Commit Graph

341 Commits

Author SHA1 Message Date
Timothy Kassis
d80ddf17c9 Merge pull request #41 from K-Dense-AI/update-writing-skills
Sync writing skills from claude-scientific-writer
2026-02-05 08:52:18 -08:00
Timothy Kassis
7f9a689126 Merge pull request #42 from fedorov/update-idc-skill-to-v1.2.0
Update imaging-data-commons skill to v1.2.0
2026-02-05 08:51:06 -08:00
Andrey Fedorov
63801af8e6 Update imaging-data-commons skill to v1.2.0
see changes in the changelog upstream:

https://github.com/ImagingDataCommons/idc-claude-skill/blob/main/CHANGELOG.md#120---2026-02-04
2026-02-04 14:35:14 -05:00
Vinayak Agarwal
5c71912049 Add infographics skill for creating visual data representations
New skill for generating scientific infographics including:
- SKILL.md with comprehensive guidelines for infographic creation
- Design principles and color palette references
- Scripts for AI-powered infographic generation
- Support for various infographic types (statistical, process, comparison, etc.)

Co-authored-by: Cursor <cursoragent@cursor.com>
2026-02-03 17:03:44 -08:00
Vinayak Agarwal
21801d71b2 Enhance literature search and research lookup documentation
- Added criteria for identifying high-quality literature, emphasizing the importance of Tier-1 journals and citation counts.
- Updated guidelines for citation finding to prioritize influential papers and reputable authors.
- Revised abstract writing instructions to reflect the preference for flowing paragraphs over structured formats.
- Included best practices for generating AI schematics, specifically regarding figure numbering and content clarity.
2026-02-03 14:31:19 -08:00
Timothy Kassis
49024095e3 Merge pull request #37 from jiaodu1307/fix/rdkit-morgan-fp
fix(rdkit): update fingerprint generation to use rdFingerprintGenerator API
2026-02-01 18:46:35 -08:00
Timothy Kassis
d17d74dc5d Add support for economic data form the Federal Reserve using FRED v2.18.0 2026-01-27 10:41:40 -08:00
jiaodu1307
06ac0af626 refactor(rdkit): update fingerprint generation to use rdFingerprintGenerator API
- Replace direct calls to AllChem, Pairs, and Torsions with rdFingerprintGenerator in similarity_search.py
- Update example code in SKILL.md to reflect the new API usage
- Maintain existing functionality while adopting the modern fingerprint generation interface recommended by RDKit
2026-01-26 20:25:28 +08:00
Timothy Kassis
a31cf4dd97 Merge pull request #35 from fedorov/add-idc-clean
Added Imaging Data Commons skill
2026-01-25 10:17:32 -08:00
Andrey Fedorov
79a598e060 Register imaging-data-commons skill in the marketplace 2026-01-23 17:10:02 -05:00
Andrey Fedorov
1d306c59cf Update to include new index available from idc-index 2026-01-23 17:05:50 -05:00
Andrey Fedorov
b71988fcdf Added Imaging Data Commons skill 2026-01-22 18:26:30 -05:00
Timothy Kassis
cd537c1af6 Replace all instances of Sonnet to Opus 2026-01-21 09:16:34 -05:00
Timothy Kassis
c5413a6b5c Remove Biomni due to incompatibilities 2026-01-21 09:11:38 -05:00
Timothy Kassis
497232fbc1 Merge pull request #32 from K-Dense-AI/add-open-source-acknowledgements
Add open source acknowledgements
2026-01-15 20:44:16 -08:00
Haoxuan "Orion" Li
2a42585d11 docs: fix README text symbols 2026-01-15 16:05:02 -08:00
Haoxuan "Orion" Li
8578c44724 Merge branch 'main' into add-open-source-acknowledgements 2026-01-15 16:01:38 -08:00
Haoxuan "Orion" Li
b4e35897ae docs: add acknowledgements and sponsor information on open source projects referenced 2026-01-15 16:00:45 -08:00
Timothy Kassis
25f29ac3db Update readme 2026-01-15 12:49:04 -08:00
Timothy Kassis
bbe8a15cf7 Update README.md to include a link to a detailed comparison of K-Dense Web and Claude, and enhance contribution guidelines for adherence to the Agent Skills Specification. 2026-01-14 09:53:20 -08:00
Timothy Kassis
955a36ac82 Update README.md to enhance plugin installation instructions and add management commands 2026-01-12 17:17:47 -08:00
Timothy Kassis
e2e00231da Add support for Rowan computational platform that provides a suite of design and simulation tools for chemical R&D v2.17.0 2026-01-12 13:22:43 -08:00
Timothy Kassis
f086d9f499 Merge pull request #31 from shao-shuai/fix/uspto-database
Add patentsview api key for patent search api
2026-01-09 08:57:21 -08:00
shao-shuai
68f8f709f3 Add patentsview api key for patent search api 2026-01-08 22:38:59 -08:00
Timothy Kassis
a7221bb237 Merge pull request #30 from marovole/fix/shell-command-injection-docs
fix(security): Replace shell=True with safe subprocess patterns in documentation
2026-01-08 08:53:35 -08:00
marovole
b6a6d698db fix(security): replace shell=True with safe subprocess patterns in documentation
## Summary
Fix command injection vulnerabilities in documentation examples by replacing
shell=True with safe list-based subprocess calls.

## Changes

### alphafold-database/SKILL.md
- Replace shell=True with list-form subprocess.run()
- Add input validation for taxonomy_id parameter
- Add security warning note with link to Python docs

### modal/references/web-endpoints.md
- Replace shell=True with list-form subprocess.Popen()
- Add security warning note

## Security
These changes prevent potential command injection if users copy these examples
with untrusted input. The new patterns follow Python security best practices.
2026-01-08 15:05:30 +08:00
Timothy Kassis
38c1560c7b Merge pull request #29 from K-Dense-AI/orion/add-k-dense-web-gif
Add K-Dense Web GIF to README
2026-01-07 20:38:47 -08:00
Haoxuan "Orion" Li
7232cf73a9 docs: add K-Dense Web GIF 2026-01-07 17:13:23 -08:00
Timothy Kassis
29536568d4 Merge pull request #28 from Jacobluke-/patch-1
Fix typo in gget/SKILL.md description
2026-01-07 08:56:08 -08:00
Jacob Luke
912bdc7afa Fix description formatting in SKILL.md
Updated description formatting in SKILL.md
2026-01-07 15:15:18 +08:00
Jacob Luke
7942c59146 Fix typo in gget/SKILL.md description
Fix typo to avoid YAML: mapping values are not allowed in this context at line 2 column 92
2026-01-07 15:08:58 +08:00
Timothy Kassis
808578ba03 Enhance README.md with detailed comparison of features between the local repo and K-Dense Web, highlighting benefits such as zero setup, cloud compute, and advanced workflows. 2026-01-06 21:01:58 -08:00
Timothy Kassis
2cb6f2e645 Bump version v2.16.1 2026-01-05 18:21:49 -08:00
Timothy Kassis
87497a3c60 Add K-Dense Web skill v2.16.0 2026-01-05 18:20:10 -08:00
Timothy Kassis
ca49c8c105 Update README.md to clarify capabilities and usage instructions for Claude Code and MCP clients 2026-01-05 17:23:58 -08:00
Timothy Kassis
9ab5b29dc5 Merge pull request #26 from K-Dense-AI/fix-writing-skills
Fix pptx-posters SKILL.md with correct content
2026-01-05 15:47:03 -08:00
Timothy Kassis
90aea1b0a5 Merge branch 'main' into fix-writing-skills 2026-01-05 15:46:55 -08:00
Timothy Kassis
5ef0ccddc2 Clean description fields v2.15.0 2026-01-05 14:29:10 -08:00
Timothy Kassis
9cb0c2f934 Disambiguate descriptions 2026-01-05 14:25:22 -08:00
Vinayak Agarwal
7fff998fe6 Fix pptx-posters SKILL.md with correct content from claude-scientific-writer 2026-01-05 14:11:43 -08:00
Timothy Kassis
15d9e4699a Update examples 2026-01-05 13:49:00 -08:00
Timothy Kassis
e268d8db9b Writing enhancements v2.14.0 2026-01-05 13:33:11 -08:00
Timothy Kassis
1d716b0375 Merge pull request #25 from K-Dense-AI/fix-writing-skills
Merge skills from claude-scientific-writer
2026-01-05 13:31:55 -08:00
Vinayak Agarwal
c127b737a5 Remove extra md files from markitdown 2026-01-05 13:07:50 -08:00
Vinayak Agarwal
5b52a8dd23 Remove test scripts and summary files 2026-01-05 13:06:20 -08:00
Vinayak Agarwal
3439a21f57 Enhance citation management and literature review guidelines
- Updated SKILL.md in citation management to include best practices for identifying seminal and high-impact papers, emphasizing citation count thresholds, venue quality tiers, and author reputation indicators.
- Expanded literature review SKILL.md to prioritize high-impact papers, detailing citation metrics, journal tiers, and author reputation assessment.
- Added comprehensive evaluation strategies for paper impact and quality in literature_search_strategies.md, including citation count significance and journal impact factor guidance.
- Improved research lookup scripts to prioritize results based on citation count, venue prestige, and author reputation, enhancing the quality of research outputs.
2026-01-05 13:01:10 -08:00
Timothy Kassis
d243a12564 Merge pull request #24 from backtrue/feature/add-nstc-support
feat(research-grants): Add comprehensive Taiwan NSTC proposal support
2026-01-05 12:38:29 -08:00
Timothy Kassis
70375367d6 Support for writing and executing MATLAB/Octave scripts v2.13.0 2026-01-05 10:15:22 -08:00
backtrue
4427270a71 feat(research-grants): Add comprehensive Taiwan NSTC proposal support
- Add new nstc_guidelines.md with official requirements and practical insights
- Include CM03 format specifications and page limits by field
- Integrate LaTeX templates (CTAN package, Overleaf templates)
- Add practical writing strategies from three expert reviewers:
  * Prof. Huang You-Ping (NPU): Scoring thresholds and section strategies
  * Prof. Guo Yao-Huang: Closed-loop logic and KPI formulation
  * President Wei Yao-Hui (Mackay): SMART principles and review dimensions
- Include budget preparation guidance and common pitfalls
- Update SKILL.md to reference NSTC in overview and agency list

This comprehensive guide provides 700+ lines of actionable guidance for
Taiwan NSTC (formerly MOST/NSC) research proposal writing.
2026-01-06 00:34:59 +09:00
Timothy Kassis
9827af22ad Update readme 2026-01-02 19:09:54 -08:00