Description
Tier 1: Basic Troubleshooting ($2,000)
The Goal: A rapid, surgical fix to “unstick” your project and restore script functionality.
- Timeline: 72-Hour Rapid Kickoff (approx. 1.5 work weeks for delivery).
- Best For: Labs with a specific “breaking point” or specific performance bottlenecks in an existing script.
- What’s Included:
- Deep-Dive Debugging: Resolution of R (Bioconductor), Python, or Bash errors, including dependency conflicts and runtime crashes.
- Parameter Optimization: Tuning tool-specific settings to ensure your pipeline is actually capturing the biological signal you’re looking for.
- Environment Standardization: Migration to a stable Conda or Docker environment to eliminate the “it works on my machine” problem.
- Resource Audit: Analysis of memory/CPU allocation to permanently prevent “Out of Memory” (OOM) kills.
- The Deliverable: A stabilized, error-free script and a technical memo outlining the fixes and optimized parameters.
Tier 2: Premium Optimization & Deployment ($5,000)
The Goal: A scalable, “Push-Button” infrastructure that saves thousands in compute costs.
- Timeline: Priority Scheduling (approx. 3 work weeks for delivery).
- Best For: Biotech startups or high-volume labs needing a production-grade pipeline for recurring use or cloud deployment (AWS/GCP/Azure).
- What’s Included:
- Full Workflow Orchestration: Re-architecting legacy code into a modular Nextflow or Snakemake pipeline with automated error-retry logic.
- Cloud Cost Optimization: Implementation of “Spot Instance” logic and data egress strategies, typically reducing cloud compute spend by 40%.
- HPC/Cloud Portability: Seamless deployment across institutional clusters or private clouds using Singularity/Docker containers.
- Benchmarking: Comparative analysis against “Gold Standard” datasets to prove your new pipeline is faster and more accurate.
- The Deliverable: A fully containerized pipeline repository (GitHub/GitLab) with comprehensive documentation for your in-house team.
