dsh-science

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A Claude Science–style research workbench for DeepSeek Harness — for genomics / pathogens / human health / bioinformatics projects.

One-liner: dsh-science — Claude Science-style research workbench for DSH: ReAct research-loop engine (research_* tools), versioned artifacts with provenance (artifact_* tools), an SSH remote-compute engine (remote_* tools, mirroring Claude Science's Computer / Remote compute clusters), and 11 science skills for genomics / pathogens / bioinformatics.

• ReAct research loop engine — research_init / research_state / research_hypothesis / research_experiment / research_findings / research_phase / research_review / research_report, persisted in a research-manifest.json state machine (Question → Hypothesis → Experiment → Observe → Analyze → Conclude → Next Question).
• Versioned artifacts with provenance — artifact_save / artifact_list / artifact_show / artifact_diff / artifact_verify / artifact_deprecate / artifact_reproduce: every result saved as artifacts/<name>/v<N>/ with per-file SHA-256, artifact.json provenance (command / inputs / environment / envFile) and an append-only provenance.md.
• Remote compute engine (SSH / HPC clusters) — 16 tools: remote_host_add / remote_host_probe / remote_host_notes / remote_run / remote_status / remote_logs / remote_pull / remote_cancel / remote_exec etc. Connect lab workstations or HPC clusters via ~/.ssh/config aliases (nothing installed on the host, zero third-party deps). Long bioinformatics jobs run as detached processes on workstations or via sbatch on SLURM — they survive connection loss; submission asks for approval by default; remote_status batch-monitors and auto-transitions state (running → succeeded/failed/killed); remote_pull fetches outputs back (files over the size threshold stay on the host with their paths recorded).
• Remote Hosts config UI (bundle/profile-level) — a Settings > 远程主机 page (the analog of Claude Science's Settings > Compute > SSH hosts): list/add/probe/edit/remove hosts, plus each project's access allowlist and job summary. Host-side REST API (webServer route /dsh-science/remote-hosts/*, engines/remote-hosts-ui.mjs) + client bundle (client/remote-hosts-ui/, built by scripts/build-client-bundle.mjs) sharing the same data files as the remote engine. Requires a web-process restart to activate (see docs/remote-hosts-ui.md).
• Model Tier router (tiered, cross-provider) — via the companion bundle dsh-model-tier: within one session, automatically routes auxiliary requests (session titles, compaction summaries) and subagent/background tasks to a light tier, keeps the main conversation on the default tier, and escalates complex work (deep subagent chains, very long inputs) to a strong tier — each tier may point at a different provider (e.g. strong GLM-5.3 / default deepseek-v4-flash / light minimax-M3), mirroring Claude Code's Opus/Sonnet/Haiku strategy. Built on DSH's native agent/request + llm/stream waterfall extension points; a no-op when the tier's provider is unregistered. Installed automatically with dsh-science, but also standalone-installable into any profile (dsh plugin add dsh-model-tier).
• 11 science skills — research-loop, science-project-setup, artifact-provenance, scientific-review

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