dsh-research-suite

dsh-research-suite

A DeepSeek Harness (DSH) plugin for the full clinical-research workflow — manuscript writing, language polishing, figures, statistics, research ideation, peer review, slides, literature search and journal formatting. Install it and it takes over research tasks automatically: no UI, no manual skill picking.

中文完整说明见 README.zh-CN.md（内容更全，含配置项、目录结构、占位符清单）。

• Package: dsh-research-suite · Version: 3.0.1 · License: MIT · DSH tested: 0.2.1-rc.5, 0.2.2-rc.1
• Requires Node ^22.19.0 || >=24.0.0, DSH >=0.2.0-0 <0.3.0
• Self-contained: all 592 source skill documents plus their bundled references/scripts/templates assets ship inside the package; nothing is read from any external skill directory at runtime.

Why capability cards instead of a skill router

The hard part of research work is not a lack of skills — it is that three to eight skills can each do the same task well in different ways. A router hands the model one "primary skill" name; the model then reads that skill's manual and improvises, losing the other skills' strengths along the way.

Instead, each capability card takes every competing skill in its group, records best_at (what it is best at), limits (what it explicitly cannot do) and take (the concrete rules, thresholds and templates lifted from it), then fuses them into one executable protocol. Every protocol step says which skill it comes from and why. The acceptance rule is strict: after reading one capability card you can finish the job without opening any original skill document.

The 592 source documents (and the 3,924 asset files they bring along) remain bundled as a deep-reading layer — for checking details, not for improvising.

How auto-takeover works

No UI, no buttons. Three pieces:

1. A system-prompt section — lib/prompt.js builds a policy named research-suite/policy at order: 650 ("after team policy, before tool docs"); lib/index.js registers it through systemPrompt.section({ name, order, text: () => buildPolicy(core) }). The policy tells the model: recognise a research task → call research_playbook first → follow the capability protocol → deep-read if needed → run research_gate before delivering.
2. 11 skills (skills/): one entry skill plus ten domain SOPs (writing / polish / figures / stats / ideation / review / slides / literature / format / data). Their content is inlined at registration time — passing a lazy load() hook fails DSH's runtime validation and silently drops every skill (the exact failure mode of v1).
3. 7 read-only tools for capability lookup, searching the 592-document catalog, deep reading (including skill-bundled assets), standards, and mechanical self-checks.

When research_playbook finds no match, the policy falls back to research_catalog + research_kb_read rather than refusing the task.

Domains

Domain	Source skills	Covers
writing	66	paper types and sections (original / review / case report / grant)
polish	12	register, de-AI-flavour, reduction, proofreading, Word reports
figures	36	data plots, statistical charts, mechanism diagrams, layout
stats	31	descriptive, comparison, regression, survival, prediction, PSM, MR, Meta, missing data, sample size
ideation	39	topic selection, novelty search, hypotheses, grants, ethics
review	21	self-review, reviewer comments, revision, rebuttal, response letters
slides	37	conference, lecture, defence, lab meeting, poster
literature	26	search strings, screening, close reading, evidence tables, recall/precision
format	51	journal formatting, references, figure/table specs, submission package
data	40	databases and omics data: GEO / TCGA / dbGaP / genotype and variant databases, omics retrieval and curation
Total	592	103 capability cards across the ten domains

toolbox is an additional index-only bucket of 233 utility skills: it feeds research_catalog and research_kb_read, and deliberately has no capability cards — a tool is a means, not a task a user asks for.

Every one of the 592 source skills has a recorded verdict in data/ledger/<domain>.json (fused — and which cards it feeds / index-only / deprecated / out-of-scope), so the "all studied, best only" claim is auditable: node scripts/verify-ledger.mjs all re-checks coverage and that every fused skill is actually a member of the card it claims. Beyond the text, skill-bundled assets ship too: 451 skills contribute 3,924 files (~29 MB) of references/, scripts/ and templates/ under knowledge/skills/<domain>/<slug>__assets/; research_kb_read(name, asset='scripts/plot.py') reads them (omitting asset lists what the skill ships with). Nine reference standards live in references/.

Tools

Tool	Purpose
research_playbook	The only entry point. Pass the user's own words; returns the 1–3 best-matching capability cards with protocol, gates, deliverables and suggested deep reads
research_capability	Expand a full capability card (member comparison, protocol, decisions, gates, outputs, kb) by id or by domain
research_catalog	Search the 592-document catalog by name/description keywords (the 233 toolbox skills included), optionally filtered by domain; each hit reports how many bundled assets it carries
research_kb_read	Read one skill document or INDEX.md/FUSION.md; the asset parameter reads a skill-bundled file such as scripts/plot.py or references/*.md (omitting it lists the skill's assets); paging and path-escape rejection included
research_standard	List or read the nine reference standards in references/
research_gate	Gate and mechanical self-check: section = all / data / selfcheck / mutex / forbidden / hard / handoffs; text checks fullwidth punctuation, superscript citation numbers, AI-cliché phrases and absolute wording
research_suite_status	Load self-check: version, per-domain capability counts, 592-entry catalog completeness, asset statistics, references, package root

Install

Published on npm as dsh-research-suite@3.0.1.

# via plugin_manager (GUI) — recommended
plugin_manager(action="install_bundle", target="dsh-research-suite@3.0.1")

# via CLI (Windows)
dsh.cmd plugin --profile desktop add dsh-research-suite@3.0.1
# via CLI (POSIX)
dsh plugin --profile desktop add dsh-research-suite@3.0.1

# from a local checkout (plugin development)
plugin_manager(action="install_bundle", target="<absolute package path>")

# from GitHub, if npm is not reachable
dsh plugin --profile desktop add github:xuzhecomeon/dsh-research-suite

Fully quit and restart DSH Desktop afterwards (closing the window is not enough — the loader reads the bundle patch layer at startup). Verify with research_suite_status.

Configuration

The plugin deliberately does not export a Config: in v2.0.0 that export (toJSON() returning JSON Schema) was hydrated by DSH's Host settings service as a schemastery envelope, crashed on schema.meta, and prevented DSH Desktop from starting. Configuration is now validated inside apply() by validateConfig().

Key	Default	Meaning
autoTakeover	true	Inject the auto-takeover prompt section; false degrades the plugin to "7 tools + 11 skills" without automatic routing
sectionOrder	650	Order of the prompt section (after team policy, before tool docs)
verbose	false	Log warnings when skill/tool/prompt registration fails

Because there is no exported Config, the DSH settings panel shows no entries for this plugin (a deliberate trade-off). Override values in the profile's cordis.patch.yml entry instead:

- id: dsh-research-suite
  config:
    autoTakeover: true
    sectionOrder: 650
    verbose: false

Documentation

• docs/CAPABILITY-SPEC.md — capability-card content contract
• docs/ARCHITECTURE.md — modules, data flow, how auto-takeover is implemented, and the v3 knowledge layer & ledger
• docs/PUBLISH.md — npm release, DSH install paths, upgrade/rollback, troubleshooting table
• CHANGELOG.md — what changed in 3.0.0

Self-checks

npm test                          # scripts/selftest.mjs — fake-ctx load smoke test
npm run verify                    # scripts/verify-package.mjs — static release checks
npm run verify:caps               # scripts/verify-capabilities.mjs all
node scripts/verify-ledger.mjs all # ledger coverage (11 domains, 592 skills) + fused check
npm run pack:check                # npm pack --dry-run (~38 MB unpacked in v3; knowledge/ included by design)

Measured on the current v3 tree (final numbers follow once every domain lands): 4,577 files / 38.62 MB on disk (scripts/verify-package.mjs count, includes .github/); the bulk is knowledge/ — 592 source documents plus 3,924 bundled asset files.

License

MIT — see LICENSE.

Scope note: MIT covers the plugin itself (lib/, data/, skills/, references/, scripts/, docs/ and the index files). The 592 skill texts and 3,924 bundled assets under knowledge/skills/ are third-party material vendored verbatim from the author's local skill collection; their licenses belong to their original authors and are not covered by MIT. Read docs/ATTRIBUTION.md before redistributing.