Seqera Co-Scientist: Your Intelligent, Collaborative Partner That Brings the Full Power of Seqera to Scientists
Today at the Nextflow Summit in Boston, we launched Seqera Co-Scientist, the intelligent, collaborative partner that brings the full power of Seqera to all scientists. Co-Scientist understands scientific context, reasons with you, and executes with intelligence – making developing, deploying, and debugging bioinformatics accessible regardless of technical experience. Best of all, Co-Scientist is built for Enterprise bioinformatics, providing deep integration with your data, compute, and internally hosted models as well as complete visibility across your entire bioinformatics stack and controls that let you lean into productivity without compromising on reproducibility or security.
Three Integrated Capabilities
Co-Scientist can work alongside you interactively or autonomously in the background. Whether you're a bench scientist launching your first pipeline, a bioinformatician debugging production workflows, or an administrator integrating custom AI agents, Co-Scientist simplifies your work:
- Self-Service Interface for Scientists – Enable bench scientists to launch pipelines, manage data, and explore results independently in a simple portal with guardrails that bioinformaticians and IT can easily configure and evolve over time.
- Interactive Research Intelligence – Build, validate, optimize, and debug pipelines through CLI, IDE, MCP, or web with full workspace context, working alongside your internal AI tools and LLMs.
- Automation with Agents (Coming Soon) – Trigger pipelines, detect and self-fix failures, and autonomously improve code with 24/7 agents. Always on, always working.
Self-Service Interface for Scientists
Scientists can now run their own analyses without waiting in the bioinformatics queue. This dramatically reduces turnaround times, increases experimental throughput, and reducing dependency on bioinformatics teams for routine pipeline launches.
Governed self-service also ensures scientists access only what bioinformatics teams provision through label-based controls. All RBAC, SSO, and security controls are inherited from Seqera Platform, and all workflow are fully audited and reproducible – delivering scientific autonomy with enterprise guardrails.
Key capabilities
- →Self-service analytics – Launch pipelines, manage datasets, and analyze results independently without bioinformatics support.
- →Your experiments, your data – Simplified interface shows only the pipelines and datasets relevant to your projects, no clutter.
- →Real-time visibility – Track pipeline status, get instant updates, and access results immediately without waiting.
- →AI-assisted interpretation – Built-in help explain reports, highlights key findings, and answers follow-up questions.
- →Automated workflows (Coming Soon) – Pipelines launch automatically when data arrives; results organized as analyses complete.
Interactive Research Intelligence
Accelerate pipeline development with AI-powered intelligence that has the full context of your Seqera workspace, enabling faster iteration cycles and seamless dev-to-production deployment. Co-Scientist handles containerization, dependency management, and environment configurations while intelligently optimizing resource allocation based on execution history.Move from conversation to results without context-switching, integrating pipeline development, debugging, and execution into a unified experience.
Key capabilities
- →Build, debug, optimize - Available through CLI, IDE, or web chat with full context across pipelines, runs, code, compute, and data.
- →Convert code to Nextflow — Transform scripts (bash, CWL, WDL) into production-ready Nextflow pipelines with high accuracy.
- →Seamless dev-to-production - Develop locally with AI assistance, test in sandboxes, deploy to production without manual configuration.
- →MCP integration - Connect AI tools to Seqera with full SSO authentication. Build custom agents that extend Co-Scientist's capabilities.
- →Action-oriented APIs - Your agents don't just get information, they launch pipelines, manage workflows, orchestrate compute directly.
- →Deploy in your infrastructure - Run as containerized services within your VPC, connecting to internal LLMs. No data leaves.
Automation with Agents (Coming Soon!)
Background agents work 24/7 to shift bioinformatics teams from firefighting production issues to building new capabilities, multiplying experimental throughput without proportional headcount growth. Unlike interactive sessions, background agents handle complex, long-running tasks autonomously, completing pipeline development, debugging, and optimization in the background while you focus on other work.
Work happens without waiting. Pipelines launch when data arrives, failures get fixed as they occur, and compute resources optimize continuously while you focus on innovation.
Key capabilities
- →Self-fixing pipelines - Detect failures, diagnose root causes, apply fixes, and restart runs autonomously. Always on, always working.
- →True autonomous execution - Background agents handle long-running tasks independently, providing the execution layer that makes custom agents truly autonomous.
- →Automate workflows - Chain pipeline executions, trigger on data arrival, orchestrate multi-step analyses automatically. No manual intervention required.
- →Autonomous code quality - Scan codebases, promote stable modules to libraries, and refactor to best practices autonomously.
The Same Frontier Intelligence However You Work
Co-Scientist positions your organization at the forefront of AI-driven bioinformatics, accelerating velocity through automation without sacrificing quality, security, or reproducibility. The same frontier intelligence powers every team, however they work. Scientists gain independence, bioinformaticians build faster, and administrators enable innovation within guardrails.
| Bench Scientists | Bioinformaticians | Administrators |
|---|---|---|
| ✔ Higher sample throughput | ✔ Faster iteration cycles | ✔ Rapid agent deployment |
| ✔ Faster turnaround time | ✔ Intelligent troubleshooting | ✔ Deploy in your infrastructure |
| ✔ No bioinformatics queue | ✔ 24/7 autonomous pipeline execution | ✔ Enterprise governance |
| ✔ Self-sufficient analysis | ✔ Auto-optimization of resources | ✔ Utilize internal LLMs |
| ✔ Increased team productivity | ✔ Reduced infrastructure overhead | ✔ Consolidated AI governance |
| ✔ Real-time analysis visibility | ✔ Self-serve scientists | ✔ Full traceability & compliance |
Scientists
Move from waiting days for pipeline launches to running analyses independently within minutes. Higher sample throughput, faster turnaround times, and the autonomy to iterate on experiments without waiting on bioinformaticians or sacrificing quality or reproducibility. Track pipeline status in real time, access results immediately, and increase your team's overall productivity through a simplified interface designed for your experiments and your data.
Bioinformaticians
Shift from repetitive launch requests and production firefighting to building new capabilities. Faster iteration cycles, automated resource optimization, and AI-powered development that understands your full workspace context. Build truly autonomous agents with MCP connectivity and utilize your internal LLMs, while enabling scientists through governed self-service. Background agents provide 24/7 execution — orchestrating, self-fixing, and optimizing continuously so you focus on innovation, not DevOps.
Administrators
Accelerate AI adoption across your organization while maintaining full control. Deploy Co-Scientist within your infrastructure using bring-your-own-key models connecting to LLMs you've already approved. No data leaves your environment. Full enterprise governance through inherited RBAC, SSO, and security controls ensures compliance without slowing teams down. Consolidate AI tool sprawl into one governed platform, accelerate adoption with rapid agent deployment, and maintain complete visibility and traceability across your bioinformatics operations.
Built for Enterprise, Deployed Your Way
Co-Scientist utilizes continuously evolving AI capabilities to accelerate discovery while guaranteeing full traceability, governance, and reproducibility through Seqera’s platform architecture. Deploy through Seqera-managed cloud infrastructure for rapid adoption, or as containerized services within your VPC connecting to internal LLMs you’ve already approved. Proprietary data and code remain protected, eliminating external data flow concerns and streamlining compliance. Your platform becomes AI-ready on day one, with the controls your organization already trusts.