Bio-Specific Usage Tips

Pipeline Generation Tips

Be Specific with Intent

The more specific your natural language description, the better the pipeline:

# Good — specific workflow with clear steps
bc7 create "RNA-seq from paired-end FASTQ to differential expression using STAR and DESeq2" \
  --target nextflow
 
# Less specific — may produce a more generic pipeline
bc7 create "RNA-seq pipeline" --target nextflow

Specify Container Preferences

Force container resolution for reproducibility:

bc7 create "variant calling pipeline" \
  --target nextflow \
  --containers docker

Use EDAM Terms for Precision

When searching, EDAM terms give more precise results than free text:

# EDAM operation search (precise)
bc7 search --operation "operation:0292"  # Sequence alignment
 
# Free text (broader)
bc7 search "alignment"

Registry Query Tips

Combine Filters

# Search by operation AND topic
bc7 search --operation alignment --topic genomics
 
# Search with format constraints
bc7 search --operation alignment --input-format fastq --output-format bam

Explore EDAM Hierarchy

EDAM is hierarchical — broader terms include narrower ones:

# See child terms
bc7 edam children "operation:0292"
 
# See parent terms
bc7 edam parents "operation:0292"

MCP Integration Tips

Prompt Patterns for Claude Code

When using BioContext7 through Claude Code's MCP integration, these prompt patterns work well:

• "Search for tools that can perform sequence alignment on FASTQ files"
• "Suggest a pipeline for RNA-seq differential expression analysis"
• "What operations does the STAR aligner support?"
• "Look up the EDAM term for variant calling"

Chaining MCP Calls

Claude Code can chain BioContext7 tools for complex queries:

1. lookup_edam("variant calling") — resolve the EDAM term
2. search_biotools(operation="operation:3227") — find tools
3. suggest_pipeline("variant calling from BAM files") — get a workflow

Performance Tips

Local Index

BioContext7 maintains a local index for fast searches. Keep it updated:

# Full sync (may take a few minutes)
bc7 sync all
 
# Quick sync (only changed tools since last sync)
bc7 sync --incremental

Caching

API responses are cached locally by default. Clear the cache if you need fresh data:

bc7 cache clear

Common Pitfalls

Missing EDAM Annotations

Some tools in bio.tools lack EDAM annotations. BioContext7 uses text-based matching as a fallback, but results may be less precise. Check tool details with bc7 info <tool> to verify annotations.

Container Availability

Not all tools have Docker/Singularity containers available. BioContext7 checks BioContainers automatically, but for tools without containers you may need to install them manually.

Pipeline Target Limitations

Each compilation target has different capabilities: