MCP server · Research
BioHarbor MCP server
by danielLuo2
Let your AI run real biology analyses on your own GPUs, like sequence checks, protein searches and structure prediction.
BioHarbor is a helper program that lets your AI actually run biology tools instead of just talking about them. You ask for an analysis, and it does the work on your own computer or lab GPU. It is handy for researchers, students and anyone who works with DNA or protein sequences and wants to skip the command line.
What is an MCP server? The 30-second version
On its own, your AI can only chat. An MCP server is a small helper program that gives your AI a new skill or a connection to a tool. BioHarbor is that helper for biology work: it connects your AI to real analysis programs like MMseqs2 and ESMFold. So when you ask a question about a sequence, the AI can actually run the analysis and bring back the result.
What this MCP server does
You ask your AI something like finding the longest gene in a DNA snippet or predicting a protein's shape. The AI passes your request to BioHarbor. BioHarbor first checks that your input makes sense, then runs the right biology tool, either right away or by waiting in line for a free GPU. When it finishes, it sends back a short summary and saves the full results as files on your computer.
What you can do with it
- Check a DNA or protein sequence and get its length, type and GC content
- Translate DNA into protein in one frame or all six frames
- Find the longest open reading frames on both strands
- Search a protein or translated DNA against a local reference database for similar sequences
- Predict a protein's 3D structure and see which parts are low confidence
- Check which GPUs are free before starting a big job
- Follow the status of a long-running job and cancel it if needed
Try asking your AI
- “Find the longest ORF in this contig and translate it”
- “Search Swiss-Prot for homologs of this protein sequence”
- “Predict the structure of this protein and tell me which regions are low confidence”
- “What is the GC content and molecular weight of this DNA sequence”
What it gives back to you
You get a short summary in the chat, like the number of homologs found or the average confidence of a predicted structure. Longer jobs give you a job ID right away, and you can ask for the result later. Full outputs such as structure files or search results are saved on disk, and the summary tells you where they are.
Before you start
What you need
- Python installed on your computer
- BioHarbor installed with pip
- A reference database set up for homology search, if you want to use that tool
- A GPU with the right setup if you want to predict structures
Good to know
This is an early alpha version, and the HTTP mode has no login protection yet, so keep it on your own machine or use an SSH tunnel.
Install it with your AI
Add BioHarbor MCP server to your AI, no technical skills needed
You don't install anything by hand. You copy one prompt, paste it into an AI that can work on your computer, and it checks, installs and connects the server for you, asking you when it needs something.
Sign in to get the install prompt
Members get a ready-made prompt that lets the Claude desktop app check BioHarbor MCP server, install it and connect it for them, step by step. You don't need any technical skills: you copy, paste and answer a few questions. Your connected AI can also find and install any of the 4,609 MCP servers here for you.
Who it's for
Biologists, bioinformatics students and lab researchers who want to run sequence and structure analyses through their AI assistant without typing commands.
