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BIF601 : Bioinformatics Computing I

Course Overview

Course Synopsis

This course aims to introduce the concepts of data representation, searching, security and ownership. Develop techniques for pattern matching, recognition and their applications in bioinformatics.

Course Learning Outcomes

At the end of the course, you will have good understanding of following modules

  • Databases and Data management
  • Networks, communications models, transmissions technology, protocols, and , geographical scope
  • Search engines. search process, search engine technology, searching and information theory
  • Computational methods, knowledge management, sequence and structure visualization
  • Data mining methods and technology
  • Pattern recognition, discovery, and pattern matching
  • Dot matrix analysis and substitution matrices
  • Dynamic programming and Scripting

Course Calendar

1 Database
2 Database Advantages

4 Database Software
3 Data Management

5 Computer Network
6 Data communication (Part I)

7 Data communication (Part II)
8 Communication tasks and protocols

9 Topology
10 Topology and Transmission modes

11 Geographical Scope and Communication Models
12 Communication Models and transmission Technology

13 Communication Models and transmission Technology-II
14 Communication Models and transmission Technology-III

15 Bandwidth/Frequency Spectrum
16 Network Security

17 Information retrieval and Search engines
18 informationretrievalintro
19 IRModels
20 IRevaluationMeasures
21 IRinBiologicalDBs

22 IRinBioinformatics
23 searchengines
24 MLEvaluation
25 searchenginecategories
26 EMRs
27 EHRs
28 Knowledge discovery
29 knowledgediscoverytechniques
30 Bayes’ theorem
31 Decision Tree
32 Neuralnetworks

33 Association rule
34 Clustering
35 Machinelearning
36 Mlapplications
37 MLOtherApplications
38 Data integration
39 Problems with data integration
40 Pattern Finding
41 Brute Force Algo
42 KMP Algo
43 KMP Prefix function

44 KMP Matcher
45 Boyer Moore Algo
46 Dot Plots
47 Scoring Scheme
48 Substitution Matrices
49 Optimal Algos
50 Needleman_wunch Algos
51 Needleman_wunch Execution
52 Smith_waterman Algo
53 PSA Complex Models
54 ComputerPrograms

55 Programminglanguages
56 JavaIntroduction
57 AnatomoyofJavaProgram
58 Introduction to BioJava
59 Alphabets, Symbols and Sequences
60 CentralDogma
61 SequenceInputOutput
62 FeaturesandAnnotations
63 Protein structure modules
64 AlignmentModule

65 Matlab introduction
66 MatlabBasics
67 BioInformaticsToolbox
68 Features and functions
69 bioinfarmaticstasks
70 Phylogenticanalysis
71 proteinsandaas
72 Intoduction To Python
73 PythonBasics
74 BioPythonBasics

75 Intoduction To BioPython
76 SequenceObject
77 Phylogenetic tree IO
78 PHP part-1-I
79 PHP part-1-II
80 PHP part-2
81 Perl Basics
82 Unix/Linux Commands
83 Shell Scripting
84 Multiple Sequence Alignment

85 More on Multiple Sequence Alignment
86 Progressive Alignment for MSA
87 MSA Example
88 CLUSTAL
89 Structure Visualization - I
90 Structure Visualization - II
91 Experimental Determination of Protein Structure
92 Protein Data Bank
93 Visualization Techniques
94 Online Resources for Protein Visualization
95 Types of Protein Visualizations

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