Topic outline

  • Welcome to Introduction to Biology & Chemistry for Computation


    • Course Instructor's Information:

      Instructor Name   : Nushrat Jahan Ria (NJR)                                              
      Designation           : Lecturer  
      Office Address       : Room 505 AB4 Building, DIU
      Contact No            : 01521201557
      Email                     : nushratria.cse@diu.edu.bd

      Website                  : https://faculty.daffodilvarsity.edu.bd/profile/cse/

      Whatsapp              : 01521201557

      Telegram               : 01521201557

      Appointment         :  


      		 Course Teacher


      Welcome Message From Your Teacher

             

           

        


      Basic Information:

      Course Code: CSE115
      Program: B.Sc in Computer Science and Engineering
      Faculty: Science and Information Technology
      Semester: Summer; Year: 2022
      Credit: 2.0; Contact Hour: 3 Hours/ Week
      Course Category: Core Engineering
       

      Course Rationale:

      Introduction to Biology & Chemistry for Computation has been the most used methods of incorporating intelligence of chemistry & the biological world to computer science. It is, therefore, necessary to develop a good understanding of their operation and how they can be used as building blocks for the computerized application of biology and chemistry. This course explores the inner workings of chemistry and biological world from the programmer’s perspective by implementing different algorithms of Computer Science.

       

      Course Objectives:

      To provide a solid conceptual understanding of biology and chemistry for computation. More specifically,

        • To gather knowledge about chemistry & biological world and relation with Computer Science and Engineering 
        • To analyze some existing methods and algorithms for specific chemistry & biological problems
        • To grow the research interest in the field of Bioinformatics, Biochemistry and the Chemical industry
        • To know the scope of the bioinformatics, bio chemistry and chemical industry research area and motivate them for research work.


      Course Learning Outcomes (CLO's):

      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.

      Assessment Strategies:



      Reference Book:

      Computational Chemistry

      An Introduction to Bioinformatics Algorithm


      Additional Support for Students



  • Week 1


    Lesson plan:

    • Lecture 01: Getting introduced to the student
    • Lecture 02: Introduction: Scope of Computer in Chemistry
    • and Biology

    Expected Learning Outcome:

    • Students will search over the internet about different aspects of Biology and chemistry for computing.

    • Introduction class

    Assignment 1 given in the class

    Additional Materials:

    Computational Chemistry at the University of Cambridge and the Essential Skills for Chemists video:


    What is COMPUTATIONAL BIOLOGY? What does COMPUTATIONAL BIOLOGY mean? video:



    • Discussion Forum

      Write 2 applications name where computation is used in chemistry or biology field?

  • Week 2, 3


    Lesson plan:

    • Lecture 01: Molecular and Cellular Biology
    • Lecture 02: Role of chemistry in computer science & engineering

    ● Uses and effects of chemistry

    ● Benefits of Chemistry

    ● Applications of Chemistry

    Expected Learning Outcome:

    • Students will learn important keywords.

    Additional Materials:


    Videos


  • Week 4

    Lesson plan:

    • Lecture 01 & 02: DNA Sequencing Techniques

    Expected Learning Outcome:

    • Review Feedback on the topic.

    Additional Materials:

    Video

  • Week 5

    Lesson plan:

    • Sequence Alignment Basics:
    • Global Alignment Basics
    • Local Alignment Basics

    Expected Learning Outcome:

    • Students will learn important keywords.

    Additional Materials:

    Video

    • Global Local Alignment Homework Assignment
      Opened: Friday, 27 May 2022, 12:00 AM
      Due: Friday, 3 June 2022, 12:00 AM

      Align the following sequences using global and local alignments:

      seq 1: AATTCA

      seq 2: AATGA

      Submit your answer here


  • Week 6

    Lesson plan:

    • Introduction to Computational Chemistry
    • Lecture 01: ● History of Computational Chemistry ● Fields of Application
    • Lecture 02: ● Computational Chemistry Methods ○ Ab Initio Methods ○ Density Functional Methods ○ Semi-empirical Methods ● Software Packages

    Expected Learning Outcome:

    • Students will learn important keywords.

    Additional Materials:

    Video

    • Midterm Week

      Midterm Exam


      • Week 7

        Lesson plan:

        • Gene Duplication and read Mapping

        Expected Learning Outcome:

        • Students will learn important keywords.


        Additional Material:

        • Week 8

          Lesson plan:

          • DNA Database Searching
                         ● FASTA

          Expected Learning Outcome:

          • Students will learn important keywords.


          • Week 9

            Lesson plan:

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

            Expected Learning Outcome:

            • Students will learn important keywords.

          • Final Week

            Final Exam


            • Topic 11

              • Topic 12

                • Topic 13

                  • Topic 14

                    • Topic 15

                      • Topic 16

                        • Topic 17

                          • Topic 18

                            • Topic 19

                              • Topic 20