ABI Bioinformatics Guide 2024
  • INTRODUCTION
    • How to use the guide
  • MOLECULAR BIOLOGY
    • The Cell
      • Cells and Their Organelles
      • Cell Specialisation
      • Quiz 1
    • Biological Molecules
      • Carbohydrates
      • Lipids
      • Nucleic Acids (DNA and RNA)
      • Quiz 2
      • Proteins
      • Catalysis of Biological Reactions
      • Quiz 3
    • Information Flow in the Cell
      • DNA Replication
      • Gene Expression: Transcription
      • Gene Expression: RNA Processing
      • Quiz 4
      • Chromatin and Chromosomes
      • Regulation of Gene Expression
      • Quiz 5
      • The Genetic Code
      • Gene Expression: Translation
    • Cell Cycle and Cell Division
      • Quiz 6
    • Mutations and Variations
      • Point mutations
      • Genotype-Phenotype Interactions
      • Quiz 7
  • PROGRAMMING
    • Python for Genomics
    • R programming (optional)
  • STATISTICS: THEORY
    • Introduction to Probability
      • Conditional Probability
      • Independent Events
    • Random Variables
      • Independent, Dependent and Controlled Variables
    • Data distribution PMF, PDF, CDF
    • Mean, Variance of a Random Variable
    • Some Common Distributions
    • Exploratory Statistics: Mean, Median, Quantiles, Variance/SD
    • Data Visualization
    • Confidence Intervals
    • Comparison tests, p-value, z-score
    • Multiple test correction: Bonferroni, FDR
    • Regression & Correlation
    • Dimentionality Reduction
      • PCA (Principal Component Analysis)
      • t-SNE (t-Distributed Stochastic Neighbor Embedding)
      • UMAP (Uniform Manifold Approximation and Projection)
    • QUIZ
  • STATISTICS & PROGRAMMING
  • BIOINFORMATICS ALGORITHMS
    • Introduction
    • DNA strings and sequencing file formats
    • Read alignment: exact matching
    • Indexing before alignment
    • Read alignment: approximate matching
    • Global and local alignment
  • NGS DATA ANALYSIS & FUNCTIONAL GENOMICS
    • Experimental Techniques
      • Polymerase Chain Reaction
      • Sanger (first generation) Sequencing Technologies
      • Next (second) Generation Sequencing technologies
      • The third generation of sequencing technologies
    • The Linux Command-line
      • Connecting to the Server
      • The Linux Command-Line For Beginners
      • The Bash Terminal
    • File formats, alignment, and genomic features
      • FASTA & FASTQ file formats
      • Basic Unix Commands for Genomics
      • Sequences and Genomic Features Part 1
      • Sequences and Genomic Features Part 2: SAMtools
      • Sequences and Genomic Features Part 3: BEDtools
    • Genetic variations & variant calling
      • Genomic Variations
      • Alignment and variant detection: Practical
      • Integrative Genomics Viewer
      • Variant Calling with GATK
    • RNA Sequencing & Gene expression
      • Gene expression and how we measure it
      • Gene expression quantification and normalization
      • Explorative analysis of gene expression
      • Differential expression analysis with DESeq2
      • Functional enrichment analysis
    • Single-cell Sequencing and Data Analysis
      • scRNA-seq Data Analysis Workflow
      • scRNA-seq Data Visualization Methods
  • FINAL REMARKS
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  • Installing a Virtual Machine
  • Accessing the ABI server

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  1. NGS DATA ANALYSIS & FUNCTIONAL GENOMICS
  2. The Linux Command-line

Connecting to the Server

PreviousThe Linux Command-lineNextThe Linux Command-Line For Beginners

Last updated 5 months ago

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For the following sections of our guide, you will need to have access a Linux command-line environment to practice with hands-on exercises. If your computer operates on a Unix system with more than 8GB RAM and 100GB storage space, you're in luck! Although real-world bioinformatics datasets require a much more space and memory for processing, you can still use your laptop for the practical exercises in this guide.

If you don't have access to a Linux environment, there are two options you can try:

  1. You can install a Linux Virtual Machine (VM) on your computer. This requires patience, as VMs can be slow ;)

  2. You can apply for access to the ABI computing resources. This will give you access to a fast server, where we will also provide example datasets used in the tutorials that follow.

Installing a Virtual Machine

Register for the following course from Johns Hopkins University here:

Then access the VMBox Download & Instructions in the Week 1 materials.

Access hints

To access this course, you’ll need to create a Coursera account. Financial aid is available, allowing you to take the course for free. The application process is simple and straightforward, so don’t hesitate—just go for it!

Accessing the ABI server

Step 1: Generate a key pair

An SSH key pair is like a lock and key for secure online access. The private key is your secret key that you keep safe, and the public key is the lock you give to the server. When they match, the server knows it's you, allowing secure access without needing a password.

Step 2: Apply for access

If you have a Windows machine, follow to generate your key pair. Remember the location of your private and public keys! You will provide your public key when requesting access. When granted access, you will need to locate your private key, so be sure to remember where you stored it for future use!

If you have a Unix Machine, you can use .

Please, make a donation of at least 10,000 AMD at as a token of gratitude and support to ABI. Then fill in to request a month-long access. You can prolong your access by filling in another form as you go. You will need to provide your public key when filling the form, so have it ready.

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