npm - @zerowall/dsh-plugin-skills - Versions diffs - 0.1.0-preview.5 → 0.1.0 - Mend

@zerowall/dsh-plugin-skills 0.1.0-preview.5 → 0.1.0

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package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-stem-cell-organoid.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Stem cell, iPSC, and organoid research — pluripotency markers, differentiation protocol pathways, lineage commitment factors, organoid model selection. Use for iPSC characterization, differentiation protocol design via developmental-pathway recapitulation, and organoid-model selection for disease modeling.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-structural-proteomics.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Structural biology plus proteomics integration for drug target validation. Combines PDB experimental structures, AlphaFold predictions, GPCRdb, SAbDab antibody structures, ProteinsPlus binding-site prediction, BindingDB ligand-affinity data, BMRB NMR data, CATH/InterPro fold classification, intrinsic-disorder prediction (MobiDB/DisProt/IUPred3), membrane-protein topology (OPM/TopDB/PDBTM/ChannelsDB), enzyme catalytic-site data (M-CSA), PDBe ligand/compound chemistry, and MD simulation trajectory metadata (MDDB). Use for druggability assessment, binding-site characterization, ligand-pocket analysis, structural-confidence scoring (resolution, pLDDT), antibody-target interface analysis, disordered-region assessment, membrane-protein topology, catalytic-mechanism lookup, and finding published MD simulations for a target.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-structural-variant-analysis.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Structural variant (SV) clinical interpretation: deletions, duplications, inversions, translocations, complex rearrangements. Applies ACMG-adapted criteria with ClinGen HI/TS dosage scores, gnomAD frequencies, and ClinVar evidence. Produces 5-tier classification with explicit per-criterion evidence. Use for clinical genomics SV review, dosage-sensitivity assessment, breakpoint analysis, and CNV pathogenicity calls. Gene-dosage-driven reasoning.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-synthetic-biology-parts.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Look up synthetic biology genetic parts (promoters, RBS, CDS/genes, terminators, reporters, composite devices) from the SynBioHub repository, including the iGEM Registry of Standard Biological Parts. Use when someone asks to "find a genetic part", "look up a BioBrick", "search SynBioHub", "get the sequence for BBa_...", "browse iGEM part collections", "find a promoter/RBS/terminator for a genetic circuit", or "what parts are available for [organism/function]". NOT for plasmid backbone/vector lookup by catalog ID (use tooluniverse-molecular-cloning's Addgene coverage), NOT for primer design once a part sequence is chosen (use tooluniverse-primer-design). Honest: SynBioHub disabled anonymous public REST access upstream — every unauthenticated call currently returns 401/HTML-login-page, verified live. This skill explains that limitation plainly and how to unlock real access (SYNBIOHUB_API_TOKEN) rather than pretending the tools work with no setup.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-systems-biology.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Systems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interaction Database. Multi-database pathway enrichment, protein-pathway relationships, network reasoning. Use for pathway analysis on a gene list, multi-source pathway concordance, and systems-level interpretation across databases.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-target-research.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Comprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD), druggability (DGIdb, ChEMBL approved drugs). 9 parallel research paths with citations. Use for full target profile reports, target characterization for drug discovery, and 'tell me about target X' queries.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-toxicology.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, toxicogenomic associations, and EPA CompTox quantitative hazard/high-throughput bioactivity data. Triangulates molecular initiating event to cellular outcome to organ-level toxicity to clinical adverse event. Use for hepatotoxicity/cardiotoxicity/nephrotoxicity prediction and toxicology reports.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-vaccine-design.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Computational vaccine candidate design: peptide/subunit vaccines via MHC-I/MHC-II epitope prediction (IEDB), population HLA coverage optimization, B-cell epitope identification, and cross-strain conservation analysis. Use for vaccine epitope prediction, HLA allele coverage, multi-epitope construct design, and immunogenicity assessment. Combines predicted MHC binding with experimentally validated IEDB epitopes for higher-confidence designs.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-variant-analysis.md CHANGED Viewed

@@ -2,7 +2,7 @@
 VCF and variant analysis — parsing, annotation, classification (synonymous, missense, frameshift, stop_gained), VAF filtering, coding vs non-coding categorization, multi-condition variant comparison, variant-notation conversion (SPDI/HGVS/VCF/rsID interconversion, ALFA per-ancestry allele frequencies), European Variation Archive (EVA) lookups (per-study cohort variant data, RS-accession resolution), HGVS validation/normalization (Mutalyzer), gene-specific curated variants (LOVD), canonical cross-database allele IDs (ClinGen Allele Registry), automated ACMG/AMP classification (GeneBe), principal-transcript selection (APPRIS), Ensembl linkage disequilibrium (LD) for GWAS/fine-mapping, GRCh37/GRCh38 coordinate liftover and protein/cDNA-to-genomic mapping, and Ensembl ID utilities (stable-ID version history, cross-references, region/gene feature overlap, assembly/species metadata). Use for VCF parsing, variant fraction calculations (denominator = coding subset only, NOT all variants), per-sample mutation profiling, converting a variant between SPDI/HGVS/VCF-coordinate/dbSNP-rsID representations, cross-checking a variant against EVA's raw submitted study cohorts, validating an HGVS string's syntax, looking up curated variants for a well-studied gene, resolving a variant to its ClinGen CA ID, getting an automated ACMG verdict, or picking a gene's principal transcript.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-variant-functional-annotation.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Functional annotation of protein variants — ProtVar structural/functional context, ClinVar clinical classifications, gnomAD population frequencies, CADD deleteriousness, ClinGen gene-disease validity, plus FAVOR one-call comprehensive GRCh38 annotation. Use for variant annotation pipelines, missense effect prediction, and protein-level variant interpretation with functional context.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-variant-interpretation.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Use for VUS classification, pathogenicity assessment with cited criteria, structure-based variant impact (AlphaFold/PDB), non-coding/regulatory variant effect prediction with sequence deep-learning models (AlphaGenome, Enformer, Borzoi, ChromBPNet, Evo 2), and producing clinical-grade variant reports for return of results or molecular tumor boards. Use this whenever a user asks about a variant's significance, an intronic/promoter/enhancer/UTR non-coding variant's functional impact, or needs ACMG classification — even if they don't say "ACMG".
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-variant-predictor-dms-validation.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Validate a variant-effect predictor (AlphaMissense, ESM-C SAE, ESM logits, EVE, conservation scores, or any per-variant numeric score) against experimental deep mutational scanning (DMS) data. Computes per-variant predictor scores, splits variants into neutral vs disruptive groups by DMS effect, runs a Mann-Whitney U test on the predictor scores, and sweeps the stratification thresholds for robustness. Use when you need to know whether a predictor's scores track real functional disruption on a specific protein.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/resources/skills/zerowall-tooluniverse/references/upstream/tooluniverse-variant-to-mechanism.md CHANGED Viewed

@@ -2,7 +2,7 @@
 End-to-end variant-to-mechanism analysis — trace a variant (rsID/coordinates) through regulatory context, target gene(s), molecular pathway(s), and phenotypic consequences. Integrates 7+ databases across 3 evidence layers (regulatory, molecular, disease) for a mechanistic model. Use for GWAS-hit-to-mechanism, eQTL-causal-gene tracing, and full causal-chain reports.
-这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 RMCP 模块。
+这是上游科学工作流的远程导航摘要。先用 research_workflow 的 tooluniverse 模块 search，再 describe 精确能力；SDK、安装及管理命令不在此处执行。目录中的候选工具需逐个核对 schema、availability 和 verification。专项分析仍使用对应 zerowallrmcp 模块。
 上游研究阶段（仅作为任务拆解线索，实际方法条件需另行核对）：

package/zerowall.plugin.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@zerowall/dsh-plugin-skills",
-  "version": "0.1.0-preview.4",
+  "version": "0.1.0",
   "host": "./lib/index.js",
   "client": "./lib/client.js",
   "remote": "./lib/typert.remote-client.js",
@@ -23,7 +23,6 @@
   ],
   "profiles": [
     "development",
-    "preview",
     "stable"
   ],
   "migrationVersion": 1,