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Computing for life
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computing.md

Computing for Life

Week-1: Linux

  • Introduction To Linux

  • Why Linux Over Windows?

  • Installing UBUNTU-19.04

    • Option-1: In VirtualBox
      • Minumum Laptop Config: RAM=4GB, PRO= i3, HDD or SSD?, SSD=MUST(For Good Performance In VirtualBox)
    • Option-2: Dual Boot(Alongside Windowns)
      • Minimum Laptop Config: RAM=4GB, PRO= i3, HDD or SSD?, SSD=Recommended, FreeSpace=50GB+
    • Option-3: Fresh Installation
      • Minimum Laptop Config: RAM=4GB, PRO= i3, HDD or SSD?, SSD=+, HDD=500GB

  • An overview of UBUNTU-19.04 & Directory Structure

  • Basic Linux Commands

    • Listing Files and Directories
    • Handling Files and Directories

  • Command Arguments

  • Finding Files

  • Selecting Lines Using grep Command

  • Redirection

  • chmod options

Week-2: Version Control & Python Environment Setup

  • Installing Anaconda Python Distribution & Jupyter Notebook
    • An Overview of Jupyter Notebook
    • Introduction To Jupyter Markdown(For Documentation)
    • Introduction To Jupyter LaTex(For Basic Maths and Chemicak Equations)
  • What is Version Control & Why it is so important?
  • Intro To Git & Github
  • Installing Git
  • Basic Git Commands
  • Branching
  • Working With Team
  • Creating a Github Repository & Push Projects

Week-3&4: Basic Math for Programming & Python

  • Introduction To Numbers

    • Integer Numbers
    • Floating Point Numbers
    • Positive Numbers
    • Negative Numbers
    • Even Numbers
    • Odd Numbers
    • Prime Numbers
    • Complex Numbers
    • Fibonacci Series
    • Logarithms
    • Sets
    • Functions

  • Python Basics

    • Variables
    • Python Keywords and Identifiers
    • Data Types
      • Numbers
      • Strings
      • List
      • Tuple
      • Dictionary
      • Sets
    • Input, Output, Import
    • Operators
      • Arithmetic operators
      • Comparison operators
      • Logical operators
      • Assignment operators
      • Identity operators
      • Membership operators

  • Python Flow Control

    • if..else
    • for loop
    • Detail About range() function
    • while loop
    • break & continue
    • pass

  • Functions

    • Built-in Functions VS User Defined Functions

  • Python Built-in Data Structure(Detail)

    • List
    • Sets
    • Dictionary
    • Tuples

  • Files Handling

    • Working with CSV files
    • Working with FASTA files
    • Working with simple text files

  • Pattern Mathcing

  • Object Oriented Concepts(Advance)

Week-5: Python for Biological Problems(Practical Problem Solving)

  • Counting Letters (A, T, C, G) in DNA Sequence
  • Calculating AT Content
  • Calculating GC Content
  • Complementing DNA
  • Restriction Fragment Lengths
  • Splicing Out Introns(Part-1)
  • Splicing Out Introns(Part-2)
  • Splicing Out Introns(Part-3)
  • Splitting Genomic DNA
  • Writing FASTA file
  • Writing Multiple FASTA Files
  • Processing DNA in a File
  • Multiple exons From Genomic DNA
  • Percentage of Amino Acid Residues(Part-1)
  • Percentage of Amino Acid Residues(Part-2)
  • Several Species
  • Lenght Range
  • AT Content
  • Complex Condition
  • High, Low, Medium
  • DNA Translation
  • Bining DNA Sequences
  • K-mer Counting

Week-6: Biopython for Bioinformatics

  • What is Biopython?
  • Advantage of Biopython
  • Working With Sequence
    • DNA Nucleotides and Strands
    • Turning DNA sequences into Protein sequences
    • RNA Transcription and Translation
    • DNA Sequence Data Analysis
    • Pairwise Sequence Alignment
    • Multiple Sequence Alignment
    • How to create a sequence object?
    • How to reverse and transcribe a DNA sequence?
    • How to translate an RNA sequence into protein?
    • How to create a sequence record?
    • How to read sequence files in different formats?
    • How to write formatted sequence files?
  • Molecular Phylogenetics using Bio.Phylo
  • Retrieving Data from Web Resources
    • How to read sequence files from web?
    • How to submit PubMed queries?
    • How to submit queries to the NCBI nucleotide database
    • How to retrieve Uniport records and write them to a file

Week-7: Statistics for Data Analysis

  • What is statistics?

  • Classification of statistics

  • What is Data?

  • Classification of Data

  • Where do data come from?

  • Variable types

  • Measures of Central Value

    • Mean, Mode, Median

  • Measures of Spread

    • The Range
    • Quartiles & Interquartile Range
    • Percentiles
    • Standard Deviation
    • Variance
    • Correlation

  • Multivariate Categorical Data

  • Univariate Categorical Data

  • Sample & Population

    • Sampling form well defined populations

  • Survey & Census

  • Probability Sampling

  • Non-Probability Smapling

  • The Binomial Distribution

  • The Normal Distribution

    Week-8: NumPy(Scientific Computing)

    • NumPy Array
    • Creating NumPy Arrays
    • Initial Placeholders
    • Saving and loading on disk
    • Data Types
    • Inspecting Array
    • Asking Help?
    • Array Mathematics
      • Arithmetics Operations
      • Comparison
      • Aggregate Functions
    • Copying Array
    • Sorting Arrays
    • Subsetting, Slicing, Indexing
    • Array Manipulation
    • Examples, Problem Solving

Week-9: Pandas(Data Analysis)

  • Pandas Data Structures
    • Series
    • DataFrame
  • Read and Write CSV
  • Read Multiple Files
  • Asking Help?
  • Selecting
  • Boolean Indexing
  • Dropping
  • Sort & Rank
  • Series & DataFrame Informations
  • Applying Functions
  • Data Alignment

Week-10: Matplotlib & Seaborn(Data Visualization)

  • Introduction To Matplotlib & Creating Publication Quality Graphs
    • Bar Graph
    • Join Bar Graph
    • Histograms
    • Line Plot
    • Scatter Plot
    • Pie Chart
    • Box Plot
    • Heatmap
    • And More...
  • Data Visualization With Seaborn(Based Matplotlib)

Week-11: Projects

  • P1-Zika Virus Dataset Analysis
  • P2-Disease Related Dataset Analysis

Week-12: Scientific Typesetting for Document Preparation

  • Intro To LaTex
  • Why LaTex?
  • Comparison With Other Typesetting System(Like MS Word)
  • Spaces, New Lines & Special Characters
  • List Item
  • Document Structure
  • Comments
  • Justifications and Alignment
  • Section, Subsection, Subsubsection
  • Tables
  • Figures
  • Matrices
  • Math Equations
  • Chemical Equations
  • Algorithms
  • Example-1: Lab Report
  • Example-2: Research Paper
  • Example-2: Presentation
  • Example-2: CV
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