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Frequently Asked Questions (FAQ)

Find answers to common questions about BioGrids installation, usage, and troubleshooting.

General Questions

What is BioGrids?

BioGrids is a comprehensive software infrastructure for computational biology that provides pre-compiled, optimized scientific software packages. It includes 500+ applications for bioinformatics, phylogenetics, genomics, proteomics, and more, along with 1,400+ R packages and 600+ Python packages.

How is BioGrids different from other package managers?

BioGrids specializes in scientific software and provides: - Pre-optimized binaries for computational biology - Comprehensive dependency management - Multiple version support with easy switching - Professional packaging and testing - Academic-focused licensing compliance

Is BioGrids free?

Yes, BioGrids is free for academic and non-profit research. The software collection is supported by Harvard Medical School and Boston Children's Hospital.

Installation Questions

Which installation method should I choose?

  • Personal Installation: Individual researchers who want specific software
  • Site Installation: Institutions needing complete software collections for multiple users
  • Cloud Deployment: Users working in cloud environments

See our installation overview for detailed guidance.

How much disk space does BioGrids require?

  • Personal Installation: 5-50 GB depending on selected software
  • Site Installation: 100+ GB for complete collection
  • Individual packages: Range from MB to several GB each

Can I install BioGrids without administrator privileges?

Yes, the personal installation manager can install to your home directory without requiring admin privileges. However, some system-wide optimizations may require administrator access.

Does BioGrids work on Windows?

BioGrids doesn't run natively on Windows, but you can use it with: - Windows Subsystem for Linux (WSL2) - Docker containers - Virtual machines running Linux

Usage Questions

How do I start using BioGrids software?

After installation, initialize the environment: 

source /programs/biogrids.shrc
Then run any BioGrids software by name. See our Quick Start Guide.

How do I see what software is available?

# List all available software
cat /programs/x86_64-linux/biogrids_x86_64-linux  # Linux
cat /programs/i386-mac/biogrids_i386-mac          # macOS

# Get information about specific software
biogrids-info -l samtools

# List executables in a package
biogrids-list samtools

How do I use a specific version of software?

Use environment variables to override default versions: 

# Linux
export SAMTOOLS_X=1.12
samtools --version

# macOS
export SAMTOOLS_M=1.12
samtools --version

The override variable name is shown in biogrids-info -l <software> output.

Can I use multiple versions of the same software?

Yes! BioGrids supports multiple versions simultaneously. Use environment variables to switch between versions, or specify versions in scripts.

Troubleshooting

BioGrids software isn't found after installation

  1. Initialize the environment: source /programs/biogrids.shrc
  2. Check installation path: ls -la /programs/
  3. Verify environment: echo $BIOGRIDS_VERSION

Software behaves differently than expected

  1. Check version: Most issues are version-related
  2. Try older version: Use environment variables to test previous versions
  3. Check dependencies: Some software requires specific libraries

Installation fails or hangs

  1. Check internet connection: Installations require downloading packages
  2. Verify disk space: Ensure adequate free space
  3. Check permissions: Installation directory must be writable
  4. Review firewall settings: Some corporate firewalls block downloads

Environment doesn't load automatically

Add the initialization command to your shell configuration: 

# For bash (add to ~/.bashrc)
if [ -f /programs/biogrids.shrc ] ; then
  source /programs/biogrids.shrc
fi

# For tcsh (add to ~/.tcshrc)
if ( -e /programs/biogrids.cshrc) then
    source /programs/biogrids.cshrc
endif

Performance Questions

Why is software startup slow?

  • First run: Initial startup may be slower due to caching
  • Network storage: Performance depends on network file system speed
  • Many modules: Loading many environment modules takes time

How can I improve performance?

  • Use local storage: Install on fast local SSDs when possible
  • Optimize network: Use high-speed connections for network installs
  • Selective loading: Only load software modules you need
  • Consider capsules: Modern capsule environment has better performance

Does BioGrids affect system performance?

BioGrids software runs with normal system performance. The environment setup has minimal overhead, and software packages are optimized for performance.

Licensing and Usage

Can I use BioGrids for commercial work?

BioGrids itself is free, but individual software packages have their own licenses. Most are free for academic use but may require commercial licenses for commercial work. Check individual software documentation.

Can I redistribute BioGrids software?

No, you cannot redistribute BioGrids packages. Users must download directly from BioGrids. However, you can share installation scripts and configurations.

How do I cite BioGrids in publications?

Include this statement in your methods or acknowledgments:

"Software used in the project was installed and configured by BioGrids (cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"

Technical Questions

What architectures does BioGrids support?

  • x86_64: Intel and AMD 64-bit processors (Linux and macOS)
  • ARM64: Apple Silicon M1/M2 processors (macOS)
  • Future: RISC-V and other architectures under evaluation

Does BioGrids work with job schedulers?

Yes, BioGrids integrates well with: - Slurm Workload Manager - PBS/Torque - SGE (Sun Grid Engine) - LSF (Load Sharing Facility)

Can I use BioGrids in containers?

Yes, BioGrids works in: - Docker containers - Singularity/Apptainer containers - Kubernetes pods - Cloud container services

Does BioGrids support GPUs?

Yes, many BioGrids applications support GPU acceleration, including: - CUDA-enabled applications - OpenCL applications - Machine learning frameworks (TensorFlow, PyTorch)

Updates and Maintenance

How often is BioGrids updated?

  • Site installations: Automatic monthly updates
  • Personal installations: Update on demand using Installation Manager
  • Security updates: Applied as needed

How do I update my installation?

  • GUI: Use the Installation Manager to check for and install updates
  • CLI: Run biogrids-cli update
  • Site installations: Updates happen automatically

Can I prevent automatic updates?

  • Personal installations: Updates are manual by default
  • Site installations: Contact administrators to disable automatic updates
  • Version pinning: Use environment variables to lock specific versions

What happens if an update breaks something?

Use environment variables to revert to previous versions while issues are resolved: 

export SOFTWARE_X=previous_version  # Linux
export SOFTWARE_M=previous_version  # macOS

Getting More Help

Where can I find more documentation?

How do I contact support?

What information should I include in support requests?

  1. Operating system and version
  2. BioGrids version (echo $BIOGRIDS_VERSION)
  3. Exact error messages
  4. Steps to reproduce the problem
  5. What you were trying to accomplish

Still have questions? Contact us at help@biogrids.org or browse our complete documentation.