BioDSH

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A bioinformatics agent for clinicians and wet-lab scientists. Describe the analysis in plain language and get the result, with no coding.

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You add your data (single-cell h5ad, count matrices, clinical tables, gene lists…) and ask a question such as "Do responders and non-responders differ in CD8A expression?" The agent loads the data, picks the right method, writes and runs the code, and reports the conclusion along with the figures, the tables and every step it took.

BioDSH runs on your own computer and is built on DeepSeek Harness (dsh). It comes in two forms: a one-click desktop app and a dsh plugin (dsh-biodsh).

_{BioDSH 1.0 skill hub (preview; catalog entries and counts are illustrative). Interactive preview}

Why BioDSH

• Plain language in, conclusions out. You don't need to write code or set up an environment. A Python analysis environment (scanpy, anndata, pandas, statsmodels, matplotlib…) installs itself on first launch.
• Validated methods instead of improvised code. It ships 17 official analysis skills: single-cell QC, clustering, annotation and treatment response; bulk RNA-seq with limma-voom; Kaplan–Meier and Cox survival; regression with robust standard errors; ANOVA designs; and more. The statistics skills were checked against R on tens of thousands of cases (for example, 101,587 survival comparisons with zero mismatches).
• The right skill picked automatically. For each request, a model selects the one or two relevant skills from the 17 official skills and a library of 2,000+ community skills, and loads only those. The context stays small and cheap.
• Low cost. BioDSH runs on DeepSeek models. On our analysis tasks its accuracy is on par with Claude Code (Sonnet/Haiku) at about 3–13× lower cost per task (see Results).
• Long analyses always finish. A convergence guard keeps the agent from running in circles. It first asks the agent to wrap up, then asks for a final answer, so you always get a result.
• Your data stays safe. Original files are never modified, and every analysis writes into a new folder. In offline mode BioDSH talks only to a model on your own machine or intranet and makes no outbound requests, which suits hospitals and labs.
• Every result can be traced. Every step goes into an append-only session log that you can review, export or hand to a reviewer.
• Reusable workflows. You can save a finished analysis as a workflow and rerun it on new data. BioDSH can also build a workflow from an existing script, notebook or methods paragraph.
• Your choice of model. BioDSH works with DeepSeek's official API, any OpenAI-compatible endpoint, or a local or intranet model, and you can configure several of them side by side.

Download

Version	Platform	Get it
1.0.0 Preview 1 (new)	Windows 10/11	BioDSH_1.0.0_x64-setup.exe
0.3.0 (stable)	Windows, macOS (Apple silicon)	Latest release

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