skills/claude-scientific-skills
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Author SHA1 Message Date
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
Timothy Kassis
29c869326e Enhance README by adding a description of K-Dense Web, clarifying its role as a hosted platform built on the scientific skills collection. This addition aims to promote the platform's features and benefits. 2026-02-28 07:23:48 -08:00
Timothy Kassis
a472690126 Revise README to streamline content and promote K-Dense Web, highlighting its features and benefits. Remove outdated sections and enhance calls to action for cloud-based execution and publication-ready outputs. 2026-02-27 13:42:12 -08:00
Timothy Kassis
c58a309012 Update README to reflect the increase in scientific skills from 148 to 250+ databases, and enhance descriptions for Python package and integration skills. Adjust badge and feature tables accordingly. 2026-02-27 13:36:31 -08:00
Timothy Kassis
6040d02c8c Update README and documentation to reflect the addition of the pyzotero skill and increment skill count from 147 to 148. Bump version to 2.24.0 in marketplace.json. v2.24.0 2026-02-27 09:38:51 -08:00
Timothy Kassis
8dc5701063 Use Nano Banana 2 2026-02-26 08:59:40 -08:00
Timothy Kassis
d4177ce3a5 Merge pull request #61 from connerlambden/add-bgpt-skill 
Add BGPT paper search skill
 2026-02-24 14:23:19 -08:00
connerlambden
f54b1bb174 Add BGPT paper search skill 2026-02-24 14:42:31 -07:00
Timothy Kassis
29ae12d2c0 Merge pull request #62 from leipzig/feature/add-tiledb-vcf-skill 
Feature/add tiledb-vcf skill
 2026-02-24 12:43:57 -08:00
Timothy Kassis
77883baba2 Merge pull request #60 from renato-umeton/main 
Fix architecture diagram
 2026-02-24 12:41:32 -08:00
Jeremy Leipzig
791fd2361c Update skill counts and add TileDB-VCF to repository documentation 
- Update skill count badges and descriptions from 146 to 147 skills
- Add TileDB-VCF to genomic tools list in bioinformatics section
- Add variant database management use case for TileDB-VCF
- Add comprehensive TileDB-VCF entry to docs/scientific-skills.md
 2026-02-24 12:07:21 -07:00
Jeremy Leipzig
730531e0d7 Remove all reference documentation files and clean up references 
- Delete references/population_genomics.md
- Remove all references to deleted documentation files
- Clean up References section since no reference files remain
- Simplify skill to standalone main file only
 2026-02-24 11:30:31 -07:00
Jeremy Leipzig
55811bdbbe Remove references/querying.md 
- Delete detailed querying reference documentation
- Update main skill to remove references to querying.md
- Leave only population_genomics.md reference file
 2026-02-24 11:29:01 -07:00
Jeremy Leipzig
c576d2e66a Remove references/export.md and references/ingestion.md 
- Delete detailed export and ingestion reference documentation
- Update main skill to remove references to deleted files
- Simplify skill to focus on core querying and population genomics
- Keep querying.md and population_genomics.md reference files
 2026-02-24 11:27:59 -07:00
Jeremy Leipzig
ba2afda31c Fix documentation URLs to point to correct TileDB Academy 
- All documentation is at https://cloud.tiledb.com/academy/
- Remove incorrect service URLs (docs.tiledb.com, support portal, etc.)
- Consolidate to academy and main platform URLs only
- Update contact information to sales@tiledb.com
 2026-02-24 11:22:34 -07:00
Jeremy Leipzig
e3a7a85122 Remove multiple advanced export sections 
- Remove VEP annotation preparation section
- Remove Cloud Export (S3) section
- Remove Export Validation section
- Remove Efficient Export Strategies section
- Simplify export guide to focus on core export functionality
- Maintain essential VCF/BCF and TSV export examples
 2026-02-24 11:17:41 -07:00