[Upstream sync] K-Dense-AI/scientific-agent-skills (github) — 45 added, 56 modified #33

Merged

promptadmin merged 101 commits from upstream-sync/scientific-agent-skills-20260808-991bd9-sesb into main

2026-08-09 18:31:46 +00:00

promptadmin commented

2026-08-08 15:47:16 +00:00

Owner

Upstream sync from `K-Dense-AI/scientific-agent-skills` (github)

Source: https://github.com/K-Dense-AI/scientific-agent-skills
Forge: github
Compare: a1b84fb2...991bd993

Scan summary

Category	Files
Prompt / Skill files	28
Catalogue / Reference files	73

Prompt files are stored under upstream/{owner}-{repo}/
Catalogue files are stored under upstream/{owner}-{repo}/catalogue/

Decision required

Option	Action
Accept	Merge this PR — changes ingested into PromptNotes
Reject	Close this PR — local version preserved unchanged
Modify	Edit files in this branch before merging

Backup rights: If the upstream repository is later deleted or made private,
the last accepted version in PromptNotes is retained under backup rights.

Files added (45)

.github/ISSUE_TEMPLATE/bug_report.yml
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/new_skill_request.yml
.github/ISSUE_TEMPLATE/skill_improvement.yml
.github/PULL_REQUEST_TEMPLATE.md
.github/workflows/skill-spec-validation.yml
.github/workflows/skill-tests.yml
AGENTS.md
CLAUDE.md
CODE_OF_CONDUCT.md
docs/security-report.json
docs/security-triage.md
skills/analytical-method-validation/SKILL.md
skills/analytical-method-validation/assets/validation-protocol-template.md
skills/analytical-method-validation/assets/validation-report-template.md
skills/analytical-method-validation/references/compendial-and-clsi.md
skills/analytical-method-validation/references/framework-selection.md
skills/analytical-method-validation/references/ich-m10-bioanalytical.md
skills/analytical-method-validation/references/ich-q2r2.md
skills/analytical-method-validation/references/source-ledger.md
skills/analytical-method-validation/references/statistics.md
skills/benchling-integration/references/core_capabilities.md
skills/bids/references/core_workflows.md
skills/cellxgene-census/references/core_workflow_patterns.md
skills/citation-management/references/best_practices.md
skills/citation-management/references/core_workflow.md
skills/citation-management/references/example_workflows.md
skills/citation-management/references/script_reference.md
skills/citation-management/references/search_strategies.md
skills/database-lookup/references/database_selection_guide.md
skills/datamol/references/core_workflows.md
skills/datamol/references/workflow_patterns.md
skills/deepchem/references/core_capabilities.md
skills/deepchem/references/typical_workflows.md
skills/deepspot-m/SKILL.md
skills/deepspot-m/references/api.md
skills/deepspot-m/references/whole_slide.md
skills/deeptools/references/core_workflows.md
skills/generate-image/references/models.md
skills/genomic-coordinates/SKILL.md
… and 5 more

Files modified (56)

.github/workflows/pr-skill-scan.yml
.github/workflows/security-scan.yml
CONTRIBUTING.md
README.md
SECURITY.md
docs/examples.md
docs/security-report.md
docs/skills.md
skills/adaptyv/SKILL.md
skills/aeon/SKILL.md
skills/anndata/SKILL.md
skills/arbor/SKILL.md
skills/arbor/references/arbor-upstream.md
skills/arboreto/SKILL.md
skills/astropy/SKILL.md
skills/autoskill/SKILL.md
skills/benchling-integration/SKILL.md
skills/bgpt-paper-search/SKILL.md
skills/bids/SKILL.md
skills/biopython/SKILL.md
skills/bioservices/SKILL.md
skills/bulk-rnaseq/SKILL.md
skills/cellxgene-census/SKILL.md
skills/cirq/SKILL.md
skills/citation-management/SKILL.md
skills/citation-management/references/citation_validation.md
skills/citation-management/references/google_scholar_search.md
skills/clinical-decision-support/SKILL.md
skills/cobrapy/SKILL.md
skills/consciousness-council/SKILL.md
skills/dask/SKILL.md
skills/database-lookup/SKILL.md
skills/datamol/SKILL.md
skills/deepchem/SKILL.md
skills/deepchem/references/workflows.md
skills/deeptools/SKILL.md
skills/depmap/SKILL.md
skills/dhdna-profiler/SKILL.md
skills/diffdock/SKILL.md
skills/docx/SKILL.md
… and 16 more

Auto-generated by PromptNotes upstream tracker v2 · 2026-08-08 15:47 UTC

## Upstream sync from `K-Dense-AI/scientific-agent-skills` (github) **Source:** https://github.com/K-Dense-AI/scientific-agent-skills **Forge:** github **Compare:** [a1b84fb2...991bd993](https://github.com/K-Dense-AI/scientific-agent-skills/compare/a1b84fb2...991bd993) --- ## Scan summary | Category | Files | |----------|-------| | Prompt / Skill files | 28 | | Catalogue / Reference files | 73 | > Prompt files are stored under `upstream/{owner}-{repo}/` > Catalogue files are stored under `upstream/{owner}-{repo}/catalogue/` --- ## Decision required | Option | Action | |--------|--------| | **Accept** | Merge this PR — changes ingested into PromptNotes | | **Reject** | Close this PR — local version preserved unchanged | | **Modify** | Edit files in this branch before merging | > **Backup rights:** If the upstream repository is later deleted or made private, > the last accepted version in PromptNotes is retained under backup rights. --- ## Files added (45) - `.github/ISSUE_TEMPLATE/bug_report.yml` - `.github/ISSUE_TEMPLATE/config.yml` - `.github/ISSUE_TEMPLATE/new_skill_request.yml` - `.github/ISSUE_TEMPLATE/skill_improvement.yml` - `.github/PULL_REQUEST_TEMPLATE.md` - `.github/workflows/skill-spec-validation.yml` - `.github/workflows/skill-tests.yml` - `AGENTS.md` - `CLAUDE.md` - `CODE_OF_CONDUCT.md` - `docs/security-report.json` - `docs/security-triage.md` - `skills/analytical-method-validation/SKILL.md` - `skills/analytical-method-validation/assets/validation-protocol-template.md` - `skills/analytical-method-validation/assets/validation-report-template.md` - `skills/analytical-method-validation/references/compendial-and-clsi.md` - `skills/analytical-method-validation/references/framework-selection.md` - `skills/analytical-method-validation/references/ich-m10-bioanalytical.md` - `skills/analytical-method-validation/references/ich-q2r2.md` - `skills/analytical-method-validation/references/source-ledger.md` - `skills/analytical-method-validation/references/statistics.md` - `skills/benchling-integration/references/core_capabilities.md` - `skills/bids/references/core_workflows.md` - `skills/cellxgene-census/references/core_workflow_patterns.md` - `skills/citation-management/references/best_practices.md` - `skills/citation-management/references/core_workflow.md` - `skills/citation-management/references/example_workflows.md` - `skills/citation-management/references/script_reference.md` - `skills/citation-management/references/search_strategies.md` - `skills/database-lookup/references/database_selection_guide.md` - `skills/datamol/references/core_workflows.md` - `skills/datamol/references/workflow_patterns.md` - `skills/deepchem/references/core_capabilities.md` - `skills/deepchem/references/typical_workflows.md` - `skills/deepspot-m/SKILL.md` - `skills/deepspot-m/references/api.md` - `skills/deepspot-m/references/whole_slide.md` - `skills/deeptools/references/core_workflows.md` - `skills/generate-image/references/models.md` - `skills/genomic-coordinates/SKILL.md` - … and 5 more ## Files modified (56) - `.github/workflows/pr-skill-scan.yml` - `.github/workflows/security-scan.yml` - `CONTRIBUTING.md` - `README.md` - `SECURITY.md` - `docs/examples.md` - `docs/security-report.md` - `docs/skills.md` - `skills/adaptyv/SKILL.md` - `skills/aeon/SKILL.md` - `skills/anndata/SKILL.md` - `skills/arbor/SKILL.md` - `skills/arbor/references/arbor-upstream.md` - `skills/arboreto/SKILL.md` - `skills/astropy/SKILL.md` - `skills/autoskill/SKILL.md` - `skills/benchling-integration/SKILL.md` - `skills/bgpt-paper-search/SKILL.md` - `skills/bids/SKILL.md` - `skills/biopython/SKILL.md` - `skills/bioservices/SKILL.md` - `skills/bulk-rnaseq/SKILL.md` - `skills/cellxgene-census/SKILL.md` - `skills/cirq/SKILL.md` - `skills/citation-management/SKILL.md` - `skills/citation-management/references/citation_validation.md` - `skills/citation-management/references/google_scholar_search.md` - `skills/clinical-decision-support/SKILL.md` - `skills/cobrapy/SKILL.md` - `skills/consciousness-council/SKILL.md` - `skills/dask/SKILL.md` - `skills/database-lookup/SKILL.md` - `skills/datamol/SKILL.md` - `skills/deepchem/SKILL.md` - `skills/deepchem/references/workflows.md` - `skills/deeptools/SKILL.md` - `skills/depmap/SKILL.md` - `skills/dhdna-profiler/SKILL.md` - `skills/diffdock/SKILL.md` - `skills/docx/SKILL.md` - … and 16 more --- *Auto-generated by PromptNotes upstream tracker v2 · 2026-08-08 15:47 UTC*

promptadmin added 101 commits 2026-08-08 15:47:21 +00:00