results and updates on the page.

• Email policy
• Include CS474 in the subject of your e-mail.
• Use TA as much as possible.

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Textbook

• Selzer, Paul M., Richard J. Marhöfer, and

Oliver Koch. Applied Bioinformatics: An
Introduction. Springer, 2018.
• Singh, Gautam B. Fundamentals of
Bioinformatics and Computational Biology.
Springer International Publishing, Switzerland,
2015.
• Durbin, Richard, et al. Biological sequence
analysis. Cambridge University Press, 1996.
• Borodovsky, Mark, and Svetlana
Ekisheva. Problems and solutions in biological
sequence analysis. Cambridge University Press,
2006.

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Evaluation and rules

• Evaluation (Tentative):
• Assignments (2) 10%, In-class Exercises (20) 30%, mid-term 20% and a Final exam
40%.
• The following rules will be strictly enforced.
• All in-class exercises are open book and open notes.
• Do not schedule any absence during the semester - there are no make-up in-class
exercises.
• All in-class exercises are unannounced.
• Due dates for assignments is STRICT.
• All in-class exercises must be received at the end of the class to receive credit.
• No late in-class exercise will be graded.
• It is your responsibility to make sure that the TA has ticked that you have submitted the
in-class exercise on the attendance sheet - TA will not be responsible for the unmarked
missing exercise later.
• All in-class exercises are to be done in pairs of two – make your group and submit it to
me by Tuesday class next week. Absent partner without prior info  absent group.

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Evaluation and rules

• Institute attendance policy to sit in final exams will be STRICTLY
enforced - 80% attendance - 36/45.
• Less than 36 lectures  NO final exam.
• Attendance will be taken at the start of class
• If you come after 5 minutes, you are not allowed to mark your presence  DO
NOT insist with TA.
• PLEASE do not put proxy of your friend OR face the music.
• If the class has started, use the back door.
• I will lock the front door at the start of each class (except today) - DO NOT try,
knock, kick or bang on it, if it is not open!
• Do not ever put your exercise/faryaad under the instructor’s/TA’s
office door.

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Evaluation and rules

• Marking is performed by the TA for the in-class exercises and assignments, and by
the instructor for mid-term and final.
• The TA shall mark the assignments and the in-class exercises within 5 days after
the submission.
• If you have a question about marking exercises/assignments, talk to TA.
• Only if something unreasonable has occurred will the instructor intervene.
• Furthermore, there is a limit of 5 days from when an exercise or assignment or
quiz or mid-term is marked (whether you are there to receive it or not including
the day) for grading problems to be dealt with.
• After that period, such will not be considered.
• The sole exception to this rule is the final examination.

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Evaluation and rules

• Cheating of any type will NOT be tolerated.
• Cheating in final exams will lead to straight F in course.
• Cheating in a in-class exercise will result in -15/30% of in-class exercise.
• Cheating in an assignment will result in -10/10% in all assignments.
• Cheating in a mid-term will result in a -20/20% in mid-term exam.
• Proxy for a friend will lead to 3 absentees for both students.
• Observe discipline of the class and do not disturb the class in any way.
• Mobile phones/tabs should preferably be not brought to class (NO CALLS).
• Put mobile phones on silent (NO VIBRATION) in case of emergency.
• Mobile phones will be confiscated for a week (SEVEN days) in case it disturbs the
class.
• Making noise in the class, and talking to a friend will get you expelled from the class
and next class without warning!
• You are allowed to sleep (if you can) but do not snore!

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Why study Bioinformatics?

• Do you want to be a Data Scientist in near future handling Big Data?
• Do you want to learn which large databases exist and how they were designed for
Biological data?
• Is designing search algorithms for large databases one of your learning objectives?
• Does recognizing patterns in data feel a very interesting job to you?
• (CS) Did Neural networks and Deep Learning make you inquisitive about the underlying
Biological model?
• Do you want to take courses that build on machine learning, data mining and software
development?
• Did you fear (hated) Biology in your F.Sc. because of the way it was taught but would like
to learn it from a cool Computer Scientist/Engineer?
• Does a Bioinformatician have career options?

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Why study Bioinformatics?

• Do you want to be a Data Scientist in near
future handling Big Data? Bioinformaticians
call themselves Biological Data Scientists
handling Biological data.
• Do you want to learn which large databases
exist and how they were designed for
Biological data? Bioinformaticians use NCBI
databases, Ensembl contains billions of
genome sequences for millions of species and
PDB structural database contains structures of
thousands of genes each with volumes of over
thousands of Terabytes. Website!

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Why study Bioinformatics?

• Is designing search algorithms for large
databases one of your learning objectives?
BLAST algorithm designed for searching
sequences from sequence database has been the
most cited paper in Bioinformatics and among
the top 12 most cited in all subjects! Website.
• Does recognizing patterns in data feel a very
interesting job to you? For example,
understanding conversion between genes, RNA
and protein sequences, understanding
inheritance mechanisms and patterns (ALS),
tracing the origins of virus outbreaks (Ebola),
tracing the pattern of evolution in famous
diseases (AIDS).

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Why study Bioinformatics?

• (CS) Did Neural networks and Deep Learning make you inquisitive about the underlying
Biological model? Inspired from Computational Biology, a twin of Bioinformatics
(specifically from Neuro Science)!
• Do you want to take courses that build on machine learning, data mining and software
development? The only option this semester is Bioinformatics!
• Did you fear (hated) Molecular Biology in your Matric because of the way it was taught,
but would like to learn it from a cool Computer Scientist/Engineer? Me too but let us give
it a try with me and Mussawar!

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Why study Bioinformatics?

• Does a Bioinformatician have career options? Lots really, a Bioinformatician is truly a
jack of many trades, can ably transform into a
• data scientist (friends doing jobs in Volvo, Swedbank and Ericsson as Data Scientists after PhD in
Bioinformatics).
• Software developer, especially database programmer (IBM).
• Computational Biologist/Bioinformatician in academia (Me!).
• Bio-statisticians.
• Bio-mechanics.
• Gene analyst, protein analyst, and/or phylogenetist.
• Pharma industry researcher, e.g., AstraZeneca in Sweden.

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Guide for successful study

• No minimalist approach
• Homework/In-class exercises would be sufficient! NOPE!!!
• Read relevant sections (previous lectures) before coming to class
• Do the homework (of course!!!)
• Work regularly
• Most lectures are building blocks for other lectures
• So you cannot catch up 2 week lectures in 2 days
• On average 8 hours EVERY week!
• Creativity
• No questions will require you to put just numbers to formula.
• Need to know how to apply! This can be improved by practice!
• Learning  Book, class exercise, note, homework
• It is combination of everything!
• Think yourself, discuss with your friends, write your own answer!

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

Course content
• Introduction to Bioinformatics (2 lectures) • Phylogenetic inference (6 lectures)
• Motivation • Background & Applications
• Definition • Data
• Representation
• Applications
• Methods & Algorithms
• Types
• Genome Assembly Problem (5 lectures)
• Relevance to you
• Background
• Data of Bioinformatics (4 lectures) • Data
• Genes, chromosomes, cells, & organisms • Types
• Graph-based solution
• Taxonomy & Nomenclature
• Microarray Expression Analysis (4 lectures)
• DNA, RNA & Proteins
• Background
• Similarity & differences with text
• Data
• Central dogma • Types
• Sequence Analysis (18 lectures) • Algorithms
• Introduction • Case studies (3 lectures)
– ALS Disease
• Pairwise & multiple sequence alignment
– Phylogeny of FERM domain
• Local & global alignment
– Development of Divvying for filtering MSAs
• Dynamic programming algorithms
• Databases in Bioinformatics (2 lectures)
• Heuristic based algorithms – BLAST
• Conclusion (1 lecture)
• Methods for multiple sequence alignments
• Filtering uncertainty in multiple sequence alignments
• Motif-finding problem & algorithms

CS474 - Bioinformatics Introduction

 Faculty of Computer Science & Engineering

QUESTIONS?

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