CE7412: Computational and Systems Biology

Introduction
Professor Jagath Rajapakse

Tuesdays 2:30 – 5:30pm at LT 11

CE7412: Computational and Systems Biology 1

 Mapping between computing and life machinery

Turing Machine Life Machinery

• Long binary tape • 3 billion letters of

A, C, G, T

• Scanning head • Scanning by ribosome

molecules

• A set of simple • “Genome” information

instructions in our cells; or proteins

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 Growth in Molecular Biology and Computer Science
Molecular Biology
Computer Science
• 1951: Helix structure of DNA • 1936: Turing machine
• 1953: Waston and Crick deduced the • 1971: microprocessor
three-dimensional structure of DNA
• Software: big systems like PC Windows,
• 1960: Elucidation of the genetic code, Unix, Linux, etc.
mapping DNA to peptide (proteins)
• Hardware: PC with 2GB memory, 3.6Ghz,
• 1970’s: DNA sequencing techniques 250GB disk, multiple-core machines
• 1985: PCR for amplifying DNA • Computer clusters, Supercomputers,
• 1980-90: Sequencing of the genomes of mid-size servers, grid computing
various organisms
• Computational structures and algorithms
• 1989: Launch of the Human Genome • Database theorems, query algorithms,
Project (HGP)
programming languages, software
• 2001: The first working draft of human engineering, artificial learning, machine
genome learning, data mining
• 2003: The reference sequence of the
human genome

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 Terms associated with computational and systems biology
• Life Sciences: associated with living organisms. Since the beginning of HGP, there have
been an explosion and implosion of life sciences data.
• Computational Biology – development of mathematical models of biological data and
processes, and design of efficient and sensitive algorithms for their analyses.
• Systems biology – the study of biological systems taking into account the interaction of
key elements such as genes, proteins, metabolites, and cells with respect to one
another.
• Bioinformatics – the marriage of computer science and biological science; application
of computational algorithms and IT infrastructure to organize, analyze, understand,
and visualize life sciences data.
• Machine Learning is the discipline of building probabilistic models and related
automated algorithms to extract useful information from a given corpus of data and
make inferences on underlying phenomena.

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 Focus of CE7412

Bioinformatics is the marriage of computer science and molecular biology

Bioinformatics == Computational biology + biological databases + web interfaces + data

management + visualization + …

Systems biology considers biological phenomena arises as a result of system of units,

interacting and functioning together.

The main focus of CE7412 is to study the use of machine learning and data mining
principles and techniques to solve problems in computational and systems biology.

Deep learning is building and learning neural network models with many layers.

CE7412: Computational and Systems Biology 5

 Workflow of computational and systems biology

Life Sciences Data

Computational
Algorithms & Tools

Knowledge, Patterns, Models, Networks

Biological Inferences

CE7412: Computational and Systems Biology 6

 Protein Structure Prediction

PISPIETVPVKLKPGMDGPKVKQWPLTEE
KIKALVEICTEMEKEGKISKIGPENPYNT
PVFAIKKKDSTKWRKLVDFRELNKRTQDF
WEVQLGIPHPAGLKKKKSVTVLDVGDAYF
SVPLDEDFRKYTAFTIPSINNETPGIRYQ
YNVLPQGWKGSPAIFQSSMTKILEPFKKQ
NPDIVIYQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGY
ELHPDKWTVQPIVLPEKDSWTVNDIQKLV
GKLNWASQIYPGIKVRQLCKLLRGTKALT
EVIPLTEEAELELAENREILKEPVHGVYY
DPSKDLIAEIQKQGQGQWTYQIYQEPFKN
LKTGKYARMPENPYNTPVFAIKKKDSTKW
RKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKENPYNTPVFAIKKKDGTKALTEVIPLT
EEAE

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 Transcription Networks

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 Problems in Computational and Systems Biology
• Sequence alignment, binding site prediction, protein 3D structure alignment
• Prediction of protein structure, prediction of RNA structure, prediction of protein
function
• Annotation of gene features, detection of genomic signals
• Clustering of gene expression data, gene regulatory networks
• Classification of tissues based on gene or protein expression, identification of disease
biomarkers
• Identification of network motifs, detection of molecular pathways
• Phylogenetic tree construction
• Computational disease diagnosis, computational disease prognosis (outcome
prediction), and bio-marker detection.

CE7412: Computational and Systems Biology 9

 Lecture Topics
0. Introduction
1. Biological foundations
2. R programming and packages
3. Probabilistic modelling
4. Models of biological sequences
5. Statistical testing in computational biology (e-learning)
6. R – Graphics (CNY: e-learning)
7. Hidden Markov models and gene structure prediction
8. High throughput counts data
9. Gene ontology and gene set enrichment analysis
[Link] learning
[Link] Networks
12. Variants calling from DNA-seq data
13. PROJECT presentations
CE7412: Computational and Systems Biology 10
 CE7412 Prerequisites and Assessment
Prerequisites:
Linear algebra, basic calculus, and programming skills

• Assessment:
– Assignments (50%) – Two assignments.
Assignments are to be done individually.

– Project (40%)
An open project: to be proposed and executed in a group of up to Three

-- Class participation (10%): Attendance to 10 in-person lectures will be taken.

7-10 marks for over 70% attendance; 5-7 marks for 50 -70% attendance; 0 marks for over 50% absence

CE7412: Computational and Systems Biology 11

 Deadlines for Assignments and Projects
Handout on Deadline on
Monday Friday
Assignment 1 Week 5 Week 8
Assignment 2 Week 9 Week 12

Project Proposal Report/codes/slides

submission and Submission on
feedback Wednesday

Week 10 Week 14

• Weeks correspond to the 13 weeks of the semester.

• Assignment solutions and project reports and codes are to be
submitted on-line via NTU Learn
CE7412: Computational and Systems Biology 12
 Project

To be proposed by students.
Need to use the principles and data types described in the class

• Projects are to be done in groups of at most three.

• You have to find partners for the project by yourself.
• There will be a peer review part which will be taken for the individual portion of
marks (25%)
• Individual members should submit solutions/reports and codes to NTU learn,
using individual accounts, and group members names should appear on the cover
page of the report.

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R Programming (version 4.4.2)

• R is the programming language

• Introductory codes and tutorial examples are given

• Download R from:
[Link]

• R-Studio is recommended IDE for code development:

[Link]

• R markdown

14
Texts for in-class Lectures

[Link]
[Link]
15
 R Programming

//[Link]/~tatiene/Disciplinas/2014.2/LivroR/R_Intro.pdf
[Link]

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 Instructor
Professor Jagath Rajapakse
• Office: Blk. S3 – B1c92
• Consultation by email appointment
• URL: [Link]
• Email: asjagath@[Link]

TAs:
Mr. Deepank Girish: DEEPANK002@[Link]
Ms Amashi Niwarthana: AMASHINI001@[Link]
• Office: Biomedical Informatics Lab, NS4-04-33

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 Thank you

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