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Superbio's Agentic Pipeline Builder is Here 🚀

Connecting the dots: our grand plan for AI models, literature search, and scientific intelligence.

Author

Superbio AI
August 04, 2025

The Road to Scientific Intelligence

Dear all,

Earlier this year, we launched the Superbio Co-pilot—our most-used product ever and the first step toward building scientific agents that accelerate research.

Today, we’re taking the next big step: introducing the Superbio Pipeline Builder.
Built on top of Co-pilot’s deep understanding of 100s of AI models on Superbio, the Pipeline Builder is a scientific agent that assembles cohesive computational workflows - not just single models.

Scientists don’t work with isolated tools, and neither should AI agents. This new feature helps you develop robust, multi-step pipelines that reflect real-world scientific reasoning - and which are entirely available to execute on Superbio.

It’s especially powerful for “generative biology” tasks, like:

  • Protein design

  • Generative chemistry

  • Biological sequence design

Agent Evaluations

We compared Superbio’s Pipeline Builder head-to-head with leading reasoning LLMs on a series of pipeline-building and parameter-setting tasks - ground truth examples we developed internally to help evaluate and improve our system.

Fig 1a. - Results from three technical replicates on a series of internal benchmarks: 42 pipeline building tasks focused on AI-native computational workflows.

Fig 1b. - Results from three technical replicates on a series of internal benchmarks: 50 parameter setting tasks requiring literature search to find biologically-relevant information.

Thanks to Superbio’s proprietary Bio-AI knowledge context and lit search capabilities, we observed our agent delivers higher accuracy answers for complex biological queries.

Key Features

🧠 Automate Workflow Suggestions
The agent suggests relevant models and assembles them into a cohesive pipeline - tailored to your specific query.

Superbio’s Pipeline Agent reasoning over app selection.

âž° Human-in-the-loop Editing
Accept the app sequence by hitting “Continue”, or suggest changes by sending a chat message (i.e. “Can you use RFAntibody instead?”)

Asking Pipeline Builder to customize the app sequence.

🤖 Intelligent Parameter Suggestions
Get context-aware parameter suggestions backed by scientific literature. Everything remains fully editable.

Editing suggested parameters in the UI.

📨 Seamless Sharing & Export
Generate polished reports and export your pipeline as a PDF - for your collaborators, presentations, or your own documentation.

Export a PDF pipeline report, complete with reasoning steps and citations.

With the Pipeline Builder, Superbio evolves from a marketplace of dispersed AI tools, into a scientific though partner capable of planning comprehensive experiments - not just individual steps.

Coming soon: automatic pipeline execution. Want early access? Reply to this email 👉

Onwards and upwards,
The Superbio Team 🚀