@nahisaho/satori 0.11.0 → 0.11.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (17) hide show
  1. package/README.md +33 -7
  2. package/package.json +1 -1
  3. package/src/.github/skills/scientific-admet-pharmacokinetics/SKILL.md +1 -0
  4. package/src/.github/skills/scientific-clinical-decision-support/SKILL.md +2 -0
  5. package/src/.github/skills/scientific-computational-materials/SKILL.md +4 -4
  6. package/src/.github/skills/scientific-deep-learning/SKILL.md +1 -0
  7. package/src/.github/skills/scientific-epidemiology-public-health/SKILL.md +1 -0
  8. package/src/.github/skills/scientific-grant-writing/SKILL.md +2 -0
  9. package/src/.github/skills/scientific-lab-data-management/SKILL.md +2 -2
  10. package/src/.github/skills/scientific-meta-analysis/SKILL.md +10 -0
  11. package/src/.github/skills/scientific-pharmacovigilance/SKILL.md +3 -0
  12. package/src/.github/skills/scientific-population-genetics/SKILL.md +2 -0
  13. package/src/.github/skills/scientific-precision-oncology/SKILL.md +1 -0
  14. package/src/.github/skills/scientific-scientific-schematics/SKILL.md +2 -2
  15. package/src/.github/skills/scientific-single-cell-genomics/SKILL.md +2 -0
  16. package/src/.github/skills/scientific-survival-clinical/SKILL.md +11 -0
  17. package/src/.github/skills/scientific-variant-interpretation/SKILL.md +1 -0
package/README.md CHANGED
@@ -23,15 +23,24 @@ hypothesis-pipeline → pipeline-scaffold → academic-writing → critical-revi
23
23
 
24
24
  ```
25
25
  research-methodology → grant-writing → hypothesis-pipeline ← [O→A 研究計画]
26
+ │ ↑ ↓
27
+ regulatory-science ───┘ scientific-schematics
28
+ (FDA/ISO/特許) (研究計画図)
26
29
  ↓
27
30
  drug-target-profiling → admet-pharmacokinetics ─→ drug-repurposing
28
31
  (標的同定) (ADMET/PK 評価) (リポジショニング)
29
- ↓ ↓
32
+ ↓ │ ↓
30
33
  protein-structure-analysis → protein-design → lab-automation
31
34
  (構造解析) (de novo 設計) (実験自動化)
35
+ │
36
+ lab-data-management
37
+ (Benchling/DNAnexus/OMERO)
32
38
  ↓
33
39
  variant-interpretation → clinical-decision-support → presentation-design
34
40
  (バリアント解釈) (臨床意思決定) (学会発表)
41
+ ↑
42
+ pharmacogenomics
43
+ (PGx 代謝型)
35
44
  ```
36
45
 
37
46
  各ステップで生成されるファイルが次のステップに自動的に引き継がれます：
@@ -41,17 +50,23 @@ variant-interpretation → clinical-decision-support → presentation-design
41
50
  ```
42
51
  pharmacovigilance ← admet-pharmacokinetics ← [P 安全性監視]
43
52
  (市販後安全性) (前臨床 ADMET) ↓
53
+ │ regulatory-science
54
+ │ (FDA/ISO/特許)
55
+ ↓ ↓
44
56
  precision-oncology → clinical-decision-support → medical-imaging
45
57
  (腫瘍プロファイル) (臨床意思決定) (画像診断)
46
- ↓ ↓
58
+ ↓ ↑ ↓
47
59
  disease-research → variant-interpretation → deep-learning
48
60
  (疾患-遺伝子) (バリアント解釈) (DL フレームワーク)
61
+ ↑ ↓
62
+ pharmacogenomics neuroscience-electrophysiology
63
+ (PGx 代謝型) (スパイクソート/EEG/HRV)
49
64
  ↓
50
65
  quantum-computing → bayesian-statistics → graph-neural-networks
51
66
  (量子計算) (ベイズ推論) (GNN 分子予測)
52
- ↓
53
- explainable-ai ← deep-learning ← [R 先端計算]
54
- (XAI 説明可能性) (DL パイプライン)
67
+ │ ↓
68
+ computational-materials explainable-ai ← deep-learning ← [R 先端計算]
69
+ (pymatgen/VASP) (XAI 説明可能性) (DL パイプライン)
55
70
  ```
56
71
 
57
72
  **次世代オミクス・疫学パイプライン（T-Z）**
@@ -60,7 +75,15 @@ quantum-computing → bayesian-statistics → graph-neural-networks
60
75
  single-cell-genomics → spatial-transcriptomics ← [T シングルセル・空間]
61
76
  (scRNA-seq QC) (Visium/MERFISH)
62
77
  ↓ ↓
63
- immunoinformatics → infectious-disease ← [U 免疫・感染症]
78
+ epigenomics-chromatin → gene-expression-transcriptomics
79
+ (ChIP-seq/ATAC/WGBS) (GEO/GTEx/DESeq2)
80
+ │ │
81
+ └─────────────┬─────┘
82
+ ↓
83
+ proteomics-mass-spectrometry → multi-omics ← [F オミクス統合]
84
+ (LC-MS/MS/PTM/GNPS) (統合解析)
85
+ ↓
86
+ immuninformatics → infectious-disease ← [U 免疫・感染症]
64
87
  (エピトープ予測) (AMR・系統解析)
65
88
  ↓ ↓
66
89
  microbiome-metagenomics → environmental-ecology ← [V マイクロバイオーム・環境]
@@ -69,8 +92,11 @@ microbiome-metagenomics → environmental-ecology ← [V マイクロバイ
69
92
  systems-biology population-genetics ← [W+Y モデル・集団]
70
93
  (SBML/FBA/GRN) (Fst/ADMIXTURE)
71
94
  ↓ ↓
72
- epidemiology-public-health → text-mining-nlp ← [X+Z 疫学・NLP]
95
+ epidemiolog-public-health → text-mining-nlp ← [X+Z 疫学・NLP]
73
96
  (RR/OR/空間クラスタ) (NER/KG/BERTopic)
97
+ ↑
98
+ clinical-trials-analytics
99
+ (ClinicalTrials.gov)
74
100
  ```
75
101
 
76
102
  | フェーズ | 生成ファイル | 参照先 |
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@nahisaho/satori",
3
- "version": "0.11.0",
3
+ "version": "0.11.1",
4
4
  "description": "SATORI — Agent Skills for Science. GitHub Copilot Agent Skills collection for scientific data analysis.",
5
5
  "main": "index.js",
6
6
  "bin": {
package/src/.github/skills/scientific-admet-pharmacokinetics/SKILL.md CHANGED
@@ -373,3 +373,4 @@ def one_compartment_pk(dose, ka, ke, vd, time_points):
373
373
  | `scientific-drug-repurposing` | → ADMET 通過化合物のリポジショニング候補評価 |
374
374
  | `scientific-clinical-decision-support` | → PK パラメータの臨床応用 |
375
375
  | `scientific-academic-writing` | → 研究成果の論文化 |
376
+ | `scientific-regulatory-science` | → FDA 規制申請・承認履歴 |
package/src/.github/skills/scientific-clinical-decision-support/SKILL.md CHANGED
@@ -300,3 +300,5 @@ Clinical decisions must be made by qualified healthcare professionals.
300
300
  | `scientific-deep-research` | ← 最新エビデンスの収集 |
301
301
  | `scientific-presentation-design` | → 臨床結果のプレゼンテーション |
302
302
  | `scientific-academic-writing` | → 研究成果の論文化 |
303
+ | `scientific-clinical-trials-analytics` | ← 臨床試験マッチング・競合解析 |
304
+ | `scientific-pharmacogenomics` | ← PGx バイオマーカー・投与量調整 |
package/src/.github/skills/scientific-computational-materials/SKILL.md CHANGED
@@ -343,10 +343,10 @@ def parse_vasp_output(vasprun_file="vasprun.xml"):
343
343
 
344
344
  | スキル | 関連 |
345
345
  |---|---|
346
- | `scientific-quantum-chemistry` | DFT / 量子化学計算 |
347
- | `scientific-molecular-dynamics` | 分子動力学シミュレーション |
348
- | `scientific-visualization` | 構造可視化 |
349
- | `scientific-data-analysis` | 材料データ統計解析 |
346
+ | `scientific-quantum-computing` | 量子計算・VQE・量子化学 |
347
+ | `scientific-cheminformatics` | 分子記述子・構造解析 |
348
+ | `scientific-publication-figures` | 構造・相図可視化 |
349
+ | `scientific-materials-characterization` | XRD・SEM・実験材料特性 |
350
350
 
351
351
  ### 依存パッケージ
352
352
 
package/src/.github/skills/scientific-deep-learning/SKILL.md CHANGED
@@ -373,3 +373,4 @@ def export_model(model, sample_input, export_dir="models"):
373
373
  | `scientific-image-analysis` | ← 画像データの CNN 応用 |
374
374
  | `scientific-medical-imaging` | → 医用画像の DL モデル |
375
375
  | `scientific-quantum-computing` | ← 量子-古典ハイブリッド ML |
376
+ | `scientific-neuroscience-electrophysiology` | ← 神経デコーディング・スパイクソート DL |
package/src/.github/skills/scientific-epidemiology-public-health/SKILL.md CHANGED
@@ -326,6 +326,7 @@ def blocks_all_backdoor(G, X, Y, Z):
326
326
  | [scientific-meta-analysis](../scientific-meta-analysis/SKILL.md) | メタアナリシス・系統的レビュー |
327
327
  | [scientific-infectious-disease](../scientific-infectious-disease/SKILL.md) | 感染症疫学 |
328
328
  | [scientific-bayesian-statistics](../scientific-bayesian-statistics/SKILL.md) | ベイズ空間モデル |
329
+ | [scientific-clinical-trials-analytics](../scientific-clinical-trials-analytics/SKILL.md) | 臨床試験レジストリ |
329
330
 
330
331
  #### 依存パッケージ
331
332
 
package/src/.github/skills/scientific-grant-writing/SKILL.md CHANGED
@@ -313,3 +313,5 @@ BUDGET_JUSTIFICATION_TEMPLATE = """
313
313
  | `scientific-hypothesis-pipeline` | ← 仮説定義・課題設定 |
314
314
  | `scientific-deep-research` | ← 文献レビュー・先行研究調査 |
315
315
  | `scientific-academic-writing` | ← アカデミックライティングスキル |
316
+ | `scientific-scientific-schematics` | ← 研究計画図・フロー図生成 |
317
+ | `scientific-regulatory-science` | ← 規制戦略セクション |
package/src/.github/skills/scientific-lab-data-management/SKILL.md CHANGED
@@ -324,10 +324,10 @@ def fork_protocol(original_protocol_id, modifications):
324
324
  | スキル | 関連 |
325
325
  |---|---|
326
326
  | `scientific-bioinformatics` | ゲノミクスデータ解析 |
327
- | `scientific-imaging-analysis` | 顕微鏡画像解析 |
327
+ | `scientific-image-analysis` | 顯微鏡画像解析 |
328
328
  | `scientific-gene-expression-transcriptomics` | RNA-seq データ管理 |
329
329
  | `scientific-single-cell-genomics` | scRNA-seq データ管理 |
330
- | `scientific-data-analysis` | データ前処理 |
330
+ | `scientific-data-preprocessing` | データ前処理 |
331
331
 
332
332
  ### 依存パッケージ
333
333
 
package/src/.github/skills/scientific-meta-analysis/SKILL.md CHANGED
@@ -355,6 +355,16 @@ def cumulative_meta_analysis(studies_df, sort_by="year", model="random"):
355
355
  | EuropePMC | `EuropePMC_search_articles` | ヨーロッパ文献検索 |
356
356
  | Crossref | `Crossref_search_works` | 出版情報検索 |
357
357
 
358
+ ### 参照スキル
359
+
360
+ | スキル | 連携 |
361
+ |---|---|
362
+ | `scientific-survival-clinical` | ← 生存解析・値引 HR |
363
+ | `scientific-statistical-testing` | ← 仮説検定・効果量算出 |
364
+ | `scientific-deep-research` | ← 系統的文献検索 |
365
+ | `scientific-clinical-trials-analytics` | ← 臨床試験結果の統合 |
366
+ | `scientific-academic-writing` | → メタアナリシス論文化 |
367
+
358
368
  #### 依存パッケージ
359
369
 
360
370
  ```
package/src/.github/skills/scientific-pharmacovigilance/SKILL.md CHANGED
@@ -514,3 +514,6 @@ def generate_pv_report(target_drug, signals_df, ebgm_df, output_dir="results"):
514
514
  | `scientific-admet-pharmacokinetics` | ← 毒性予測・代謝経路情報 |
515
515
  | `scientific-clinical-decision-support` | → シグナル情報の臨床意思決定への反映 |
516
516
  | `scientific-deep-research` | ← 安全性文献の深層リサーチ |
517
+ | `scientific-clinical-trials-analytics` | ← 臨床試験データベース照会 |
518
+ | `scientific-regulatory-science` | → FDA/FAERS 規制データ統合 |
519
+ | `scientific-pharmacogenomics` | ← PGx 代謝型別安全性評価 |
package/src/.github/skills/scientific-population-genetics/SKILL.md CHANGED
@@ -330,6 +330,8 @@ def selection_scan(haplotype_matrix, positions, method="ihs"):
330
330
  | [scientific-disease-research](../scientific-disease-research/SKILL.md) | 疾患-遺伝子関連 |
331
331
  | [scientific-statistical-testing](../scientific-statistical-testing/SKILL.md) | 統計検定 |
332
332
  | [scientific-pca-tsne](../scientific-pca-tsne/SKILL.md) | 次元削減 |
333
+ | [scientific-pharmacogenomics](../scientific-pharmacogenomics/SKILL.md) | PGx 集団頻度差 |
334
+ | [scientific-epigenomics-chromatin](../scientific-epigenomics-chromatin/SKILL.md) | エピゲノム集団差 |
333
335
 
334
336
  #### 依存パッケージ
335
337
 
package/src/.github/skills/scientific-precision-oncology/SKILL.md CHANGED
@@ -422,3 +422,4 @@ def generate_mtb_report(patient_id, variants, civic_data, oncokb_data,
422
422
  | `scientific-drug-target-profiling` | ← 標的ドラッガビリティ評価 |
423
423
  | `scientific-disease-research` | ← がん種の疫学・遺伝的背景 |
424
424
  | `scientific-deep-research` | ← 腫瘍学最新文献リサーチ |
425
+ | `scientific-pharmacogenomics` | ← PGx 代謝型・投与量調整 |
package/src/.github/skills/scientific-scientific-schematics/SKILL.md CHANGED
@@ -325,11 +325,11 @@ def generate_tikz_figure(tikz_code, output_file="figures/tikz_figure.tex",
325
325
 
326
326
  | スキル | 関連 |
327
327
  |---|---|
328
- | `scientific-visualization` | データ可視化全般 |
328
+ | `scientific-publication-figures` | データ可視化全般 |
329
329
  | `scientific-clinical-trials-analytics` | CONSORT 図のデータソース |
330
330
  | `scientific-grant-writing` | 研究計画図 |
331
331
  | `scientific-network-analysis` | ネットワーク図 |
332
- | `scientific-presentation` | プレゼン素材 |
332
+ | `scientific-presentation-design` | プレゼン素材 |
333
333
 
334
334
  ### 依存パッケージ
335
335
 
package/src/.github/skills/scientific-single-cell-genomics/SKILL.md CHANGED
@@ -355,6 +355,8 @@ def sc_visualization_panel(adata, deg_df=None, save_dir="figures"):
355
355
  | [scientific-network-analysis](../scientific-network-analysis/SKILL.md) | 遺伝子制御ネットワーク |
356
356
  | [scientific-deep-learning](../scientific-deep-learning/SKILL.md) | scVI / scGPT 等の深層学習モデル |
357
357
  | [scientific-pca-tsne](../scientific-pca-tsne/SKILL.md) | 次元削減手法 |
358
+ | [scientific-gene-expression-transcriptomics](../scientific-gene-expression-transcriptomics/SKILL.md) | バルク RNA-seq 差次発現 |
359
+ | [scientific-epigenomics-chromatin](../scientific-epigenomics-chromatin/SKILL.md) | エピゲノム-発現統合 |
358
360
 
359
361
  #### 依存パッケージ
360
362
 
package/src/.github/skills/scientific-survival-clinical/SKILL.md CHANGED
@@ -245,6 +245,17 @@ def bayesian_sequential_update(successes_list, trials_list,
245
245
  | GDC | `GDC_search_cases` | TCGA 臨床データ |
246
246
  | PubMed | `PubMed_search_articles` | 臨床文献検索 |
247
247
 
248
+ ### 参照スキル
249
+
250
+ | スキル | 連携 |
251
+ |---|---|
252
+ | `scientific-causal-inference` | ← 傾向スコア・因果推論 |
253
+ | `scientific-meta-analysis` | ← 統合解析・エビデンス統合 |
254
+ | `scientific-statistical-testing` | ← 仮説検定・多重比較 |
255
+ | `scientific-clinical-trials-analytics` | ← ClinicalTrials.gov 試験データ |
256
+ | `scientific-pharmacovigilance` | → AE データの安全性解析 |
257
+ | `scientific-clinical-decision-support` | → 生存解析結果の臨床応用 |
258
+
248
259
  #### 参照実験
249
260
 
250
261
  - **Exp-03**: Kaplan-Meier + Cox PH（がん生存解析）
package/src/.github/skills/scientific-variant-interpretation/SKILL.md CHANGED
@@ -324,3 +324,4 @@ def pgx_recommendation(gene, phenotype, drug):
324
324
  | `scientific-data-preprocessing` | ← バリアントデータの前処理・正規化 |
325
325
  | `scientific-clinical-decision-support` | → バリアント解釈結果の臨床意思決定 |
326
326
  | `scientific-academic-writing` | → 研究成果の論文化 |
327
+ | `scientific-pharmacogenomics` | ← Star アレル・代謝型・薬理ゲノミクス |