1 Introduction

This webpage provides tutorials introducing remote computing and command-line tools commonly used in genomics and bioinformatics. The tutorials focus on practical workflows using Linux computers running the Ubuntu distribution.

The material presented here is especially relevant for:

These tutorials will help you develop the computational skills required to connect to remote computers, manage long analyses, and navigate the command-line environment used in genomics research.

2 Learning Outcomes

After completing these tutorials, you will be able to:

  1. Remotely access Linux computers using the ssh protocol.
  2. Safely run long analyses (aka computer jobs) using tmux sessions.
  3. Use common Bash command-line tools to organize files and perform genomics analyses.

3 Workflow

These tutorials are organized to guide you through the essential steps required to work on remote Linux systems and perform genomics analyses using the command line.

The material is structured into the following sections:

  1. Remotely access Linux computers
    In this section, you will learn how to connect to remote computers using the ssh protocol and understand the basic concepts required for secure remote access.

  2. Safely run computer jobs
    This section introduces the tmux tool, which allows you to run and manage long computational jobs in persistent terminal sessions.

  3. Bash command-line reference
    This section provides a practical overview of commonly used Bash commands for navigating the file system, managing files, and supporting genomics analyses.

  4. File Exchange
    This section provides a practical overview of how to conduct file exchange using FileZilla.

  5. Group Exercises 1: Building a Shared Bioinformatics Workflow
    This section provides group activities to help you learn and master skills related to remotely accessing Linux computers, running safe jobs, and using Bash commands.

  6. Group Exercises 2: File Exchange Using FileZilla
    This section provides group activities to help you learn how to transfer files between your computer and a remote server.

4 Groups

4.1 Group Organization and Structure

Each group is composed of 5 to 6 students, with a mix of undergraduate and graduate students to promote peer learning and knowledge exchange.

Each group is divided into two subgroups (A and B). Both subgroups will perform the same analyses in parallel, working independently at first.

This structure is designed to:

  • Encourage fact-checking by comparing results between subgroups
  • Improve accuracy and reproducibility
  • Build confidence in computational results through independent validation

4.2 Group Accounts

Each group has been assigned two accounts:

  • One account for Subgroup A
  • One account for Subgroup B

Each subgroup must use its assigned account to complete the group activities.

You will access the Linux systems using the ssh protocol. Details on your account information are available here.

4.3 Group Collaboration Guidelines

  • Each subgroup works independently using its assigned account
  • Analyses are conducted in parallel by Subgroup A and Subgroup B
  • All accounts within a group share the same computational resources
  • Coordinate within your subgroup to avoid conflicts when running intensive jobs
  • After completing tasks, compare results between subgroups to verify accuracy
  • Discuss and resolve any discrepancies before moving forward

4.3.1 Technical Notes

  • All accounts use the same password for simplicity
  • Accounts have access to the bioinformatics software required for the course
  • File permissions allow collaboration within each account environment
  • Contact the instructor if you experience connection issues

5 Remotely Access Computers

To remotely access your assigned Linux computer accounts using the ssh protocol, you need the following information:

  1. Your user ID and password (see the Google document).
  2. The IP address of the computer you want to connect to.

If you want to remotely access the lab computers from a Windows machine, please read the protocol described below before continuing.

Important: If you are accessing the Linux computers outside of the BSU campus network, you will need to connect through the BSU VPN.

5.1 What is an IP Address?

An Internet Protocol (IP) address is a numerical label assigned to each device connected to a computer network that uses the Internet Protocol for communication.

An IP address serves two main functions:

  1. Network interface identification
  2. Location addressing

5.2 How to Find the IP Address?

The procedure summarized here shows how to retrieve a computer’s IP address on the Ubuntu operating system (Figure 5.1):

  1. Open the System Settings application from the desktop sidebar.
  2. Select the Network tab located under the Hardware section.
  3. Select the Wired tab.
  4. The computer’s IP address appears under the IPv4 Address field.
Screenshot of Ubuntu desktop showing how to retrieve the IP address.

Figure 5.1: Screenshot of Ubuntu desktop showing how to retrieve the IP address.

5.2.1 Command Lines to Get the IP Address

You can also retrieve the IP address from the command line by typing the following commands in a Terminal:

# Get IP address
hostname -I | awk '{print $1}'
ip a
ifconfig -a

5.3 The ssh Protocol

The Secure Shell (ssh) protocol is a method used for secure remote login from one computer to another (Figure 5.2). It protects communication using strong encryption and allows users to remotely execute commands on another machine.

Overview of ssh protocol.

Figure 5.2: Overview of ssh protocol.

Once you have gathered the required information (IP address and username), open a Terminal and type:

# General command
ssh USER_ID@IP

# Example
ssh bioinformatics@132.178.143.53
Example of an ssh connection from a Terminal.

Figure 5.3: Example of an ssh connection from a Terminal.

5.4 Install Putty on Windows

If you are using Windows, you can use Putty to establish SSH connections.

Download the software here: http://www.putty.org

When launching Putty (Figure 5.4):

  1. Enter user@IP in the Host Name field.
  2. Set Port to 22.
  3. Select SSH as the connection type.
Putty configuration window.

Figure 5.4: Putty configuration window.

6 Safely Run Computer Jobs

Some analyses performed in genomics can take several hours or even days to complete. To avoid interrupting these analyses, it is important to run them in a persistent terminal environment.

The tool we will use for this purpose is tmux, which allows multiple terminal sessions to run simultaneously.

6.1 The tmux protocol

tmux is a terminal multiplexer for Unix-like systems. It allows users to create multiple independent terminal sessions within a single window.

Key advantages:

  • Run long analyses safely
  • Disconnect from a remote computer without stopping jobs
  • Manage multiple command-line tasks simultaneously

6.1.1 Install tmux on Mac

brew install tmux

6.2 How to Operate tmux Sessions

6.2.1 Create a New Session

tmux

6.2.2 Detach from a Session

Press:

Ctrl+b then d

6.2.3 Reattach to a Session

tmux attach

6.2.4 Create and Name a Session

tmux new -s JOB1

6.2.5 List Sessions

tmux list-sessions

6.2.6 Attach to a Specific Session

tmux attach -t JOB1

6.2.7 Kill a Session

tmux kill-session -t JOB1

Warning: Killing a session will terminate any running analysis.

7 Bash Command-Line Reference

Below is a collection of common Bash commands used to navigate the file system and manage computational analyses.

7.1 File System

  • ls — list files in a directory
  • cd — change directory
  • pwd — print working directory
  • mkdir — create a directory
  • rm — remove a file
  • cp — copy files
  • mv — move or rename files
  • cat — display file contents
  • less — view files page by page
  • head — show the first lines of a file
  • tail — show the last lines of a file

7.2 System

  • whoami — display current user
  • date — display date and time
  • exit — exit terminal
  • df -h — disk usage
  • free — memory usage

7.3 Process Management

  • ps — list active processes
  • top — show running processes
  • htop — interactive process viewer
  • kill PID — terminate process

7.4 Networking

  • ssh user@host — connect to remote host
  • scp — transfer files between machines
  • wget — download files
  • curl — download files

7.5 Searching

  • grep — search text patterns
  • find — locate files
  • sed — text substitution

7.6 Compression

  • tar — archive files
  • gzip — compress files

8 File Exchange

8.1 Learning Objectives

By the end of this section, you will be able to:

  • Explain what SFTP is and why it is used
  • Connect to a remote server using FileZilla
  • Transfer files between your local computer and a remote system
  • Verify successful file transfers

8.2 Why File Transfer Matters

In bioinformatics, analyses are often conducted on remote computing systems, while data visualization and reporting are performed locally. Efficient and reliable file transfer is therefore essential for:

  • Moving input datasets to remote systems
  • Retrieving analysis results
  • Sharing files between collaborators

Developing good file management and transfer practices is critical for ensuring reproducibility and data integrity.

8.3 What is SFTP?

SFTP (Secure File Transfer Protocol) is a network protocol used to securely transfer files between your local computer and a remote server.

Unlike older file transfer methods (such as FTP), SFTP encrypts both the data and the login credentials during transmission. This ensures that your files and passwords are protected from unauthorized access.

8.3.1 Key Features of SFTP

  • Secure communication: All data is encrypted
  • Authentication: Requires a username and password (or SSH key)
  • Reliable transfers: Reduces the risk of data corruption
  • Integration with SSH: Uses the same protocol as ssh (port 22)

8.4 SFTP in FileZilla

FileZilla is a graphical SFTP client that simplifies file transfer between your computer and a remote server.

When you connect using FileZilla:

  • You are using SFTP by default (when connecting via port 22)
  • Your connection is secured using the same system as your ssh login
  • You can upload and download files using a drag-and-drop interface

8.4.1 Why SFTP is Important in Bioinformatics

  • Protects sensitive datasets and research results
  • Ensures secure access to remote computing systems
  • Enables efficient transfer of large genomic datasets

In this course, you will use SFTP through FileZilla to move data between your local computer and remote Linux systems.

8.5 Download and Install FileZilla

FileZilla is a free, open-source SFTP client available for Windows, macOS, and Linux.

8.5.1 Steps

  1. Go to the official FileZilla website:
    https://filezilla-project.org/
  2. Click Download FileZilla Client
  3. Select the version for your operating system:
    • Windows
    • macOS
    • Linux
  4. Run the installer and follow the installation instructions
  5. Launch FileZilla after installation

Notes:

  • Select the FileZilla Client, not the Server version
  • Avoid installing optional bundled software if prompted
  • Administrator privileges may be required

8.6 Connecting with FileZilla

8.6.1 Connection Details

To connect using FileZilla, you will need:

  • Host: your remote server address
  • Username: your assigned account
  • Password: your assigned password
  • Port: 22 (SFTP)

8.6.2 FileZilla Interface Overview

Once connected, the FileZilla interface is divided into several panels:

  • Quickconnect bar (top): Enter host, username, password, and port
  • Left panel: Local file system (your computer)
  • Right panel: Remote file system (server)
  • Bottom panel: File transfer queue and status

8.7 Good Practices for File Transfer

  • Always verify files after transfer (e.g., check file size or contents)
  • Use clear and consistent file names
  • Keep your directories well organized
  • Avoid overwriting important files unless intended
  • Transfer only necessary files to reduce clutter

9 🤝 Group Exercises 1: Building a Shared Bioinformatics Workflow

9.1 Learning Outcomes

These exercises reinforce:

  • Remote computing skills (ssh)
  • Linux navigation and file management
  • Safe job execution using tmux
  • Collaborative bioinformatics workflows

9.2 Activity Overview

In this 50-minute group activity, you will work in groups of 5–6 students, divided into two subgroups (A and B), to build and manage a shared bioinformatics workspace on a remote Linux system.

Through this activity, you will:

  • Practice connecting to a remote system using ssh
  • Navigate and manage files using essential Linux commands
  • Collaboratively create and organize a shared working directory
  • Create, verify, and delete files within a shared environment
  • Use tmux to safely run and manage persistent computational jobs
  • Develop communication and coordination skills required in real-world bioinformatics workflows

This activity is designed to simulate how bioinformatics teams collaborate on shared computing infrastructure. You will experience the importance of clear communication, careful file management, and responsible use of shared resources.

By the end of this session, you will be prepared to confidently work on remote systems, manage your own analysis environment, and collaborate effectively on computational genomics projects.

9.4 Instructions

These exercises are designed to simulate real-world bioinformatics collaboration.

You will work in:

  • 3 groups (5–6 students each)
  • Each group has:
    • 2 accounts
    • 1 per subgroup (A and B)

⚠️ Important:

  • Only ONE terminal session per subgroup
  • You must coordinate, communicate, and trust each other
  • Mistakes affect everyone — just like in real research

9.5 Phase 1 — Establishing Access (Trust & Communication) (15 minutes)

Goal: Successfully access your shared system

9.5.1 Tasks

  1. Connect to the remote server using ssh. See here for account details. Once you have gathered the required information (IP address and username), open a Terminal and type (see here if you use Putty):
# General command
ssh USER_ID@IP

# Example
ssh bio_40@132.178.143.53
  1. Confirm your identity and current directory:
# Retrieve your username
whoami

# Retrieve your current path
pwd
  1. Exit the ssh connection:
exit

👉 Deliverable: Shared notes describing the login procedure

9.6 Phase 2 — Shared Workspace Construction (Coordination) (15 minutes)

Goal: Build a common working directory

9.6.1 Tasks

  1. Connect to the remote server using ssh

  2. Navigate to your home directory

cd ~
  1. Create a new folder:
mkdir Tutorial_genomics
  1. Verify the directory structure:
# Basic listing
ls

# Detailed listing
ls -lh
  1. Create and remove a test file inside the folder:
# Move into the directory
cd Tutorial_genomics

# Create a test file
touch test_file.txt

# Verify it exists
ls -lh

# Remove the file
rm test_file.txt

# Confirm deletion
ls
  1. Exit the ssh connection

👉 Discussion:

  • What are the differences between ls and ls -lh?
  • Why does directory structure matter in genomics pipelines?
  • Why is it important to verify file creation and deletion?

9.7 Phase 3 — Safe Job Execution (Shared Responsibility) (15 minutes)

Goal: Run persistent jobs safely using tmux

9.7.1 Tasks

  1. Connect to the remote server using ssh

  2. Start a tmux session:

tmux new -s GENOMICS_JOB
  1. Run a dummy job:
sleep 300
  1. Detach from the session:
Ctrl + b, then d
  1. Reattach to the session:
tmux attach -t GENOMICS_JOB
  1. Exit the ssh connection

👉 Discussion:

  • Why is tmux essential in genomics workflows?
  • What could happen if a long job is run without it?

9.8 Phase 4 — Reflection (Building Trust) (5 minutes)

9.8.1 Group Discussion

  1. What worked well in your collaboration?
  2. Where did communication break down?
  3. Did you trust the other subgroup?
  4. What would happen in a real research project?

10 🤝 Group Exercises 2: File Exchange Using FileZilla

10.1 Learning Outcomes

By completing these exercises, you will be able to:

  • Transfer files between your local computer and a remote Linux system
  • Connect to a remote server using an SFTP client (FileZilla)
  • Organize files for bioinformatics workflows
  • Verify successful file transfers

10.2 Activity Overview

In this 25-minute group activity, you will work in groups of 5–6 students, divided into two subgroups (A and B), to learn how to transfer files between your local computer and the remote system, and verify file integrity.

The key takeaways from this activity are as follows:

  • File transfer is a critical component of bioinformatics workflows
  • Always verify file integrity after transfer
  • Maintain clear file naming conventions to avoid confusion
  • Combine graphical tools (FileZilla) with command-line tools for flexibility

10.3 Tasks

10.3.1 Prepare a File Locally

Each subgroup should:

  • Create a simple text file on your computer (e.g., groupA_test.txt or groupB_test.txt)
  • Add the following content:
This is a test file for file transfer.
Subgroup: A or B

10.3.2 Upload the File to the Remote Server

Using FileZilla:

  • Navigate to your home directory on the remote system
  • Upload your file into the folder:
~/Tutorial_genomics

10.3.2.1 Steps

To upload your file to the remote server, do the following steps:

  1. Open FileZilla. See here for more detials on how to use FileZilla.

  2. Enter your connection details in the Quickconnect bar. See here for account details.

  3. Click Quickconnect

  4. Navigate:

    • Local files (left)
    • Remote files (right)

10.3.3 Verify the File on the Remote System

Connect via ssh and run:

cd ~/Tutorial_genomics
ls -lh
cat groupA_test.txt   # or groupB_test.txt

10.3.4 Modify and Download the File

  • Edit the file on the remote system using a command-line editor (e.g., vim, nano):
vim groupA_test.txt
  • Add one additional line, save, and exit

10.3.5 Download the Updated File

  • Use FileZilla to download the modified file back to your local computer

10.3.6 Confirm Changes Locally

  • Open the downloaded file
  • Verify that your modification is present

10.3.7 Discussion

  • What are the advantages of using FileZilla compared to the command line?
  • When would command-line tools (e.g., scp, rsync) be preferable?
  • How can file mismanagement impact reproducibility in bioinformatics?

10.3.8 Next Step

Use the protocol you just learned to transfer the ORF map from Module 2 to your local computer.