High-Performance, Reliable, & Scalable Bioinformatics Systems
Internal tools | pipelines | dashboards | web servers
Diagnose | rescue | build
We build bioinformatics systems optimized for performance, correctness, and maintenance cost. Whether you need to diagnose, rescue, or build, we help you reach production-grade reliability without constant rewrites.
They Are All System Design Issues
All the situations above boil down to whether your systems are high-performance, reliable, and scalable. Such systems:
Remain correct as data volume grows
Are safe to change and extend
Can support real users, not just the original author
Move from research into production without constant rewrites
By building performant, robust systems, we solve the underlying problems that keep operations reactive instead of predictable.
Are You in Any of These Situations?
When you recognize one or more of the following situations, it may be time to reach out to us.
Build a New Bioinformatics System
For Example:
- ◆ You are planning a new internal tool, pipeline, or platform
- ◆ You want to start with a production-grade architecture rather than a quick prototype
- ◆ You expect the system to grow in data volume, users, or scope over time
- ◆ You want to avoid costly rewrites, performance cliffs, or reliability issues later
- ◆ You need a system that can move cleanly from research into long-term production use
Turn an Internal System into a Platform or Product
For Example:
- ◆ An internal pipeline or tool is becoming a product or core company asset
- ◆ External users, customers, or partners will depend on the system
- ◆ You need clearer boundaries between core logic, interfaces, and infrastructure
- ◆ Reliability, upgrade paths, and long-term maintainability now matter
- ◆ You want to build a foundation that supports future features and teams
Scale and Stabilize a Growing Pipeline
For Example:
- ◆ A pipeline originally written for one project is reused by multiple projects and the original author is no longer available
- ◆ Systems that span research, clinical, or commercial environments
- ◆ Pipelines that integrate with EHRs, LIMS, or external data providers
- ◆ Data flows crossing teams, organizations, or compliance boundaries
- ◆ Increasing expectations around auditability, traceability, or governance
Improve Performance, Reliability, and Cost
For Example:
- ◆ Turnaround times increase as sample volume grows
- ◆ Pipelines require frequent reruns
- ◆ Cloud costs rise without clear explanation
- ◆ Adding resources no longer solves the problem
- ◆ Where is time or money actually being spent?
- ◆ Are we wasting computation or storage?
- ◆ Is this system fundamentally inefficient?
- ◆ Can we make this predictable rather than reactive?
Need Clarity About Your Systems
For Example:
- ◆ PIs, lab directors, or program leads
- ◆ Startup founders or CTOs
- ◆ Core facility managers
- ◆ Is this system safe to keep using?
- ◆ What are the biggest risks right now?
- ◆ Do we need to rebuild this, or can it be stabilized?
- ◆ What is a realistic path forward?
What We Do
Oak Bioinformatics helps teams design, build, and evolve bioinformatics systems across their full lifecycle:
From exploratory research to sustained production
From scripts to applications and services
From individual use to multi-user environments
Our work emphasizes system structure, clear interfaces, and production-oriented engineering practices.
We Help in These Ways
Bioinformatics Systems Design and Build
For teams that want to build bioinformatics applications, services, or platforms on solid foundations.
We help with:
- ◆ System architecture and data model design
- ◆ High-performance pipelines and services
- ◆ Backend systems, APIs, and web servers
- ◆ Production-grade dashboards and interfaces
We use languages and tools appropriate for long-term reliability, including Rust where it provides clear advantages.
A system that lowers operational stress and enables confident scaling.
Production Upscaling of Research Products
For teams moving beyond exploratory analysis.
We help:
- ◆ Wrap research logic with production infrastructure
- ◆ Create a transition plan without unnecessary rewrites
- ◆ Introduce workflow, validation, and deployment patterns
A system that the public or collaborators can use with confidence.
Performance and Cost Optimization
For teams under pressure to deliver faster results or control infrastructure costs.
We help:
- ◆ Profile performance and resource usage
- ◆ Identify bottlenecks and structural inefficiencies
- ◆ Refactor workflows and data flow for predictable scaling
A faster turnaround system with reliable performance and consistent costs.
Genomic Data Analysis and Interpretation
For teams needing careful, high-confidence analysis of genomic or transcriptomic data.
We help:
- ◆ Perform expert genomic and omics analysis
- ◆ Design analysis and interpretation workflows
- ◆ Deliver clear, structured results suitable for downstream use
Results that can be trusted and built upon.
Why We Are Right Fit
We have deep experience designing and implementing bioinformatics platforms.
We have:
- 1.
Served as lead architect for widely used genomic analysis platforms
- 2.
Built end-to-end annotation and analysis systems from the ground up
- 3.
Designed software intended to be used, extended, and maintained by others
We focus on making complex bioinformatics workflows understandable, operable, and safe to evolve over time.
We use modern, production-oriented technologies chosen to match the problem at hand:
- Rust for performance-critical and reliability-sensitive components
- Python and established bioinformatics tooling where flexibility and ecosystem matter
- Workflow engines, cloud infrastructure, and web technologies appropriate for long-lived systems
The goal is systems that behave predictably under real use.
Dr. Ryangguk Kim
Bioinformatics Systems Builder
Oak Bioinformatics is led by Dr. Ryangguk Kim, a bioinformatics systems builder who works directly with clients. Ryangguk has spent his career designing and building genomic analysis platforms that other researchers and teams depend on, including serving as lead architect of OpenCRAVAT and developing OakVar and ScanVar. His background spans biology, computational biology, and software engineering, with a focus on making complex bioinformatics systems understandable, maintainable, and safe to evolve as they move beyond individual use.
Ready to Start Conversation?
Most engagements begin with a focused assessment or design phase.
We start by understanding your current system, constraints, and goals. From there, we outline risks, tradeoffs, and realistic next steps before committing to deeper work.
Our engagements are designed to be:
- • Transparent in scope and expectations
- • Collaborative with your internal team
- • Structured so you can make informed decisions early
If you want a clear, grounded view of where your system stands and what it would take to move forward safely, we should talk. Message us for a no commitment, 30-min initial talk: