An Introduction to application of MATLAB in biological realms

 

An Introduction to application of MATLAB in biological realms: programming skills and bioinformatics toolbox

By Oveis Jamialahmadi, M.Sc. student of Biotechnology Engineering, Tarbiat Modares University.

 

Room# 5002

Faculty of  Biological Sciences

Tarbiat Modares Universitty

 

**  For registration contact with N. Niknam (niloofae_niknam {at} yahoo.com)

 

Oct. 18, 2012

8 – 8:45

An introduction to MATLAB software:

·           What is MATLAB and what are its benefits to scientific and engineering fields?

·           Advantages or programming with MATLAB over other programming languages.

·           Getting familiar with MATLAB: Command window, Workspace, Command history and Scripts.

·           How to learn MATLAB by getting a little assistance from MATLAB Help.

Using MATLAB as a tool for programming:

·           What is programming and how a program is created?

·           MATLAB, a flexible tool for programming: Scripts, Functions and Toolboxes.

 

8:45 – 9

Break

9 – 9:45

An introduction to programming with MATLAB: programming fundamentals

·           Basic programming components.

·           Program control statements:

–          Operators and special characters.

–          Conditional control.

–          Loop control.

9:45 – 10

Break

10 – 10:45

Matrices:

·           Importance of matrix as a basic concept of programming with massive data information.

10:45 – 11:15

Break

11:15 – 12

Matrices:

·           Begin to input and interpret matrices in MATLAB.

Strings:

·           Creating character arrays.

 

13:30 – 14:15

Structures:

·           What are structures and why they are important to handle massive data?

14:15 – 14:30

Break

 

14:30 – 15:15

Structures:

  • How to create structures and manipulate them.
  • How they can be useful to bioinformatics?

Cell arrays:

·         What is a cell array?

 

15:15 – 15:30

Break

 

15:30 – 16:15

Cell arrays:

  • Cell array operations
  • Examples

 

16:15 – 16:30

Break

 

16:30 – 17:15

Functions:

  • How to write, recall and manipulate them.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Oct. 20, 2012  

8 – 8:45

An introduction to Bioinformatics toolbox of MATLAB:

  • What are features of Bioinformatics toolbox of MATLAB?

–          Data formats and databases and manipulate them.

  • Data formats and databases: how to work with?

–          Web-based databases: GeneBank, EMBL, PDB…

–          Reading and writing data formats.

 

8-45 – 9

Break

 

9 – 9:45

Sequence alignments:

  • Functions needed to do this purpose, an example.

Sequence utilities and statistics:

  • Manipulate and analyze sequences.

 

9:45 – 10

Break

 

10 – 10:45

Sequence utilities and statistics:

  • Sequence conversion, manipulation and statistics.

Protein property analysis:

  • Some useful functions.

10:45 – 11:15

Break

 

11:15 – 12

Protein property analysis:

  • Protein plot and Molecular viewer: two graphical user interfaces for protein analysis.
  • Visualizing the three-dimensional structure of a molecule, a good example of molecular viewer.

 

13:30 – 14:15

Phylogenetic analysis. 

14:15 – 14:30

Break

 

14:30 – 15:15

An introduction to Graph Visualization, view relationship between your own data.Figures: Why they are important? 

 

15:15 – 15:30

Break

 

15:30 – 17

Review some advanced demo of bioinformatics toolbox examples