Plugins

Bioinformatics agent preset with 17 BioDSH analysis skills (single-cell, bulk RNA-seq, survival, regression, ANOVA), a 2000+ skill library searched by a skill_library tool, per-message skill selection and a time/step convergence guard.

BioDSH for DeepSeek Harness: a bioinformatics agent preset with BioDSH skills, a 2000+ skill library, automatic skill selection and a convergence guard

Claude Science-style research workbench: ReAct research-loop engine (research_* tools), versioned artifacts with provenance (artifact_* tools), and 10 science skills for genomics/pathogens/bioinformatics.

Reproducible science workbench: agent-driven cells, inline figures with feedback/rerun, manifest provenance, environment snapshots, and publication-grade figure skills (9 bio_* tools + workbench UI).

Literature research toolset registering 26 model tools over PubMed, Europe PMC, OpenAlex, PubTator3 and Semantic Scholar: field-syntax search, ID conversion, bibliographic lookup, citation formatting, MeSH and related-article walking, PubTator bioconcept resolution and relation queries, Europe PMC and Semantic Scholar paging, full-text retrieval, and open-access PDF discovery with optional download. A unified search deduplicates hits across sources and orders results by cross-source hits, then relevance, then citation count; a session knowledge graph with PubTator concept enrichment commits to a persistent user graph and renders as Mermaid. Most sources need no key.

Whole-report verification for scientific reports: per-claim checks against Crossref, PubMed (retraction scan), ClinicalTrials.gov, UniProtKB, GEO/SRA and PatentsView, URL accessibility and title agreement, claim-vs-source meaning at temperature 0, and a durable restartable audit ledger with an annotated report.

Assembly-aware strawberry research evidence tools for DeepSeek Harness

Biomedical research plugin for DeepSeek Harness (dsh): biomcp MCP server tools, scientific plotting skills, and deep-research subagent

生物信息学「许愿式分析」插件：BioPython 全功能覆盖（任意代码执行器 bio_python + 14 个领域 skill）+ 高频语义化工具 + 零依赖自举 Python 环境（uv + venv + biopython 自动下载到插件私有目录）。用户下载安装即可许愿式分析。

Runs OmicVerse/OmicOS bioinformatics analyses in a persistent Python kernel, with capability-catalog search, kernel inspection and an account tab.

Single-cell RNA-seq workbench usable from the Harness UI or from agent tools: imports h5ad, 10x, loom, Seurat RDS and archive files, runs QC, filtering, normalisation, highly variable genes, PCA, neighbour graph, clustering, UMAP/t-SNE, marker genes and cell-type annotation, offers resolution scans and saved marker panels, and exports h5ad, result tables and reports.

GEO and bulk transcriptomics workbench backed by a local Python and R engine: search and download GEO series, import your own counts or TPM matrix, then run QC, filtering, normalisation, batch correction, PCA, differential expression, GO/KEGG/GSEA enrichment, immune infiltration, survival and prognosis, signature mapping onto single-cell data, and circRNA, miRNA, lncRNA, fusion and alternative-splicing modules.

WispOps (dsh-wisp-ops): multi-host server operations plugin for DeepSeek Harness — fleet inspection, disk & recent-file analysis with omics cleanup advice, security triage, scheduled per-server reports, human-approved sudo

蛋白质结构预测与设计插件：序列设计（ProteinMPNN/SolubleMPNN/LigandMPNN）、结构预测（ESMFold）、复合物界面筛选、序列理化打分与多样性聚类——零手动自举（本地 CPU/GPU 自适应），供 dsh-bio-genie 消费 | Protein structure prediction & design toolkit for dsh (sequence design, folding, interface screening)

Bioinformatics workflow catalog, WDL bundle store, and declarative preflight for DeepSeek Harness.