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1 - Introduction To Computational Biology

This document provides an introduction to computational biology and bioinformatics, covering topics such as overlapping fields, applications, history, computers and operating systems used, internet resources, cheminformatics, and common Linux terminal commands. Key applications of computational biology include drug design, sequence analysis, and clinical uses like disease prediction. The growth of internet resources and availability of biological databases online have been crucial to enabling the field of bioinformatics.

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Alisha
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148 views22 pages

1 - Introduction To Computational Biology

This document provides an introduction to computational biology and bioinformatics, covering topics such as overlapping fields, applications, history, computers and operating systems used, internet resources, cheminformatics, and common Linux terminal commands. Key applications of computational biology include drug design, sequence analysis, and clinical uses like disease prediction. The growth of internet resources and availability of biological databases online have been crucial to enabling the field of bioinformatics.

Uploaded by

Alisha
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Computational Biology &

Drug Design
DISCIPLINE SELECTIVE ELECTIVE (CREDIT : 6)
2

You may visit with me about questions or


concerns any time we are not in the middle
of direct instruction, or I am not helping
other students.
How and when
to contact me?
You may email or text me if necessary, and
I will respond when I am able.
[email protected]
9560632181
3

eAssignment 1:
Continuous Submit by 8th January 2019

evaluation
(10 marks
each) Test: 26TH February
Syllabus covered uptil 19th February 2019
4
Introduction to Computational Biology

 Computational Biology and Bioinformatics?


 Internet and Bioinformatics
 Chemoinformatics
 Linux
5
OVERLAPPING FIELDS
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Computational Biology and
Bioinformatics: similar/different??
Definition
8
Applications

 Turns ideas into a testable hypothesis (Cell genetic heterogeneity and drug resistance in cancer)
 Lead/hypothesis generation for wet lab experiments (Identifying disease associating mutations)
 Sequence Homology Analysis (Phylogeny)
 Drug design (Identification of target/novel drug/modifications in lead molecule)
 Predictive functions (hypothetical proteins)
 Clinical (disease prediction, biomarkers)
 Intellectual Property Rights (patents, information, security)

SAVES TIME AND RESOURCES


History 9
10
11
12
13
14
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Computers and Programs

 Computer  Electronic machine to store information and process it in the binary mode.
 Information retrieval and analysis require  programs
 Software  Collective term for various programs that can run on computers
 System software (computer’s operating system and any other program required to run applications)
 Application software ( installed by user for specific purposes)
 Programming languages (Machine code, assembly, and Higher-level language) :::: It comprises
of a set of instructions that produce various kinds of output. Eg. C, C++, R, etc.
 Markup language :::: It allows document annotation in a way that is syntactically distinguishable
from the text. Unlike programming language, they are designed to create a structure, identify
data rather than executing or performing an action. Eg. Hypertext makrup language (HTML),
Bioinformatic sequence markup language (BSML)
 Scripting language :::: It is a programmimg language that is designed for integrating and
communicating with other programming languages. Eg. JAVA script, Python etc.
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Operating systems

 OS is a master program that manages all peripheral hardware and allows other software applications to
run.
Examples:
 BIOS (Basic-Input Output Operating system) :
 low level OS entirely stored in ROM
 It decides : switch on/off, reading and writing to disks, responding to input, displaying readable charcters on
monitor
 WINDOWS
 A higher level OS than BIOS which provides a typical graphical user interface
 UNIX
 OS for multi-user component environment (software that powers web was invented on UNIX)
 Rich in commands and possibilities ranging from networking software to word processing softwares and from
emails to newsreaders.
 Many Varities and versions
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LINUX : open source variation of UNIX

 It can be downloaded and installed free of cost (www.linuxfoundation.org)


 History (UNIX inception in 1969  AT&T’s and Bell Laboratory antitrust case over UNIX  1984, case
finished, Bell lab’s proprietariship started  GNU (GNU’s not UNIX) project started  led to the
development of LINUX)
 First released on September 17, 1991 by Linus Torvalds.
 Used in  Cloud computing, mainframe computers, mobile devices, PC’s, ervers, supercomputers
 As an OS, Linux is software that sits underneath all of the other software on computer, receiving
requests from those programs and relaying these requests to the computer’s hardware.
 It is enabled with several packages (sets of programs and tools)  Linux Kernel, GNU/Linux
 As compared to other OS, it is extremely customizable. Users can choose applications (like word
processor and web browser) and core components
 Linux Kernel is mainly written in the C programming language.
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Common terminal commands of
LINUX

 cat : to Concatenate or merge  grep: to search for specified text in a file


multiple files into one file  wc: to count the no. of characters,
 less: to View the files instead of words in a file
opening it  ls: to get the list of all the files or folders
 head: to print the first N lines of a file  cd: to change the directory
 mkdir: to create a directory  du: to show disk usage
 cp: to copy the file from source path  pwd: to show present working directory
to directory path
 man: to show manual of any command
 mv: to move the files present in Linux
 rm: to remove files or directory  rmdir: to delete a directory if it is empty
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Internet and Bioinformatics

 Interplay of Internet, World wide web (WWW), and global network of biological information and service
providers has made the bioinformatics revolution possible.
 Internet  is a global network of computers and computer network that links government, academic
and business institutions.
 Transmission control protocol/Internet protocol (TCP/IP) : the communication sharing protocol followed
by networks which allows different types of machines to speak to each other in a common way.
 Computers within the network  nodes
 For transfer, data is first broken into small packets (units of information)  sent independently 
reassemble at destination
 TCP determines how data are broken into packages and reassembled
 IP determines how the packets of information are addressed (IP address) and routed over the network
 Packets might reach destination after passing through several computers. Even if any of the nodes on
the way is down, the network protocols are designed to find an alternative route.
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Internet and Bioinformatics
 Internet originated  ARPAnet (US department of defense, 1969)  BITnet (1981)
 Internet provides a means to distribute software and enables researchers to perform sophisticated analysis on
remote servers.
 Late 1980’s  email servers, File transfer protocol (FTP), and TELNET server
 World wide web (www)
 way of exchanging information over the internet using a program called browser
 Developed by European Nuclear Research Council (CERN) in 1989
 First molecular biology web server : Expasy (Expert protein analysis system), 1993
 Webpage and website  hyperlinks  each hypertext document has a unique address : URL (Uniform Resource
locator). URLs take the format http://restofaddress
 Communication protocol used by web servers  Hyper text transport protocol (http)
 Language for hypertext documnts  HTML
 Internet explorer (1995 by Microsoft)  hypermedia browser
 Mozilla Firefox, Google chrome
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Cheminformatics

 Chemoinformatics, chemioinformatics and chemical informatics


 Use of computer and informational techniques applied to a range of problems in the field of
chemistry.
 Applications:
 Storage and retrieval (chemical structures are in silico represented in XML-based chemical markup
language or SMILES format)
 Virtual libraries
 Virtual screening (docking)
 Quantitative structure-activity relationship (QSAR)
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Q1. What are the merits and limitations of Linux? [3]

Q2. List and give function of at least 30 common terminal


commands of linux? [15]

Assignment Q3. Define: Algorithm, Program, Intranet, Sequence alignment,


Sanger sequencing, Microarray, Evolution, Phylogeny,
• Electronic submission by 8th January Homology modelling, Molecular Docking, [10]

Q4. Define and give 2 example each of - literature, sequence,


structure, medical, enzymes and metabolic pathways
databases [12]

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