Getting Started Guide¶

Initial Setup¶

Request Access¶

Currently we do not offer access to the public. Since the resources are limited, only approved individuals may access this server. New users will receive separate instructions about their credentials.

Accessing the Server¶

Web-Based Services (No Configuration Required)¶

These services are immediately accessible with your system credentials:

RStudio Server¶

URL: rstudio.bioinfospace.com - Full RStudio IDE in your browser - Pre-installed R packages plus user library for custom packages - Keep page open to avoid idle disconnection - Remember to close session when done

JupyterHub¶

URL: jupyter.bioinfospace.com - Interactive notebooks with multiple kernels - System Python kernel plus custom conda environments - Keep projects in different environments to avoid conflicts - Supports bash commands in notebooks

Cockpit Web Interface¶

URL: monitor.bioinfospace.com - Web-based terminal access - File upload/download interface - System usage monitoring - Service status overview

SSH Access¶

On-Campus Connection¶

Direct connection when on campus or using ND VPN:

ssh [email protected]
# or
ssh username@[server-ip-address]

Off-Campus Connection (CloudFlare Tunnel)¶

Install cloudflared on your local machine (download here)
Generate SSH keys:

ssh-keygen -t ed25519 -C "[email protected]"
# Press Enter to accept default location
# Enter passphrase (optional but recommended)

Add public key to server via Cockpit web terminal:

echo "ssh-ed25519 <your-public-key>" >> ~/.ssh/authorized_keys

Configure SSH client (~/.ssh/config):

Host ssh.bioinfospace.com
    User <your_username>
    ProxyCommand cloudflared access ssh --hostname %h
    IdentityFile ~/.ssh/id_ed25519
    StrictHostKeyChecking no
    UserKnownHostsFile /dev/null

Connect:

ssh ssh.bioinfospace.com

First-Time Setup¶

1. Change Your Password¶

It is adviced to change your password upon first log in. If you forgot your password, you may contact support to help you reset to the default password. Changing password does not require sudo previledges.

SSH terminal:

passwd
# Follow prompts for strong password

2. Explore Available Resources¶

# Your home directory
ls /home/username

# Your data directory
ls /data/username

# Shared resources directory
ls /shared

# List available software modules
module avail

# View system resources
htop

# Check your environment
echo $PATH
which python
which R

Quick Start Examples¶

Example 1: R Analysis in RStudio¶

# Test R environment
R.version
sessionInfo()

# Load sample data and create plot
library(ggplot2)
data(mtcars)
ggplot(mtcars, aes(x = hp, y = mpg)) +
    geom_point() +
    geom_smooth(method = "lm") +
    labs(title = "Test Plot")
ggsave("~/results/figures/test_plot.png")

Example 2: Python in Jupyter¶

# Test Python environment
import sys
print(f"Python: {sys.version}")

# Test scientific packages
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt

# Create sample visualization
data = pd.DataFrame({
    'x': np.random.randn(100),
    'y': np.random.randn(100)
})
plt.scatter(data['x'], data['y'])
plt.savefig('~/results/figures/test_scatter.png')

Example 3: Command Line Analysis¶

# Load bioinformatics module
module load samtools
samtools --version

# Submit a test job
bioqueue -n "test_job" "echo 'Job completed' > ~/test.txt"
bioqueue -l  # Check status

# Create persistent session
screen -S analysis
# Run commands...
# Detach: Ctrl+A, D
# Reattach: screen -r analysis

Storage Guidelines¶

Location	Quota	Purpose	Backup
`/home/username`	None	Scripts, notebooks, small files	No
`/data/username`	None	Large datasets, analysis results	No
`/tmp`	Shared	Temporary processing files	No
`/shared`	Shared	Shared resources	Limited

Important: We will not provide backup of personal data. Always maintain your own backups of critical data.

Resource Allocation¶

Currently, all resources are shared and there are no explicit limit in CPU/RAM or storage quota. However, please be considerate and coordinate with other users if there is a conflict. We might consider adding resource limits in the future.

Common Commands Reference¶

# File management
ls -lah               # List files with details
du -sh directory/     # Check directory size
df -h                 # Check disk usage

# Module system
module avail          # List available software
module load <name>    # Load software
module list          # Show loaded modules

# Job management
bioqueue submit script.sh    # Submit job
bioqueue -l                 # List jobs
bioqueue -kill <job_id>     # Cancel job

# Session management
screen -S name        # Create named session
screen -ls           # List sessions
screen -r name       # Reattach to session

# System monitoring
htop                 # Interactive process viewer
nvidia-smi          # GPU usage
free -h             # Memory usage

Requesting system package or software¶

Contact admin if you need additional system packages or modules to be installed.

Disclaimer: This documentation is still under construction. For questions or clarifications, please contact support. | Last Updated: August 2025