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

  
  

  Fatema Tuj Johora
  

  Assistant Professor
  

  Computer Science & Engineering 
  Daffodil International University

  Office: Room # 705, AB-4, Daffodil Smart City(DSC)

             Cell Number  : +880 1315689508

             Email: fatema.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 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 section Important Tasks Along with Date

  Important Tasks Along with Date

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• Select section Week 1: Getting Introduced

  Week 1: Getting Introduced

  • Select activity Introduction to Biology &amp; Chemistry for Computation

    

    Introduction to Biology & Chemistry for Computation Page

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  • Select activity All Resources - Click Here

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    All Resources - Click Here

• Select section Assignment and Presentation

  Assignment and Presentation

  • Select activity Assignment on Bio Informatics

    

    Assignment on Bio Informatics

    Opened: Monday, 24 February 2025, 12:00 AM

    Due: Saturday, 15 March 2025, 12:00 AM

    Completion

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    Collect the Previous 2 semester's questions (Final Exam) and submit them as an assignment (pdf)

  • Select activity Presentation

    

    Presentation Assignment

    Opened: Monday, 24 February 2025, 12:00 AM

    Due: Saturday, 22 March 2025, 12:00 PM

    Completion

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    Mark as done
• Select section Week 1 &amp; 2 (Lecture 1.1, 1.2 &amp; 1.3)

  Week 1 & 2 (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
    

    Importance of Computers in Chemical Industries
    

           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 Demo Quiz || Wait for Announcement

  Demo Quiz || Wait for Announcement

  • Select activity First Demo Quiz CSE 115

    

    First Demo Quiz CSE 115

    Opened: Thursday, 6 February 2025, 9:00 AM

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• Select section Week 3 (Lecture 2.1 and Lecture 2.2)

  Week 3 (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 Lecture 2.2

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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 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 activity APPlication Name Assignment 1 | 65-E

    

    APPlication Name Assignment 1 | 65-E

    Opened: Saturday, 25 January 2025, 11:00 PM

    Due: Sunday, 2 February 2025, 1:00 PM

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• Select section Week 4 &amp; 5 (Lecture 3.1 and Lecture 3.2)

  Week 4 & 5 (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 Lecture 3.2

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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 Quiz 1 | 65-E

    

    Quiz 1 | 65-E Assignment

    Opened: Saturday, 1 March 2025, 10:00 PM

    Due: Sunday, 9 March 2025, 1:00 PM

    Completion

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    Mark as done
• Select section Week 7 (Lecture 5.1 and Lecture 5.2)

  Week 7 (Lecture 5.1 and Lecture 5.2)

  • Select activity Lecture 5.1

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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 (Molecular Mechanics & Quantum Mechanics)

    Computational Chemistry Methods (MM & QM)
    

    • Click here to download Lecture 5.1

    • Click here to download Lecture 5.2

    
    

• Select section Week 8: Students Discussion &amp; Forum

  Week 8: Students Discussion & Forum

  • Select activity Discussion About Sequence Alignment Technique

    

    Discussion About Sequence Alignment Technique Forum

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• Select section Week 9: Review Class &amp; Mid-Term Examination

  Week 9: Review Class & Mid-Term Examination

  • Select activity Attend Review Class

    

    Attend Review Class Page

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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 10 (Lecture 4.1 and Lecture 4.2)

  Week 10 (Lecture 4.1 and Lecture 4.2)

  • Select activity Lecture 4.1

    Completion

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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 section Week 10 (Lecture 6.1)

  Week 10 (Lecture 6.1)

  • Select activity Lecture 7 Gene Duplication and Read Mapping

    Completion

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    Lecture 7 Gene Duplication and Read Mapping

  • Select activity Lecture 6.1 Gene Duplication and Read Mapping

    

    Lecture 6.1 Gene Duplication and Read Mapping Page

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    Click here to download the slide

  • Select activity Video Presentation on Lecture 6.1

    

    Video Presentation on Lecture 6.1 Page

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    Keyword Tree || Read Mapping ||Genome Indexing

    Burrows Wheeler Transform(BWT) 
    

    
    

  • Select activity Gene Duplication

    

    Gene Duplication Forum

    Completion

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    Please Reply The Forum Question. 

  • Select activity Class Recording 1st October, 2023

    

    Class Recording 1st October, 2023 URL

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• Select section Week 12 (Lecture 6.2 DNA Database Searching)

  Week 12 (Lecture 6.2 DNA Database Searching)

  • Select activity Lecture 8: DNA Database Searching

    Completion

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    Lecture 8: DNA Database Searching

  • Select activity Lecture 6.2 DNA Database Searching

    

    Lecture 6.2 DNA Database Searching Page

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    DNA Database Searching

    ● FASTA
    

    Click here to download slide on lecture 6.2

    Practice:

    1. Discover the similarity between the two sequences by applying FASTA:
    
    Sequence 1 (Tiger): TAACGAC
    Sequence 2 (Cat): CAGTAAC

    2.  Apply FAASTA algorithm, for the given sequences:
    Sequence 1 (Tiger): GAATCAAT
    Sequence 2 (Cat): CAATGAC
    

  • Select activity Video Presentation on Lecture 6.2: FASTA

    

    Video Presentation on Lecture 6.2: FASTA Page

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  • Select activity Online class recording | 15th Noember

    

    Online class recording | 15th Noember URL

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• Select section Week 12 (Lecture 7.1 Importance of Computation in Chemical Industries)

  Week 12 (Lecture 7.1 Importance of Computation in Chemical Industries)

  • Select activity Lecture 7.1 Importance of Computation in Chemical ...

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    Lecture 7.1 Importance of Computation in Chemical Industries

  • Select activity Lecture 7.1 Importance of Computation in Chemical Industries

    

    Lecture 7.1 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 7.1

  • Select activity Video presentation on Lecture 7.1

    

    Video presentation on Lecture 7.1 Page

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  • Select activity 16th November class |

    

    16th November class | URL

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• Select section Quiz Test (Online Mood) || Wait for Announcement

  Quiz Test (Online Mood) || Wait for Announcement
• Select section Week 13 (Lecture 10: Computer graphics for Molecular modelling)

  Week 13 (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 8.1: Computer graphics for Molecular modelling

    

    Class Lecture Slide on Lecture 8.1: Computer graphics for Molecular modelling Page

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    Computer graphics for Molecular modelling
    

    Click here to download the slide on Lecture 8.1

  • Select activity Video Presentation on Lecture 8.1 (Computer graphics for Molecular modelling)

    

    Video Presentation on Lecture 8.1 (Computer graphics for Molecular modelling) Page

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• Select section Week 14 (Presentation and Quiz)

  Week 14 (Presentation and Quiz)

  • Select activity Online Presentation on Gene Duplication and FASTA

    Completion

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    Online Presentation on Gene Duplication and FASTA

  • Select activity Quiz 3 MCQ | Online attempt | 9.00 PM to 9.15 PM

    

    Quiz 3 MCQ | Online attempt | 9.00 PM to 9.15 PM URL

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    Quiz Form 

    https://forms.gle/Ru3YS7j5jKTviSBb8
    

• Select section Week 15 (Review Class)

  Week 15 (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 activity Assignment

    

    Assignment

    Opens: Saturday, 31 May 2025, 1:59 AM

    Due: Saturday, 7 June 2025, 1:59 PM

    Completion

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• Select section Week 16 (Final Exam)

  Week 16 (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.