Page 52 - Handbook Bachelor Degree of Science Academic Session 20202021

Faculty of Science Handbook, Academic Session 2020/2021

SIV 3003 ANALYSIS OF MOLECULAR SEQUENCE Main References:
1. Zvelebil M. & Baum J. O. (2008). Understanding
This course emphasizes the basic understanding and Bioinformatics. Garland Science, USA.
knowledge required to analyse different types of molecular 2. Stryer L. (2015). Biochemistry. Freeman and Co., NY.
sequences. In practice, students will be introduced to 3. Leach, A.R. (2010). Molecular Modelling- Principles
databases, methods of searching and matching, and Applications. Addison Wesley Longman.
exploration of molecular information using predictive
methods, and molecular phylogenetics for both nucleic
acids and protein sequences. SIV 3006 GENOMICS

Assessment Methods: This course covers the following topics: Organismic
Continuous Assessment: 40% genomes; Genome anatomy, mapping, evolution, analysis
Final Examination: 60% and rearrangements; Genome databases; Genome and
transcriptome sequencing technology.
Medium of Instruction:
English Assessment Methods:
Continuous Assessment: 30%
Main References: Final Examination: 70%
1. Tore S. (2012). Genomics and Bioinformatics: An
Introduction to Programming Tools for Life Scientists. Medium of Instruction:
Cambridge University Press. English
2. Ziheng Yang (2014). Molecular Evolution: A Statistical
Approach. Oxford University Press. Main References:
3. Micheal Agostino (2012). Practical Bioinformatics. 1. Bruce R. Korf and Mira B. Irons (2013). Human
Garland Science. Genetics and Genomics.
2. Nancy Craig, Rachel Green, Carol Greider and Gisela
Storz (2014). Molecular Biology: Principles of Genome
SIV 3004 PROGRAMMING IN BIOINFORMATICS Function.
3. Leland H. Hartwell, Michael Goldberg, Janice Fischer
This course aims to provide specific knowledge required for and Charles (Chip) Aquadro (2014). Genetics: From
bioinformatics students to learn advanced aspects in Genes to Genomes.
bioinformatics programming. It covers the techniques used
for bioinformatics programming; and instruction on the
techniques and the use of tools for accessing, searching SIV 3011 CURRENT TOPICS IN BIOINFORMATICS
and retrieving information from biological databases and
the submission of new entries. Besides that, it also This course covers special topics concerning currents
introduces the scripting languages commonly used in issues in Bioinformatics. It headed towards special topics
Bioinformatics such as Perl, Python and Java. The libraries that introduce bioinformatics. Importance is as well given to
and toolkits relating to the scripting languages will be also the latest research areas in bioinformatics. Topics are
introduced such BioPerl, Biopython and BioJava. Various delivered in a series of seminars followed by exercises and
problems related to Bioinformatics are considered to be assignments.
solved using one of the scripting programming languages.
Assessment Methods:
Assessment Methods: Continuous Assessment: 100%
Continuous Assessment: 60%
Final Examination: 40% Medium of Instruction:
English
Medium of Instruction:
English SIV 2012 BIOIMAGE PROCESSING AND ANALYSIS

Main References: This course aims to introduce the concepts in image
1. Keith Bradnam and Ian Korf (2012). UNIX and Perl to processing and analysis, specifically on biological images.
the Rescue: A Field Guide for the Life Sciences. It covers the introduction of the digital image
Cambridge University Press representation, processing and analysis. Various problems
2. Brian D foy, Randal L. Schwartz and Tom Phoenix related to biological images are considered to be solved
(2011). Learning Perl. Sixth Edition. O'Reilly Media using programming language such as Matlab and C++, as
3. Mitchell L Model (2010). Bioinformatics Programming well as image processing and analysis software such as
Using Python. O’Reilly Media. ImageJ and Adobe Photoshop.

Assessment Methods:
SIV 3005 BIOMOLECULAR MODELLING
Continuous Assessment: 60%
This course covers the following topics: The concepts of Final Examination: 40%
molecular viewer and protein databases; The structure of
biomolecules especially proteins; Protein structure Medium of Instruction:
determination and prediction; Applications of biomolecular English
modeling in drugs and vaccine development and design.
Main References:
Assessment Methods: 1. Rafael C. Gonzalez & Richard E. Woods (2012).
Continuous Assessment: 40% Digital Image Processing. 3rd ed. Pearson Education.
Final Examination: 60% 2. Chris Solomon & Toby Breckon (2013). Fundamental
of Digital Image Processing: A Practical Approach with
Medium of Instruction: Examples in Matlab. Wiley-Blackwell.
English 3. Omer Demirkaya, Musa H. Asyali, Prasanna K. Sahoo
(2012). Image Processing with MATLAB: Applications
in Medicine and Biology. CRC Press.

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