Section outline

• Select section Welcome to Introduction to Biology and Chemistry for Computation Theory Course

  Welcome to Introduction to Biology and Chemistry for Computation Theory Course

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  Course Instructor Information

  Welcome, Message!!!

  
  

  Mayen Uddin Mojumdar

  Lecturer 
  Computer Science & Engineering 
  Daffodil International University

  Office: Room # 505, AB-4, Daffodil Smart City(DSC)

             Cell Number (WhatsApp & Telegram) : +880 1402113506

             Email: mayen.cse@diu.edu.bd

  
  

  
  

  
  

  Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences. It also exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.

  This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps.
  

  Today, we have new types of surveys and laboratories including “in silico studies” and “dry labs” in which bioinformaticians conduct their investigations to gain invaluable outcomes. These features have led to 3-dimensioned illustrations of different molecules and complexes to get a better understanding of nature.

  
  

  Course Learning Outcome: (at the end of the course, students will be able to do :) 
  

  CLO1	Understanding the implications, impacts and benefits of Chemistry and Biology for Computation.
  CLO2	Learn the basics of Molecular and Cellular Biology.
  CLO3	Differentiate among different Computational Chemistry methods.
  CLO4	Implement Different Algorithms related to Computational Biology.
  CLO5	Be familiar with the importance of computation in Chemical Industries.

  
  
  

  
  Grading System:

  Theory Course	Lab Course
  Class Attendance: 7%	Class Attendance: 10%
  Class Tests/Quizes: 15%	Lab Final + Viva: 40%
  Assignment: 5%	Lab Performance & Lab Assignment: 25%
  Presentation: 8%	Project Submission + Viva: 25%
  Midterm Examination: 25%
  Final Examination: 40%

  
  Attendance: will be based on class attendance and weekly class feedback
  Class Test/Quiz: will be based on the BLC online test
  Assignment: will be based on class performance and assignment submission
  Presentation: will be based on the team presentation
  Mid and Final Exam: open book class studies
  Lab: will be based on project work, performances, tests, and Viva
  

  Academic Honesty
  1. Ensure Plagiarism < 20%
  2. Reflect on self-understanding
  3. Avoid all unfair means to ensure the growth of your positive mindset

  
  

  • Select activity Announcements

    

    Announcements Forum
  • Select activity Announcements

    

    Announcements Forum
  • Select activity CO-PO, Course Outcome and Contents with Completion Plan

    

    CO-PO, Course Outcome and Contents with Completion Plan File

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    Please download the file and read before starting the course. By downloading this file, you'll know about the course plans and other information.

  • Select activity Book References

    

    Book References Page

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    Click here to download the books: "Introduction to Computational Chemistry"
    

    Click here to download the books: "An Introduction to Bioinformatics Algorithm"

    
    
    

  • Select activity Assignment no:01

    

    Assignment no:01

    Opened: Monday, 26 September 2022, 12:00 AM

    Due: Tuesday, 27 September 2022, 10:00 AM

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  • Select activity Class Test :03

    

    Class Test :03 Quiz

    Opened: Friday, 9 December 2022, 11:30 AM

    Closed: Friday, 9 December 2022, 11:50 AM

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  • Select activity Assignment :01

    

    Assignment :01

    Opened: Friday, 9 December 2022, 12:00 AM

    Due: Sunday, 11 December 2022, 12:00 AM

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  • Select activity Presentation

    

    Presentation Assignment

    Opened: Friday, 9 December 2022, 12:00 AM

    Due: Friday, 16 December 2022, 12:00 AM

    Completion

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    Mark as done
• Select section Week 1 (Lecture 1.1, 1.2 &amp; 1.3)

  Week 1 (Lecture 1.1, 1.2 & 1.3)

  • Select activity Lecture 1.1, 1.2 &amp; 1.3

    

    Lecture 1.1, 1.2 & 1.3 Page

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    Introduction to Chemistry & Biology for Computation

          Click here to download Lecture 1.1
    

    Role of chemistry in Computer science
    

           Click here to download Lecture 1.2

    Role of chemistry in computer science & engineering 
    

           Click here to download Lecture 1.3

    
    

  • Select activity Video Lecture: Introduction to Computational Chemistry

    

    Video Lecture: Introduction to Computational Chemistry Page

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  • Select activity Video Lecture: Introduction to Computational Biology

    

    Video Lecture: Introduction to Computational Biology Page

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• Select section Discussion Forum

  Discussion Forum

  • Select activity Understanding Bioinformatics

    

    Understanding Bioinformatics Forum

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    Do you want to be a Bioinformatician? If yes/no, write shortly regarding your opinion.

• Select section Demo Quiz

  Demo Quiz

  • Select activity First Demo Quiz CSE 115

    

    First Demo Quiz CSE 115

    Opened: Sunday, 16 October 2022, 7:00 PM

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• Select section Week 2 (Lecture 2.1 and Lecture 2.2)

  Week 2 (Lecture 2.1 and Lecture 2.2)

  • Select activity Lecture 2.1

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    Lecture 2.1

  • Select activity Lecture 2.1

    

    Lecture 2.1 Page

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    Role of chemistry in computer science & engineering
    

    Click here to download Lecture 2.1
    

  • Select activity Video Lecture 2.1 Role of chemistry in computer science &amp; engineering

    

    Video Lecture 2.1 Role of chemistry in computer science & engineering Page

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  • Select activity Lecture 2.2

    Completion

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    Lecture 2.2

    
    

  • Select activity Lecture 2.2 Presentation Slide

    

    Lecture 2.2 Presentation Slide Page

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    Molecular and Cellular Biology (DNA Double Helix, DNA Replication )

    Click here to download Lecture 2.2

  • Select activity Video Lecture 2.2 Molecular and Cellular Biology (DNA Replication)

    

    Video Lecture 2.2 Molecular and Cellular Biology (DNA Replication) Page

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• Select section Discussion Forum

  Discussion Forum

  • Select activity Regarding DNA Replication

    

    Regarding DNA Replication Forum

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    If DNA replication is stopped! Then is it okey for biological world? 

• Select section Week 3 (Lecture 3.1 and Lecture 3.2)

  Week 3 (Lecture 3.1 and Lecture 3.2)

  • Select activity Lecture 3.1

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    Lecture 3.1

  • Select activity Presentation Slide on Lecture 3.1

    

    Presentation Slide on Lecture 3.1 Page

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     DNA Sequencing (Sanger Method)
    

    Click here to download Lecture 3.1

  • Select activity Video Presentation of Lecture 3.1 DNA Sequencing (Sanger Method)

    

    Video Presentation of Lecture 3.1 DNA Sequencing (Sanger Method) Page

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  • Select activity Lecture 3.2

    Completion

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    Lecture 3.2

  • Select activity Presentation Slide on Lecture 3.2

    

    Presentation Slide on Lecture 3.2 Page

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    DNA Sequencing (First, Second & Third Generation Sequencing)

    Click here to download Lecture 3.2

    
    

  • Select activity Video Presentation on Lecture 3.2 DNA Sequencing (First, Second &amp; Third Generation Sequencing)

    

    Video Presentation on Lecture 3.2 DNA Sequencing (First, Second & Third Generation Sequencing) Page

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• Select section Class Test/Quiz

  Class Test/Quiz

  • Select activity Class/Quiz Test 2

    

    Class/Quiz Test 2 Page

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    Offline Quiz Test 

    Date: 25.09.2022, Time: 30 Minutes, Marks: 15

    Syllabus: Lecture 1.1, 1.2, 1.3, 2.1, 2.2 (See Google Drive Link & BLC)

• Select section Week 4 (Lecture 4.1 and Lecture 4.2)

  Week 4 (Lecture 4.1 and Lecture 4.2)

  • Select activity Lecture 4.1

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    Lecture 4.1

  • Select activity Presentation Slide on Lecture 4.1

    

    Presentation Slide on Lecture 4.1 Page

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    Sequence Alignment (Global And Local)
    

    Click here to download Lecture 4.1

  • Select activity Video Presentation on Lecture 4.1 DNA Sequence Alignment (Needleman-Wunsch)

    

    Video Presentation on Lecture 4.1 DNA Sequence Alignment (Needleman-Wunsch) Page

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  • Select activity Video Presentation on Lecture 4.2 DNA Sequence Alignment (Smith-Waterman) Method

    

    Video Presentation on Lecture 4.2 DNA Sequence Alignment (Smith-Waterman) Method Page

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• Select section Week 5 (Lecture 5.1 and Lecture 5.2)

  Week 5 (Lecture 5.1 and Lecture 5.2)

  • Select activity Lecture 5.1

    Completion

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    Lecture 5.1

  • Select activity Presentation Slide on Lecture 5.1 &amp; 5.2

    

    Presentation Slide on Lecture 5.1 & 5.2 Page

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    Computational Chemistry Methods (MM & QM)
    

    • Click here to download Lecture 5.1 & 5.2
      

    
    
    

  • Select activity Video Presentation on Lecture 5.1 Computational Chemistry Methods (Molecular Mechanics, Molecular Dynamics, Quantum Mechanics)

    

    Video Presentation on Lecture 5.1 Computational Chemistry Methods (Molecular Mechanics, Molecular Dynamics, Quantum Mechanics) Page

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  • Select activity Video Presentation on Lecture 5.2 Quantum Mechanics, AB Initio Method, Hartree Fock, Density Functional Theory &amp; Semi-Empirical Method

    

    Video Presentation on Lecture 5.2 Quantum Mechanics, AB Initio Method, Hartree Fock, Density Functional Theory & Semi-Empirical Method Page

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• Select section Week 6: Quiz/Class Test

  Week 6: Quiz/Class Test

  Quiz/Class Test Details 

  
  

  Your Quiz/Class Test will be taken with the following syllabus:

  Slides: Introduction, Role of Chemistry in Computer Science, Molecular and Cellular Biology (DNA Replication) and DNA Sequencing.

  (Lecture 2.1 to Lecture 3.2 in BLC)

  Please see the slides in BLC along with existing videos.

  
  

  Youtube Channel Link https://www.youtube.com/channel/UCjsgqdQzzpejXrHGXRMhHNA

  
  

  Question Pattern: 

  MCQ, Fill in the Blank, True/False, Short Question

  Total Marks: 20 (Will be Converted to 15)

  
  Exam Time: 19.8.2022 at 08:00PM (BDT), Place: BLC Module
  
• Select section Week 6: Quiz/Class Test (Click Below to Start Quiz Test)

  Week 6: Quiz/Class Test (Click Below to Start Quiz Test)

  • Select activity Quiz/Class Test

    

    Quiz/Class Test

    Opened: Sunday, 20 November 2022, 8:00 PM

    Completion

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    Quiz/Class Test Marks Distribution

    MCQ - 7 Question (1 Marks Equivalent) =7

    True/False- 2 (1 Marks Equivalent) =2

    Short Question- 3+3+5= 11

    Total Marks= 20 (Will be converted to 15)

    Time: 40 Minutes

    
    

• Select section Week 6: Review Class

  Week 6: Review Class

  • Select activity Attend Review Class

    

    Attend Review Class Page

    Completion

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    Dear Students,

    Your formal classes before midterm examination has been ended. Please be prepared yourself for the review classes that will be held next.

    You can download and view all slides and youtube contents too.

    Youtube Channel Link https://www.youtube.com/channel/UCjsgqdQzzpejXrHGXRMhHNA
    

• Select section Week 6: Students Discussion &amp; Forum

  Week 6: Students Discussion & Forum

  • Select activity Discussion About Sequence Alignment Technique

    

    Discussion About Sequence Alignment Technique Forum

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• Select section Week 8 (Lecture 8)

  Week 8 (Lecture 8)

  • Select activity Lecture 7 Gene Duplication and Read Mapping

    Completion

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    Lecture 7 Gene Duplication and Read Mapping

  • Select activity Lecture 7 Gene Duplication and Read Mapping

    

    Lecture 7 Gene Duplication and Read Mapping Page

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    Click here to download the slide

  • Select activity Video Presentation on Lecture 7

    

    Video Presentation on Lecture 7 Page

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    Keyword Tree || Read Mapping ||Genome Indexing

    Burrows Wheeler Transform(BWT) 
    

    
    

• Select section Week 9 (Lecture 8 DNA Database Searching)

  Week 9 (Lecture 8 DNA Database Searching)

  • Select activity Lecture 8: DNA Database Searching

    Completion

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    Lecture 8: DNA Database Searching

  • Select activity Lecture 8 DNA Database Searching

    

    Lecture 8 DNA Database Searching Page

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    DNA Database Searching

    ● FASTA
    

    Click here to download slide on lecture 8

  • Select activity Video Presentation on Lecture 8: FASTA

    

    Video Presentation on Lecture 8: FASTA Page

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• Select section Week 10 (Lecture 9 Importance of Computation in Chemical Industries)

  Week 10 (Lecture 9 Importance of Computation in Chemical Industries)

  • Select activity Lecture 9 Importance of Computation in Chemical In...

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    Lecture 9 Importance of Computation in Chemical Industries

  • Select activity Lecture 9 Importance of Computation in Chemical Industries

    

    Lecture 9 Importance of Computation in Chemical Industries Page

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    Importance of Computation in Chemical Industries:
       ● DCS (distributed control system)
            ○ Fertilizer ○ Water Treatment ○ Chemical Plant
       ● Chromatography
    
    

    Click here to download the slide on lecture 9

  • Select activity Video presentation on Lecture 9

    

    Video presentation on Lecture 9 Page

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• Select section Week 11 (Lecture 10: Computer graphics for Molecular modelling)

  Week 11 (Lecture 10: Computer graphics for Molecular modelling)

  • Select activity Lecture 10: Computer graphics for Molecular modell...

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    Lecture 10: Computer graphics for Molecular modelling

  • Select activity Class Lecture Slide on Lecture 10: Computer graphics for Molecular modelling

    

    Class Lecture Slide on Lecture 10: Computer graphics for Molecular modelling Page

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    Computer graphics for Molecular modelling
    

    Click here to download the slide on Lecture 11

  • Select activity Video Presentation on Lecture 10 (Computer graphics for Molecular modelling)

    

    Video Presentation on Lecture 10 (Computer graphics for Molecular modelling) Page

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• Select section Week 12 (Presentation and Assignment)

  Week 12 (Presentation and Assignment)

  • Select activity Physical Presentation on Gene Duplication and FAST...

    Completion

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    Physical Presentation on Gene Duplication and FASTA

• Select section Week 13 (Review Class)

  Week 13 (Review Class)

  • Select activity Review Class on Midterm Exam TopicsReview Class on...

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    Review Class on Midterm Exam Topics

    Review Class on Final Exam Topics
    

• Select section Week 14 (Final Exam)

  Week 14 (Final Exam)

  • Select activity Final Examination(40 Marks)Read thoroughly the lec...

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    Final Examination
    

    (40 Marks)

    Read thoroughly the lecture slides as well as videos too.

    
    

    Thanks for staying with me.