Getting Started with BioGrids

Once BioGrids is installed, you can start using the software collection immediately. This guide will help you set up your environment and run your first BioGrids application.

Setting Up Your Environment

Initialize BioGrids

The BioGrids software collection is installed at /programs. To use any BioGrids software, you must first initialize the environment in your terminal.

For Bash users:

source /programs/biogrids.shrc

For tcsh/csh users:

source /programs/biogrids.cshrc

Upon initialization, you'll see the BioGrids welcome message:

********************************************************************************

                          **Software Support by BioGrids**

********************************************************************************

 Developed with support from HMS Tools-and-Technologies fund.

 If your use of BioGrids compiled software was an important element in 
 your publication, please include the following statement in your work:

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

********************************************************************************

This BioGrids installation last updated: 2025-03-21

 Please submit bug reports and help requests to:  help@biogrids.org.

           **For additional information visit https://biogrids.org/wiki**

********************************************************************************

Automatic Environment Loading

To automatically load the BioGrids environment when you open a new terminal, add the initialization command to your shell configuration file.

For Bash users (add to ~/.bashrc):**

if [ -f /programs/biogrids.shrc ] ; then
  source /programs/biogrids.shrc
fi

For tcsh users (add to ~/.tcshrc or ~/.cshrc):**

if ( -e /programs/biogrids.cshrc) then
    source /programs/biogrids.cshrc
endif

Setting Up an Alias

If you prefer to load BioGrids on demand, you can create an alias for convenience:

For Bash:

alias biogrids='source /programs/biogrids.shrc'

For tcsh:

alias biogrids 'source /programs/biogrids.cshrc'

Then simply type biogrids to initialize the environment.

Exploring Available Software

List All Available Software

Linux systems:

cat /programs/x86_64-linux/biogrids_x86_64-linux

macOS systems:

cat /programs/i386-mac/biogrids_i386-mac

Get Software Information

Use biogrids-info to get detailed information about any software package:

biogrids-info -l samtools

This will show: - Default version - Currently active version
- All installed versions - Available versions - Override variable name

Example output:

Version information for: /programs/x86_64-linux/samtools

Default version:                    1.21
In-use version:                     1.21

Installed versions:                 1.21 1.20 1.19.2 1.18 1.17 1.16.1 1.16 1.15.1 1.15 1.14 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 0.1.19_r8
Other available versions:           1.20 1.19.2 1.18 1.17 1.16.1 1.16 1.15.1 1.15 1.14 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19 0.1.19_r8 
Overrides use this shell variable:  SAMTOOLS_X

List Executables in a Package

Find out what command-line tools are included in a software package:

biogrids-list samtools

Example output:

ace2sam         md5fa           samtools.pl
blast2sam.pl    md5sum-lite     seq_cache_populate.pl
bowtie2sam.pl   novo2sam.pl     soap2sam.pl
export2sam.pl   plot-ampliconstats   wgsim
fasta-sanitize.pl   plot-bamstats   wgsim_eval.pl
interpolate_sam.pl  psl2sam.pl      zoom2sam.pl
maq2sam-long    sam2vcf.pl
maq2sam-short   samtools

Using Software Versions

Default Versions

By default, BioGrids uses the most recent stable version of each software package. Simply run the software by name:

samtools --version

Using Specific Versions

You can override the default version using environment variables:

On Linux (use TITLE_X format):

export SAMTOOLS_X=1.12
samtools --version

On macOS (use TITLE_M format):

export SAMTOOLS_M=1.12
samtools --version

The override variable name is shown in the biogrids-info output.

Running Your First Application

Let's run a simple example with SAMtools:

Initialize BioGrids:
```
source /programs/biogrids.shrc
```
Check available versions:
```
biogrids-info -l samtools
```
Run SAMtools:
```
samtools
```

You should see the SAMtools help message, confirming that the software is working correctly.

Common Workflows

Sequence Analysis Example

# Initialize environment
source /programs/biogrids.shrc

# Use BWA for alignment
bwa mem reference.fa reads_1.fq reads_2.fq > alignment.sam

# Convert to BAM format with SAMtools
samtools view -bS alignment.sam > alignment.bam

# Sort the BAM file
samtools sort alignment.bam -o alignment_sorted.bam

# Index the sorted BAM file
samtools index alignment_sorted.bam

Data Analysis Example

# Initialize environment
source /programs/biogrids.shrc

# Use R for statistical analysis
R --vanilla < analysis_script.R

# Use Python for data processing
python data_analysis.py

Troubleshooting

Environment Issues

If you encounter problems:

Verify installation:
```
ls -la /programs/
```
Check environment:
```
echo $BIOGRIDS_VERSION
```
Reinitialize environment:
```
source /programs/biogrids.shrc
```

Getting Help

Software-specific help: Most applications include built-in help (--help or -h)
BioGrids support: Email help@biogrids.org
Community support: Join our mailing list
Documentation: Check our FAQ

Next Steps

Now that you're set up with BioGrids:

Explore the software catalog: Browse available software
Learn about capsules: Understanding BioGrids capsules
Get help: Support resources

Questions? Contact us at help@biogrids.org