BIO-350

Bioinformatics Database Development

by
Waseem haider, PhD
Associate Professor,

Computational Biology and Bioinformatics Group (CBBG)

Dept. of Biosciences CUI, Islamabad-Pakistan
CEO Next Gen. Solutions (NGS)
 Waseem Haider, PhD

• MSC Biology Quaid-i-Azam University QAU (1999)

• M.Phil Biochemistry/Molecular biology QAU (2002)
• Masters in Computer sciences BIIT (2008)
• PhD University of Illinois at Urbana Champaign, USA (2014)
• 25 years of Teaching/Research experience
Research Interests
 High Throughput Sequencing Data Analysis
 Statistical and computational Genomics
 Applied Statistics
 Software development
 Web/Database development
 About COMSATS

Commission on Science and Technology for

Sustainable Development in the South
In 1994, representatives from several developing
countries met on 4th and 5th October in Islamabad and
agreed to establish the Commission
 CUI Bioinformatics Faculty
Faculty Degree Research Domain Faculty Degree Research
Domain

Dr. Muhammad Muddassar Dr. Muhammad Sajjad Plant Genetics/

PhD (S.Korea) PhD (UAF, PK)
Postdoc Computer-Aided Drug muhammad.sajjad@comsats.e Genomic
(Japan) Designing, Protein du.pk & Genome Editing
mmuddassar@comsats.edu.pk Modeling

Bioinformatics & Dr. Waseem Haider Genomics

Dr. Abdul Rauf Biophysics, Structure and PhD (USA) Transcriptomics
Siddiqui Modeling, Database and haider.waseem@gmail.com Using NGS
PhD/Postdoc (France) Tool Development, Machine Learning
araufsiddiqi@comsats.edu.pk Crystallography

Dr. M. Qaiser Fatmi

PhD (Austria) Biomolecular Modeling & Dr. Zoya Khalid Proteomics,
Postdoc (USA) Simulation, Computer-
PhD Machine
qaiser.fatmi@comsats.edu.pk Aided Drug Designing
(Sabanci, Turkey) Learning

Dr. Farhan Haq Dr. Saira Amir

PhD (S.Korea) Cancer Genomics Functional
CUI Alumnus PhD (CUI) Genomics, ML
saira_amir@comsats.edu.pk
 Next Gen. Solutions (NGS)
 NGS data analysis training and consultation
company
 Raised at COMSATS University Islamabad (CUI)
https://www.facebook.com/Next-Gen-Solutions-NGS
 Profit money from our workshops is channelized into social
welfare projects through Capt. Tasleem Haider Fund
Major projects include;
• Free Medical camps
• Food distribution drives
• Financial Assistance to needy students
• Helping Rural Health and Development (RHDF)
educate underprivileged children
Hands-on training workshops
Hands-on training workshops
Hands-on training workshops
 Hands-on training workshops
UHS LHR, Dec 21

AKU Dec 23 RMU, March 24

9
Persons trained >
1500

10
Community service projects
Community services projects

Medical Camp
10000

VTC Computers
48000 50000
Student As-
sistantships Food packs
3,67000 1,25000

Helping needy
1,10000
 BIO-350
Bioinformatics Database Development

Lecture # 1
 Required Text Book
• Book Authors
– Connolly, T. M., and Begg, C. E.
• Book Title
– Database Systems
A Practical Approach to Design,
Implementation, and Management
• Book Edition and Publisher
– 4th Edition, Addison Wesley, 2005.
 Reference Books
• Book Authors
– Hoffer, Jeffrey A., and Prescott, Mary B., and
McFadden, Fred R.
• Book Title
– Modern Database Management
• Book Edition and Publisher
– 7th Edition, Prentice Hall, 2005.
 Reference Books
• Book Author
– Kroenke, David M.
• Book Title
– Database Processing
Fundamentals, Design and
Implementation
• Book Edition and Publisher
– 10th Edition, Prentice Hall, 2006.
 Reference Books
• Book Author
– Date, C. J.
• Book Title
– An Introduction to Database Systems
• Book Edition and Publisher
– 8th Edition, Addison Wesley, 2003.
 Course Objectives
• To be able to understand the underlying
concepts of database, and database
management system (DBMS)
• To introduce students to the concepts of
relational data model
• Analysis and design of database application or
information system
 Course Objectives..
• Experience with SQL
• Implementation of database using SQL
• Learn to work with My SQL
 Course Contents at a Glance
• Introduction to Database Concepts
• Database Environment
• The Relational Model
• Relational Algebra
• SQL: Data Manipulation
• SQL: Data Definition
 Course Contents at a Glance..
• Entity-Relationship Model
• Enhanced E-R Model
• Normalization
 Marks Distribution
• Quizzes/Assignments 25%
• Mid-Term 25%
• Final 50%
Introduction to Databases

Chapter 1
 Chapter 1 - Objectives
• Some common uses of database systems
• Characteristics of file-based systems
• Problems with file-based approach
• Meaning of the term database (DB)
• Meaning of the term Database Management
System (DBMS)
 Chapter 1 - Objectives
• Typical functions of a DBMS.
• Major components of the DBMS environment.
• Personnel involved in the DBMS environment.
• History of the development of DBMSs.
• Advantages and disadvantages of DBMSs.
 Examples of Database Applications
• Purchases from the supermarket
• Purchases using your credit card
• Booking a holiday at the travel agents
• Using the campus library
• Taking out insurance
• Using the Internet
• Studying at university
 File-Based Systems
• Early attempt to Computerize the manual
filing system
• Collection of application programs that
perform services for the end users (e.g.
reports).
• Each program defines and manages its own
data.
 Manual Filing Systems
• Works well
– while number of items to be stored is small
– For only storage or retrieval functionality of
large number of items
 File-Based Systems
• Consider DreamHome example for file-
based systems
– Sales Department : responsible for selling and
renting of properties
– Contract Department: responsible for handling
lease agreements
 Sales Department
• PropertyForRent
(propertyNo, street, city, postcode, type, rooms, rent,
ownerNo)
• Client
(clientNo, fName, lName, telNo, preftype, maxRent)
• PrivateOwner
(ownerNo, fName, lName, address, telNo)
PropertyForRent
propertyNo street city postcode type rooms rent ownerNo

PA14 … Aberdeen … House 6 650 CO46

PL94 … London … Flat 4 400 CO87

PG4 … Glasgow … Flat 3 350 CO40

PG36 … Glasgow … Flat 3 375 CO93

PG21 … Glasgow … House 5 600 CO87

PG16 … Glasgow … Flat 4 450 CO93

PrivateOwner
ownerNo fName lName address telNo
CO46 Joe Keogh … 01224-861212
CO87 Carol Farrel … 0141-357-7419
CO40 … … … …
CO93 … … … …
Client

clientNo fName lName telNo prefType maxRent

CR76 John Kay 0207-774-5632 Flat 425
CR56 Aline Stewart 0141-848-1825 Flat 350
CR74 Mike Ritchie 01475-392178 House 750
CR62 Mary Tregear 01224-196720 Flat 600
 Contract Department

• Lease
(leaseNo, propertyNo, clientNo, rent , paymentMethod, deposit,
paid, rentStart, rentFinish, duration)
• PropertyForRent
(propertyNo, street, city, postcode, type, rooms, rent)
• Client
(clientNo, fName, lName, telNo, preftype, maxRent)
 PropertyForRent

propertyNo street city postcode type rooms rent

PA14 … Aberdeen … House 6 650

PL94 … London … Flat 4 400

PG4 … Glasgow … Flat 3 350

PG36 … Glasgow … Flat 3 375

PG21 … Glasgow … House 5 600

PG16 … Glasgow … Flat 4 450

Lease

leaseNo propertyNo clientNo rent --- rentStart rentFinish duration

10024 PA14 CR62 650 1-Jun-05 31-May-06 12
… … … … … … … …
Client
clientNo fName lName telNo
CR76 John Kay 0207-774-5632
CR56 Aline Stewart 0141-848-1825
CR74 Mike Ritchie 01475-392178
CR62 Mary Tregear 01224-196720
File-Based Processing
 Limitations of File-Based Approach

• Separation and isolation of data

– Each program maintains its own set of data.
– Users of one program may be unaware of
potentially useful data held by other programs.
– For example, if we want to produce a list of all
houses that match the requirements of the clients.
• Duplication of data
– Decentralized approach taken by each department.
– Same data is held by different programs.
– Wasted space and potentially different values
and/or different formats for the same item.
 Limitations of File-Based Approach..

• Data dependence
– File structure is defined in the program code.

• Incompatible file formats

– Programs are written in different languages, and so
cannot easily access each other’s files.

• Fixed Queries/Proliferation of application

programs
– Programs are written to satisfy particular functions.
– Any new requirement needs a new program.
 Database Approach
• Arose because:
– Definition of data was embedded in application
programs, rather than being stored separately and
independently.
– No control over access and manipulation of data beyond
that imposed by application programs.

• Result:
– the database and Database Management System
(DBMS).
 Database
• Shared collection of logically related data, and a
description of this data, designed to meet the
information needs of an organization.
• System catalog (metadata) provides description
of data to enable program-data independence.
• Logically related data comprises entities,
attributes, and relationships of an
organization’s information.
 Database Management System (DBMS)

• A software system that enables users to

define, create, maintain, and control access
to the database.

• (Database) application program: a

computer program that interacts with
database by issuing an appropriate request
(SQL statement) to the DBMS.
Database Management System (DBMS)..
 Database Approach
• Data definition language (DDL).
– Permits specification of data types, structures and any
data constraints.
– All specifications are stored in the database.

• Data manipulation language (DML).

– General enquiry facility (query language) of the data.
 Database Approach..
• Controlled access to database may include
– A security system
• Which prevents unauthorized users accessing the database
– An integrity system
• Which maintains the consistency of stored data
– A concurrency control system
• Which allows shared access of the database
– A recovery control system
• Which restores the database to a previous consistent state in case of
hardware or software failure
– A user-accessible catalog
• Which contains description of the data in the database
 Views
• Allows each user to have his or her own
view of the database.

• A view is essentially some subset of the

database.
 Views - Benefits
• Reduce complexity
• Provide a level of security
• Provide a mechanism to customize the
appearance of the database
• Present a consistent, unchanging picture of
the structure of the database, even if the
underlying database is changed
 Summary
• Introduction to DB and DBMS
• File-based systems and their limitations
• Database approach