BioDSH tech preview · the first bioinformatics plugin ecosystem for DeepSeek Harness

Everything is a plugin. Every analysis is a sentence.

BioDSH is the bioinformatics agent desktop for clinicians and wet-lab scientists: built on DeepSeek Harness, it turns single-cell, bulk RNA-seq, clinical statistics, public databases, literature, Zotero, Excel — even your mouse and keyboard — into plugins of a DeepSeek agent.

No coding: drop in data, say what you need, read the conclusion. Runs locally, never modifies your originals, fully offline inside hospital intranets.

Skill store · 2,183 plugins GitHub

Download for Windows · x64 installer · double-click

Windows 10/11. On first run click "More info → Run anyway". Updates itself afterwards.

Download for macOS · Apple silicon · dmg

macOS 12+. If it says the app is “damaged”, open Terminal and run sudo xattr -cr /Applications/BioDSH.app then reopen (normal Gatekeeper block for unsigned apps).

On an Intel Mac? Other platforms (Intel Mac / Linux)

AGENT = DEEPSEEK + HARNESS + BIODSH

BioDSH
keeps bioinformatics running in real labs

The model is the soul of an agent.

Harness gives it hands; BioDSH gives it bioinformatics: skills, databases, literature, desktop control.

DeepSeek Harness core

DSH CORE

The core only loads plugins and keeps an append-only session log. BioDSH does not change a single line of it.

Bio capabilities as plugins

CAPABILITIES AS PLUGINS

Single-cell, literature, databases, Zotero, Excel, desktop control — 2,183 skill plugins install in one click, official skills included out of the box.

Ready out of the box

READY OUT OF THE BOX

Ships with a Python analysis environment, 9 evaluated official skills and 4 real example projects. No coding required.

Product approach

Everything is a plugin. Every step is reproducible.

Everything is a plugin

BioDSH stands on the DeepSeek Harness plugin system: the best 2,174 open-source bio skills have been collected, translated and organised into 10 domains × 40 topics, plus 9 offline-reproducible official skills. Whatever you need, one click in the store installs it.

Every analysis is traceable

Everything the model sees goes into an append-only session log: system prompts, reasoning, tool calls and results. In the chat, the intermediate steps fold into one line — “BioDSH finished N steps” — and expand level by level. Conversations export for your advisor or reviewers; projects snapshot in one click.

Four real example projects

They are in your project list the moment you install, each a real recorded conversation: single-cell analysis and plotting, literature review, public database retrieval, desktop control with Zotero. Just ask the same way.

BioDSH skill store: official skills and 2,174 community skills organised by domain

BioDSH chat: intermediate steps folded into one line, expandable level by level

Single-cell analysis & plots

PBMC 3k raw counts → QC → clustering → annotation → UMAP, then double-check whether CD8 T and NK cells were confused.

Literature review

Search the PubMed / Europe PMC APIs, build a DOI-annotated table and a review outline, and pick what deserves a close read.

Public database retrieval

NCBI / UniProt annotation tables, Hallmark enrichment, GTEx expression heatmaps; local reference packs work offline.

Desktop control & Zotero

Add papers to Zotero by DOI, open Excel, paste a table and save — with a “BioDSH is controlling the computer” banner on screen.

Product approach

Everything is a plugin. Every step is reproducible.

Everything is a plugin

BioDSH stands on the DeepSeek Harness plugin system: the best 2,174 open-source bio skills have been collected, translated and organised into 10 domains × 40 topics, plus 9 offline-reproducible official skills. Whatever you need, one click in the store installs it.

BioDSH skill store: official skills and 2,174 community skills organised by domain

Every analysis is traceable

Everything the model sees goes into an append-only session log: system prompts, reasoning, tool calls and results. In the chat, the intermediate steps fold into one line — “BioDSH finished N steps” — and expand level by level. Conversations export for your advisor or reviewers; projects snapshot in one click.

BioDSH chat: intermediate steps folded into one line, expandable level by level

Four real example projects

They are in your project list the moment you install, each a real recorded conversation: single-cell analysis and plotting, literature review, public database retrieval, desktop control with Zotero. Just ask the same way.

Single-cell analysis & plots

PBMC 3k raw counts → QC → clustering → annotation → UMAP, then double-check whether CD8 T and NK cells were confused.

Literature review

Search the PubMed / Europe PMC APIs, build a DOI-annotated table and a review outline, and pick what deserves a close read.

Public database retrieval

NCBI / UniProt annotation tables, Hallmark enrichment, GTEx expression heatmaps; local reference packs work offline.

Desktop control & Zotero

Add papers to Zotero by DOI, open Excel, paste a table and save — with a “BioDSH is controlling the computer” banner on screen.

Customize your BioDSH

Fully offline

OFFLINE MODE

Inside a hospital intranet, connect a local or intranet model, or your lab’s Linux server.

MCP integration

MCP SERVERS

Plug Zotero, PubMed and your lab’s own services into the agent.

One-click migration

MIGRATE SKILLS

Bring existing skills over from Claude Code, Codex, OpenCode or Cursor.

Get started

Up and running in three minutes

Download and install

Double-click the installer — no admin rights needed, it updates itself afterwards.

Download for Windows Download for macOS

Add a key, install the environment

Get an API key from the DeepSeek open platform and paste it in; the app ships its own Python toolchain and installs the analysis packages in one click.

More → API key → Environment → one-click installGet a DeepSeek key

Join the BioDSH plugin ecosystem

BioDSH is still a technical preview; the official skills and the desktop app will keep evolving. We look forward to working with clinicians, wet-lab scientists and bioinformatics developers to turn bioinformatics analysis into plugins anyone can use, on top of DeepSeek Harness’s open, reusable, composable infrastructure.

GitHub Download Skill store