1

VISVESVARAYA TECHNOLOGICAL UNIVERSITY

BASICS OF COMPUTER APPLICATIONS 06BT45

Hrs to be

taught Portion to be covered Book Name/ web

site address

Unit 1: Basics of Linux (5 hours)

1 Introduction to Linux, Basic commands (creating user/ passwds, ls,

man, whatis, apropos, cp, rm, cat, sort, echo)

2 Working with files, file attributes , installing programs using rpm, Basic

editors (awk, vi and sed) and their features[read, write, append, execute,

copy, undo, repeatfactor, breaking and joining lines]

3 Introduction to Shellscripts, types [bash and csh], uses of pipes, aliases,

and wildcards. Killing processes

4 Decision making statements: If-then, else-if, test, while-do-done, until-

do-done, for-in-do-done, case-in-esac, select-in-do

5 Basic regular expressions, grep command, applications towards string

search

B1

Unit 2: Basics of XML (6 hours)

6 Structured and Unstructured data, XML fundamentals

7 XML documents and XML files, elements and character tags, attributes,

XML names

8 CDATA sections, XML declarations, DTD element declarations,

attribute declarations, namespaces, parsing

9-10 Programming applications of XML, General features of NCBI’S

molecular biology data model

11 General features of BioXML, NeuroML, Chemical Markup Languages

(CML)

12 General features of MicroarrayML(MAML), RiboML and SBML

B2

Unit 3: Basics of Internet (7 hours)

13 Internet address, protocol, Transport layer

14 Upper layer protocols, Internet access and applications.

15 Overview of HTML and HTTP, Web servers, Web access

16 security, WWW proxies, HTML technology and applications,

17 Novell’s WWW service, web applications

18 Search engines of biological relevance (MEDMINER, SCIRUS),

19 Legal and ethical issues.

B3

Unit 4: Basics of Databases (7 hours)

20 Introduction to Databases, flat files

21 Concepts of DBMS and RDBMS,

22 E-R relationship, Introduction to MS-ACCESS

23 Introduction to SQL, using basic SQL commands in MS-ACCESS

24 Tables in MS-ACCESS-creation, Modification, and joining two tables

25 Simple queries using SQL, Concept of joins, inner and outer joins with

examples.

26 Data sorting and filters.

B4

Unit 5: Applications-1 (7 hours)

27 C-Program using Numerical analysis towards solving the Differential

B5

2

Text books and Website references:

Unit-1 B1:

Books:

1. Unix programming by Sumithabadas

2. Linux , the complete reference, Richard Peterson, TMH, 1998

3. Unix Programming Environment, kerningham and pike

Website references:

1. Linux Basics: First steps in to Linux: http://www.freeos.com/articles/4414/

2. Introduction to Linux: http://tldp.org/LDP/intro-linux/html/

3. Linux Knowledge base and Tutorial: http://www.linux-

tutorial.info/modules.php?name=MContent&pageid=

4. Linux Online-Getting started with Linux:

http://www.linux.org/lessons/beginner/toc.html

equations (Runge kutta II order)

28-33 Applications of differential equations to biotechnology (thermal death

kinetics of microorganisms, holding time for sterilization, estimating the

length of the lag phase, calculation of specific growth rate, doubling

time and substrate to cell yield coefficient)

Unit 6: Applications-2 (7 hours)

34-35 Introduction to OOPs concepts with respect to C++ (Encapsulation,

Polymorphism, Inheritance, Abstraction, Dynamic binding), data types,

arrays.

36 C++ Program to find the optimum Ph and temperature for maximum

enzyme activity,

37 C++ program to derive the column height needed to achieve the

specified degree of conversion in a fluidized bed reactor.

38 C++ program to find the optimal rate for maximum cell productivity

39-40 Usage of NCBI’s C++ toolkit to demonstrate certain features of

sequence analysis

B6

Unit 7: Basics of Ontologies (7 hours)

41 Overview of Ontologies, gene ontologies, Open biological

Ontologies(OBO)

42-43 TAMBIS ontology, cell cycle ontology, Gene X ontology, Building

ontology, feature of Ontology development tools (protégé 2000, GKB

editor, OilEd).

44-45 Ontology Integration, applications of bio ontologies

46-47 Data formats- types (CSV and tabbed formats for general file

representation, data cleaning, flat file)

B7

Unit 8: MATLAB (5 hours)

48-49 Introduction to MATLAB, features (Arithmetic and graphical utilities

only) of MATLAB toolbox

51-52 Introduction to MS-EXCEL, EXCEL spreadsheets utilities, and

operations (Towards descriptive statistical applications, graphing

utilities, association and comparative statistics).

53 Usage of Matlab toolboxes towards Biochemical applications

B8

3

Unit-2 B2:

Books:

1. Essential XML: Beyond Markup, Dox Box, Aaron Skonnard and John Lam,

Pearson Education

2. HTML and XML for beginners: Michael Morrison, Microsoft Press, 2001

3. Beginning XML: David Hunter, 3rd Ed.

Website references:

1. BioXML basics

http://www.biosino.org/mirror/www.bioxml.org/wiki/html/BioXML/BioXMLArc

hitecture.html

2. A collection of tutorials in Markup Languages

http://www.biotech.unl.edu/bioinformatics/tutorial.html

Unit-3 B3:

Books:

1. Data communications and Networks, 2nd Edition by Behrouz A. Ferouzan

2. Internet, The complete Reference, Margaret Levine Young, TMH, 1999

3. Computer Networds, Tanenbaum, IV edition, Pearson Ed. Asia, 2002

4. Communication Networks-Fundamental concepts and key architechtures, Alberto

Leon, TMH, 2000

Website references:

1. Search engines: http://en.wikipedia.org/wiki/Search_engine

2. Medminer: An internet Text-mining tool for biomedical information:

http://discover.nci.nih.gov/host/medminer_manuscript.pdf

3. Scirus: for scientific information : http://www.scirus.com/srsapp/aboutus/

Unit-4 B4:

Books:

1. Database System Concepts, 3rd Edition, Abraham Silberchatz, Henry F. Korth and

S. Sudarshan

2. SQL simplified: Learn to read and write SQL: Cecelia. L. Allison, Aug 2003

3. A first course in database systems (2nd ed.), Jeffrey D. Ullman and Jeniffer D.

Widon

4. An Introduction to Database Systems, 6th Edition, C. J. Date

5. Fundamentals of Database Systems by Ramez Elmasri

Website references:

1. Database Basics- a Primer

http://www.smallbusinesscomputing.com/emarketing/article.php/3364381

2. Databases: Step by step guide http://www.geekgirls.com/menu_databases.htm

Unit-5 B5:

Books:

1. Programming for Chemical Engineers using C, C++ and MATLAB, Raul Kapuno

ISBN: 9781934015094, Transatlantic Publishers group

4

2. Let us C: Yeshwanth Kanitkar

3. Programming in ANSI C, E. Balaguruswamy

4. Comprehensive programming in C and Numerical analysis, J. B. Dixit, Laxmi

publications

5. Numerical methods for Engineers, S. C. Chapra and R. P. Canale, TMH, 1990

Website references:

1. Numerical recipes in C: http://www.nrbook.com/a/bookcpdf.php

2. Numerical analysis programs in C: http://www.aei.mpg.de/~jthorn/C.html

Unit- 6 B6:

1. C++ primer by Stanley B. Lipman & Josee, Addison Wesley III Edition

2. C++, The complete Reference by Herbert Schmildt, TMH, 3rd Edition

Website references:

1. http://www.glue.umd.edu/%7ENSW/ench482/ench482.htm

2. NCBI C++ toolkit book:

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.TOC

3. Varsity notes: Chemical Engineering,

http://www.varsitynotes.com/chemical_engineering/

Unit-7 B7:

Books:

1. A study in Ontology: Peter Simons, Oxford Press.

Website references:

1. What is ontology and why do we need it available at the URL

http://protege.stanford.edu/publications/ontology_development/ontology101-noy-

mcguinness.html

2. Basics of ontology and its biological applications available at the URL

http://boole.cs.iastate.edu/baojie/pub/2006-02-25_cs672.ppt

3. Ontology in a nutshell available at the URL

http://www.knowledgeboard.com/doclibrary/knowledgeboard/day_5_ontology_in

_a_nutshell.pdf

4. Basics of Ontology modeling http://www.upriss.org.uk/teaching/ka1web.pdf

5. An introduction to Gene Ontology http://www.geneontology.org/GO.doc.shtml

6. Biological ontological databases http://www.ebi.ac.uk/Databases/ontology.html

7. History of Ontologies in Bioinformatics

http://www.mged.org/Meetings/mged3ontologies.ppt

8. aspects of ontology integration

http://www.meteck.org/AspectsOntologyIntegration.pdf

9. Integration with ontologies

http://www.ontoprise.de/documents/integration_with_ontologies.pdf

10. Ontology integration: Some challenges

http://ianlumb.wordpress.com/2006/09/08/ontology_integration_challenges/

11. Data formats-CSV http://www.creativyst.com/Doc/Articles/CSV/CSV01.htm

12. Data formats-CSV http://edoceo.com/utilis/csv-file-format

13. DBMS-Dealing with dirty data http://www.dbmsmag.com/9609d14.html

14. Simple data cleaning tools and methodologies:

http://www.tdwg.org/2003meet/EV/TDWG_2003_EV_Chapman_1.ppt

5

Unit-8 B8:

Books:

1. The matlab Expo, stablefield, willia, 1993

2. Mastering MATLAB, Hanselman and Dua, 1996

3. Programming in MATLAB, K. V. Krishnamurthy, 2003

4. Excel 2002 power programs, John Walkenbach, 2002

5. Essential MATLAB for scientists and Engineers, Arnold/ Wiley, NY

Website References:

1. A practical introduction to MATLAB:

http://www.math.mtu.edu/~msgocken/intro/intro.html

2. MATLAB Tutorials: http://www.math.siu.edu/matlab/tutorials.html

3. MATLAB primer: http://math.ucsd.edu/~driver/21d-s99/matlab-primer.html

4. Excel Tutorial: http://www.usd.edu/trio/tut/excel/

5. Excel Tutorial: http://einstein.cs.uri.edu/tutorials/csc101/pc/excel97/excel.html

6. Excel tutorial on Statistics:

http://phoenix.phys.clemson.edu/tutorials/excel/stats.html

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VISVESVARAYA TECHNOLOGICAL UNIVERSITY

SUBJECT DISCUSSION WORKSHOP (03rd -04

th October, 2007)

Subject Name : Basics of Computer Applications

Subject Code : BT45 I. A. Marks :25

Hrs/ Week : 04 Exam Hrs. :03

Total Hours : 52 Exam Marks : 100

Model Question Paper-1

NOTE: 1) Answer any five questions selecting two from each part

Part – A

1. (a) Write a shell script for comparing file permissions of two files (6 marks)

(b) Write short notes on GREP command. Explain the modes of functioning of vi

editor (7 marks)

(c) Write an AWK program to process employee details for generating the

payslip for Employees. (7 marks)

2. (a) Write a note on Structured and Unstructured Data (7 marks)

(b) Explain the salient features of DTD in an XML document (7 marks)

(c) Write short notes on (i) BioXML and (ii) NeuroML (6 marks)

3. (a) What is an IP Address? Describe the significance of Subnet mask (6 marks)

(b) Explain all seven layers of OSI Reference model (7 marks)

(c) Explain the working of search engines (7 Marks)

4. (a) List the disadvantages of file processing systems (6 marks)

(b) Define database. Write the procedure to create table using MS-ACCESS

(7 marks)

(c) Create a table (student) with suitable columns and appropriate constraints and

insert 10 records (7 marks)

Part – B

5. (a) Write a C program to find the volume of the batch reactor for production of

lactase using Lactobacillus microorganism? (7 marks)

(b) An engineer wants to find the batch time for the reactor for production of a

bio-product using biological methods. Which growth phase of microorganism

he will be interested and hence write a C program to find this ?(7 marks)

(c) Write a C program to estimate the doubling time and substrate to cell yield

Coefficient (6 marks)

7

6. (a) Describe the basic features of NCBI C++ toolkit (7 marks)

(b) Explain briefly Encapsulation and polymorphism. (7 marks)

(b) Write a C++ program to derive the column height needed to achieve the

specified degree of conversion in a fluidized bed reactor. (6 marks)

7. (a) What are Ontologies? Describe briefly Open Biological Ontologies (6 Marks)

(b) Describe in detail about the developing/ building an Ontology (7 Marks)

(c) Describe the basic features of a flatfile (7 Marks)

8. (a) Describe the basic arithmetic operations using MATLAB (6 marks)

(b) Describe the usage of MATLAB toolboxes in Chemical engineering (7 marks)

(c) Explain the various sorting mechanisms available in EXCEL to remove the

Redundancy / sort the data (7 marks)

*****

8

VISVESVARAYA TECHNOLOGICAL UNIVERSITY

SUBJECT DISCUSSION WORKSHOP (03rd -04

th October, 2007)

Subject Code : BT45 I. A. Marks :25

Hrs/ Week : 04 Exam Hrs. :03

Total Hours : 52 Exam Marks : 100

Model Question Paper-2

NOTE: 1) Answer any five questions selecting two from each part

Part – A

1. (a) Write a shell script to check whether a given string is palindromic or not.

(6 marks)

(b) What are wild card characters? Explain how they are used for pattern

Matching (7 marks)

(c) Explain repeated pattern matching and tagged expressions with respect to SED

(7 marks)

2. (a) Describe the general features of NCBI’s Molecular biology datamodel

(6 marks)

(b) What is DOM & how does it relate to XML (7 marks)

(c) What are Namespaces, Explain at least four of them in detail citing an

example (7 marks)

3. (a) Give the overview of HTML technology and its applications (6 marks)

(b) What are web servers, explain the need of a proxy server (7 marks)

(c) Explain the working of search engines (7 Marks)

4. (a) What is meant by Data Dictionary (6 marks)

(b) Explain Entity-Relationship (E-R) model and its related properties (7 marks)

(c) Construct the following SQL queries for the STUDENT table: (7 marks)

(i) Find the total number of students those who got distinction in the

subject BT-45

(ii) List the student names those who passed in all the subjects

Part – B

5. (a) Write a C program to find the specific growth rate of microorganism in a

bioreactor? (7 marks)

(b) Write a C program to find the solution of an ordinary differential equation

9

2

3y

xdx

dy+= , given 1.0,1)0( == hy using Runge kutta II order (7 marks)

(c) Write a C Program to find the doubling time for any microorganisms to grow

using substrate? (6 marks)

6. (a) Write a C++ program to find optimum pH and Temperature for

microorganisms to grow in a bioreactor for the given specific growth rate?

(7 Marks)

(b) Write a C++ program to find the hold up time in sterilizer for media?

(7 marks)

(c) Explain the concept of Inheritance in C++. (6 marks)

7. (a) Describe Gene Ontology in detail. (6 Marks)

(b) Describe briefly Ontology integration. Discuss three applications of bio-

ontologies (7 Marks)

(c) Describe the basic features of a CSV and Tabbed format file representation

(7 Marks)

8. (a) Explain the usage of Trigonometric and Mathematical functions in EXCEL

(6 Marks)

(b) Write a program in MATLAB for a 3 X 3 matrix multiplication (7 Marks)

(c) Explain the graphical utilities present in MATLAB (7 Marks)

*****