skills/claude-scientific-skills
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Author SHA1 Message Date
Timothy Kassis
04a7be2319 Add Security Disclaimer section to README 
Introduced a new section outlining the security implications of using agent skills, emphasizing the importance of reviewing skills before installation. Included recommendations for safe usage and a reminder of the review process for contributions.
 2026-03-25 09:31:25 -07:00
Timothy Kassis
cb364cc3d8 Bump version v2.30.1 2026-03-23 16:27:05 -07:00
Timothy Kassis
f93d13b08e Improve token discovery for Modal 2026-03-23 16:26:43 -07:00
Timothy Kassis
b75f4e8d08 Update Modal skill v2.30.0 2026-03-23 16:21:31 -07:00
Timothy Kassis
71e26ffa6d Add planning with files skill from @OthmanAdi v2.29.0 2026-03-23 14:34:03 -07:00
Timothy Kassis
1531326a59 Add K-Dense BYOK AI co-scientist to README with features and links 2026-03-22 17:50:53 -07:00
Timothy Kassis
903caa6a26 Add writing skills 2026-03-20 09:59:52 -07:00
Timothy Kassis
1346c01d9d Bump version v2.28.0 2026-03-18 12:22:31 -07:00
Timothy Kassis
4b90d0ca5b Merge pull request #100 from mwiewior/polars-bio 
feat: Add polars-bio skill for genomic interval operations and bioinformati…
 2026-03-18 12:19:58 -07:00
Marek Wieiwórka
436c8608f2 Add polars-bio skill for genomic interval operations and bioinformatics I/O 
Adds a new skill covering polars-bio (v0.26.0), a high-performance library
for genomic interval arithmetic and file I/O built on Polars, Arrow, and
DataFusion. All code examples verified against the actual API at runtime.

SKILL.md covers overlap, nearest, merge, coverage, complement, subtract,
cluster, count_overlaps operations plus read/scan/write/sink for BED, VCF,
BAM, CRAM, GFF, GTF, FASTA, FASTQ, SAM, and Hi-C pairs formats.

References: interval_operations, file_io, sql_processing, pileup_operations,
configuration, bioframe_migration.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-03-14 10:27:11 +01:00
Timothy Kassis
575f1e586f Merge pull request #91 from alif-munim/main 
feat: Add arXiv database search skill
 2026-03-11 09:59:08 -07:00
Alif Munim
4f46196223 Add ArXiv skill 2026-03-10 08:42:20 +00:00
Timothy Kassis
81589710a5 Merge pull request #87 from Cervolve/feat/primekg-skill 
feat: add PrimeKG Precision Medicine Knowledge Graph skill
 2026-03-09 10:46:16 -07:00
Eamon
a8b937c56b feat: add PrimeKG Precision Medicine Knowledge Graph skill 2026-03-09 05:29:46 -04:00
Timothy Kassis
c84622c08a Merge pull request #70 from urabbani/feature/geomaster-skill 
Add GeoMaster: Comprehensive Geospatial Science Skill
 2026-03-06 14:39:13 -08:00
Timothy Kassis
3ff22d0c3a Merge branch 'main' into feature/geomaster-skill 2026-03-06 14:39:04 -08:00
urabbani
2c7ffbbf6d Remove GEOMASTER_IMPROVEMENTS.md 2026-03-06 10:41:43 +05:00
Timothy Kassis
20e1be89f3 Merge pull request #80 from fedorov/update-idc-1.4.0 
Update imaging-data-commons skill to v1.4.0
 2026-03-05 14:06:03 -08:00
Timothy Kassis
d965eb83bc Upgrade to Nano Banan 2 2026-03-05 10:08:17 -08:00
Timothy Kassis
1299970688 Update marketplace.json to version 2.27.0 and streamline document skill paths for improved organization. v2.27.0 2026-03-05 08:01:31 -08:00
Timothy Kassis
204314ea22 Remove obsolete DOCX documentation and related files, including tutorials, license, and schema definitions, to streamline the project structure. 2026-03-05 07:59:40 -08:00
Timothy Kassis
e46b77d962 Refactor descriptions in markdown-mermaid-writing and timesfm-forecasting skills for clarity and conciseness, removing redundant details while maintaining essential information. 2026-03-05 07:57:07 -08:00
Timothy Kassis
cfffe4d166 Refactor torch_geometric skill references and update skill name to 'torch-geometric' for consistency. Remove obsolete files related to the skill, including documentation and scripts. 2026-03-05 07:54:41 -08:00
Timothy Kassis
2f3d0d724e Update PyMC skill name and description for clarity and consistency 2026-03-05 07:53:32 -08:00
urabbani
85591617fc Improve GeoMaster skill with Rust support, troubleshooting, and modern workflows 
Major improvements to the GeoMaster geospatial science skill:

### New Features
- Added Rust geospatial support (GeoRust crates: geo, proj, shapefile, rstar)
- Added comprehensive coordinate systems reference documentation
- Added troubleshooting guide with common error fixes
- Added cloud-native workflows (STAC, Planetary Computer, COG)
- Added automatic skill activation configuration

### Reference Documentation
- NEW: references/coordinate-systems.md - CRS fundamentals, UTM zones, EPSG codes
- NEW: references/troubleshooting.md - Installation fixes, runtime errors, performance tips
- UPDATED: references/programming-languages.md - Now covers 8 languages (added Rust)

### Main Skill File
- Streamlined SKILL.md from 690 to 362 lines (500-line rule compliance)
- Enhanced installation instructions with uv and conda
- Added modern cloud-native workflow examples
- Added performance optimization tips

### Documentation
- NEW: GEOMASTER_IMPROVEMENTS.md - Complete changelog and testing guide
- UPDATED: README.md - Highlight new capabilities

### Skill Activation
- Created skill-rules.json with 150+ keywords and 50+ intent patterns
- Supports file-based and content-based automatic activation

The skill now covers 8 programming languages (Python, R, Julia, JavaScript,
C++, Java, Go, Rust) with 500+ code examples across 70+ geospatial topics.
 2026-03-05 14:26:09 +05:00
Andrey Fedorov
0c4a7eaf16 Update imaging-data-commons skill to v1.4.0 
Release notes:
- Bump idc-index requirement to 0.11.10
- digital_pathology_guide.md: add "Filter by specimen preparation" section
  with H&E staining and FFPE/frozen embedding query examples (array column syntax)
- digital_pathology_guide.md: add "Identifying Tumor vs Normal Slides" section
  covering primaryAnatomicStructureModifier_CodeMeaning (all SM collections)
  and TCGA barcode parsing via ContainerIdentifier (TCGA-specific)
- digital_pathology_guide.md: add "Finding Pre-Computed Analysis Results" section
  for discovering derived datasets (nuclei segmentations, TIL maps) via
  analysis_results_index
- digital_pathology_guide.md: document per-annotation measurements in DICOM ANN
  objects (extraction via highdicom post-download, link to tutorial notebook)
- digital_pathology_guide.md: update sm_index description with new columns
  (container/slide ID, tissue type, anatomic structure, diagnosis)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-03-04 17:26:57 -05:00
Timothy Kassis
fc60a11f85 Merge pull request #78 from small-thinking/feat/support-gemini-cli 
docs: add support and installation guide for Gemini CLI
 2026-03-04 09:28:11 -08:00
Yxjiang
3454f76e88 docs: add support and installation guide for Gemini CLI 2026-03-04 07:21:30 -08:00
Timothy Kassis
29c3240f1a Update .gitignore to include scan_skills.py and ensure .env is ignored 2026-03-03 15:42:17 -08:00
Timothy Kassis
f198f38b22 Add social media links to README for enhanced visibility 2026-03-03 14:35:19 -08:00
Timothy Kassis
4b7c910bb5 Add Skill scanner 2026-03-03 08:29:54 -08:00
Timothy Kassis
69fbf862bd Add skills scanning 2026-03-03 08:26:21 -08:00
Timothy Kassis
c61a6a2ee0 Cleanup 2026-03-03 08:20:03 -08:00
Timothy Kassis
3ed035e64c Added around 23 new skills contributed by the community! v2.26.0 2026-03-03 08:17:25 -08:00
Timothy Kassis
d452499891 Merge pull request #68 from salmanmkc/upgrade-github-actions-node24 
Upgrade GitHub Actions for Node 24 compatibility
 2026-03-03 07:55:04 -08:00
Timothy Kassis
24ee2e3c49 Merge pull request #69 from salmanmkc/upgrade-github-actions-node24-general 
Upgrade GitHub Actions to latest versions
 2026-03-03 07:54:36 -08:00
Timothy Kassis
5dfb909509 Merge pull request #72 from ashrafkahoush-ux/feat/cognitive-science-skills 
Add dhdna-profiler and what-if-oracle as cognitive science skills
 2026-03-03 07:53:43 -08:00
Timothy Kassis
a4eabbb519 Merge pull request #75 from kuanlinhuang/main 
Add 12 new scientific skills
 2026-03-03 07:52:27 -08:00
Timothy Kassis
5642c61b33 Merge pull request #66 from K-Dense-AI/add-parallel 
Add parallel-web skill and update research-lookup
 2026-03-03 07:47:29 -08:00
huangkuanlin
7f94783fab Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation 
- Introduced a comprehensive RNA velocity analysis pipeline using scVelo, including data loading, preprocessing, velocity estimation, and visualization.
- Added a script for running RNA velocity analysis with customizable parameters and output options.
- Created detailed documentation for IQ-TREE 2 phylogenetic inference, covering command syntax, model selection, bootstrapping methods, and output interpretation.
- Included references for velocity models and their mathematical framework, along with a comparison of different models.
- Enhanced the scVelo skill documentation with installation instructions, use cases, and best practices for RNA velocity analysis.
 2026-03-03 07:15:36 -05:00
Timothy Kassis
b271271df4 Support for Ginkgo Cloud Lab v2.25.0 2026-03-02 09:53:41 -08:00
ashrafkahoush-ux
6e29728849 feat: add cognitive science skills — consciousness-council, dhdna-profiler, what-if-oracle 
Three research-backed cognitive science skills:

- consciousness-council: 12-archetype Mind Council deliberation for structured multi-perspective analysis
- dhdna-profiler: cognitive fingerprinting across 12 dimensions (DOI: 10.5281/zenodo.18736629)
- what-if-oracle: multi-branch scenario analysis with probability weighting (DOI: 10.5281/zenodo.18736841)

Each includes reference documentation. All MIT licensed.
Source: https://github.com/ashrafkahoush-ux/Claude-consciousness-skills
 2026-03-02 17:16:09 +02:00
urabbani
e67029685b Update README to include GeoMaster skill 
- Update skill count from 148 to 149
- Add GeoMaster to Data Analysis & Visualization section
- Add geospatial science domain to the main domains list
- Update skill count across all relevant sections

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
 2026-03-02 14:32:35 +05:00
Salman Muin Kayser Chishti
e62b0eb98b Upgrade GitHub Actions to latest versions 
Signed-off-by: Salman Muin Kayser Chishti <13schishti@gmail.com>
 2026-03-02 09:20:16 +00:00
Salman Muin Kayser Chishti
5e62d71168 Upgrade GitHub Actions for Node 24 compatibility 
Signed-off-by: Salman Muin Kayser Chishti <13schishti@gmail.com>
 2026-03-02 09:20:08 +00:00
Timothy Kassis
b0923b2e06 Merge pull request #67 from 04cb/fix/docs-pymatgen-computedentry-energy 
Fix docs: correct ComputedEntry energy parameter description
 2026-03-01 18:00:44 -08:00
Timothy Kassis
0cec94a92a Merge pull request #65 from urabbani/feature/geomaster-skill 
Add GeoMaster: Comprehensive Geospatial Science Skill
 2026-03-01 18:00:30 -08:00
04cb
2585a40ab5 Fix docs: correct ComputedEntry energy parameter description 2026-03-02 07:30:43 +08:00
Vinayak Agarwal
f72b7f4521 Added parallel-web skill 
Refactor research lookup skill to enhance backend routing and update documentation. The skill now intelligently selects between the Parallel Chat API and Perplexity sonar-pro-search based on query type. Added compatibility notes, license information, and improved descriptions for clarity. Removed outdated example scripts to streamline the codebase.
 2026-03-01 07:36:19 -08:00
urabbani
4787f98d98 Add GeoMaster: Comprehensive Geospatial Science Skill 
- Added SKILL.md with installation, quick start, core concepts, workflows
- Added 12 reference documentation files covering 70+ topics
- Includes 500+ code examples across 7 programming languages
- Covers remote sensing, GIS, ML/AI, 30+ scientific domains
- MIT License

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Dr. Umair Rabbani <umairrs@gmail.com>
 2026-03-01 13:42:41 +05:00