BioinfoSpace Server Documentation

Overview

This documentation provides comprehensive information about the BioinfoSpace bioinformatics server. This is a personally hosted and maintained computational resource, provided complimentary to Notre Dame bioinformatics users.

Important Notice: This server is not affiliated with, managed by, or supported through the University of Notre Dame or any other institution. It is an independent resource maintained on a voluntary basis. Access to computational resources is restricted to authorized users. For public applications and blog content, please visit bioinfospace.com.

Service Endpoints

The following services are available to authorized users:

Service URL Description
RStudio Server https://rstudio.bioinfospace.com Web-based R development environment with Bioconductor packages
JupyterHub https://jupyter.bioinfospace.com Interactive computational notebooks supporting Python and R kernels
Cockpit Monitor https://monitor.bioinfospace.com System monitoring and file management interface
SSH Access ssh.bioinfospace.com and ssh2.bioinfospace.com Secure shell access for command-line operations

System Specifications

Hardware Configuration

The BioinfoSpace server runs on the following hardware:

  • System: Dell Precision Tower 7910 Workstation
  • Processors: Dual Intel Xeon E5-2690 v4 (14 cores per CPU, 28 physical cores, 56 threads total, 2.6 GHz base frequency)
  • Graphics Processing: NVIDIA GeForce RTX 5060 with 8GB GDDR7 memory
  • Memory: 512 GB RAM (DDR4 ECC)
  • Storage:
    • Total SSD: ~1TB (2x 476GB SSDs for system and shared resources)
    • Total HDD: ~12TB (7.3TB data drive + 3.6TB LVM volume from 2x 1.8TB drives)
  • Operating System: Ubuntu 24.04.3 LTS (Kernel 6.14.0-28-generic, x86_64 architecture)

Software Environment

Programming Languages and Frameworks

  • R 4.5.1 with Bioconductor packages
  • Python 3.12.3 with scientific libraries
  • Conda/Miniconda 24.9.2 available via module system (module load conda)

Bioinformatics Tools (via Environment Modules)

Available through the module system: - Sequence alignment: BWA, Bowtie2, STAR - Quality control: FastQC - Transcriptomics: Salmon, Cell Ranger - Utilities: SAMtools, SRA Toolkit - Programming: Java, Conda - Workflows: RNAseq pipeline

Usage: Load tools on-demand with module load <toolname> (e.g., module load samtools)

Development and Analysis Environments

  • RStudio Server 2025.05.0 (Mariposa Orchid) - Web-based R IDE
  • JupyterHub - Multi-user notebook server (managed via systemd service)
  • Jupyter Notebooks - Available through conda environments
  • X11 Forwarding Support - Run GUI applications remotely:
    • Enabled by default on the server
    • X11 utilities installed (xauth, x11-apps)
    • Connect with ssh -X or ssh -Y to forward display
    • Supports GUI applications like plots, Firefox, and graphical tools
  • GNU Screen 4.09.01 - Terminal multiplexer for persistent sessions
  • Development Tools:
    • Compilers: GCC, G++
    • Build tools: Make, CMake
    • Version control: Git
    • Text editors: nano, vim

Container Support

  • Podman 4.9.3 for rootless container execution
  • Docker-compatible container runtime
  • Additional container tools available upon request

Documentation Structure

This documentation is organized into the following sections:

Getting Started

Getting Started Guide - Detailed account setup, workspace organization, environment testing, and troubleshooting

Core Services

  • Services Overview - Detailed information about RStudio, JupyterHub, SSH, and monitoring tools
  • File Management - Data transfer methods, directory structure, storage policies, and quota system

Technical Resources

  • Linux Command Line - Essential Unix/Linux commands for bioinformatics workflows
  • Software and Tools - Available packages, module system, and software installation procedures
  • Job Scheduling - Using the bioqueue system for batch processing and resource management
  • Containerization - Working with Docker, Podman, and Singularity containers

Guidelines and Support

  • Best Practices - Recommended workflows, resource usage guidelines, and troubleshooting procedures

Support and Contact Information

Communication Channels

Primary Support

  • Email: [email protected]
  • Response time is not guaranteed, but we will try our best to get to you as soon as possible.

Real-time Communication

  • Google Chat: Join the "BioinfoSpace Users" space for:
    • Quick issue reporting and troubleshooting
    • System outage notifications
    • Package installation requests
    • Community support from other users
    • Admin assistance for urgent matters

Future Platforms

  • Discord/Slack: Community channels are planned for future implementation to provide additional real-time support options

Disclaimer and Usage Policies

IMPORTANT - PLEASE READ CAREFULLY:

  1. Independent Service: This server is personally owned, hosted, and maintained. It is NOT a University of Notre Dame resource, nor is it affiliated with any institutional IT services.

  2. No Warranty: This service is provided "AS IS" without warranty of any kind, either expressed or implied, including but not limited to:

    • Service availability or uptime guarantees
    • Data integrity or recovery capabilities
    • Fitness for any particular purpose
    • Security or confidentiality assurances

  3. User Responsibility: By using this service, users acknowledge and accept that:

    • They assume ALL risks associated with using this server
    • They are solely responsible for backing up their data
    • They must comply with all applicable laws and regulations
    • They should not store sensitive, confidential, or regulated data (HIPAA, FERPA, etc.)
    • Any data loss, corruption, or security breach is their sole responsibility

  4. Service Limitations:

    • Access may be revoked at any time without notice
    • The server may be unavailable for maintenance or other reasons
    • Resources are shared and subject to fair use policies
    • No technical support is guaranteed

  5. Complimentary Access: This service is provided free of charge as a courtesy to Notre Dame bioinformatics users. It may be discontinued at any time.

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