Illumina
Illumina
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Proto Tools
A lot of computational biology looks like this: find a tool that does what you need, spend half a day getting it to install, spend another day figuring out how to call it, then reformat the output so the next tool can use it. Every tool has its own opinions about Python versions, CUDA, weight paths, and input formats.Proto Tools implements these tools so they all behave the same way. Each one is a Python function with a Pydantic input and output. Fold a protein with AlphaFold3, sample sequences with ProteinMPNN, search with BLAST; the shape of the call is the same, and the first invocation quietly sets up the environment and weights in isolation.Use it on its own, or as the tools layer of the broader Proto framework.Key Features
A quick tour of what proto-tools handles for you. Each card opens a deeper guide.Unified Interface
Consistent Python APIs with standardized Pydantic Input/Config/Output models across all tools
Isolated Environments
Each tool gets its own virtual environment; weights and dependencies are fetched and cached on first use
Device Management
Automatic GPU allocation, LRU eviction, and multi-GPU routing
Parallel Execution
Fan a single tool call out across every visible GPU with ToolPool
Tool Catalog
Every tool we implement, at a glance. Select any to open its page.Get Started
Installation
Set up the package and optional dependencies
Quickstart
Run your first tool in 5 minutes
Concepts
Understand the tool pattern and execution model