borealBytes
b376b40f59
docs(pr): add PR record for markdown-mermaid writing skill
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Skeleton PR document following the Everything is Code convention.
Contains full changes inventory, impact classification, testing steps,
architecture diagram showing integration with existing skills, and
design decision notes.
Files touched: docs/project/pr/pr-00000001-markdown-mermaid-skill.md
2026-02-19 18:24:45 -05:00
borealBytes
3d4baba365
docs(issues): add feature request for markdown-mermaid writing skill
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Documents the feature request to add a skill establishing markdown+Mermaid
as the canonical source format for scientific documentation. Includes the
originating K-Dense Discord conversation, three-phase workflow diagram
(Mermaid → Python → AI images), acceptance criteria, and technical spec
for the skill directory structure.
Files touched: docs/project/issues/issue-00000001-markdown-mermaid-skill.md
2026-02-19 18:23:43 -05:00
Timothy Kassis
22b0ad54ab
Bump version number to 2.20.0 in marketplace.json
2026-02-17 16:35:03 -08:00
Timothy Kassis
9d0125f93b
Update readme
2026-02-17 16:34:41 -08:00
Timothy Kassis
326b043b8f
Merge pull request #46 from fedorov/update-idc-v1.3.0
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update imaging-data-commons skill to v1.3.1
2026-02-16 10:24:23 -08:00
Andrey Fedorov
5a471d9c36
update to v1.3.1
2026-02-11 09:42:22 -05:00
Andrey Fedorov
2597540aa1
update imaging-data-commons skill to v1.3.0
2026-02-10 18:12:49 -05:00
Timothy Kassis
3a5f2e2227
Bump version number
2026-02-05 08:53:47 -08:00
Timothy Kassis
d80ddf17c9
Merge pull request #41 from K-Dense-AI/update-writing-skills
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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
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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
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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
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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
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- 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
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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
2026-01-27 10:41:40 -08:00
jiaodu1307
06ac0af626
refactor(rdkit): update fingerprint generation to use rdFingerprintGenerator API
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- 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
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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
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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
2026-01-12 13:22:43 -08:00
Timothy Kassis
f086d9f499
Merge pull request #31 from shao-shuai/fix/uspto-database
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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
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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
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## 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
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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
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Fix typo in gget/SKILL.md description
2026-01-07 08:56:08 -08:00
Jacob Luke
912bdc7afa
Fix description formatting in SKILL.md
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Updated description formatting in SKILL.md
2026-01-07 15:15:18 +08:00
Jacob Luke
7942c59146
Fix typo in gget/SKILL.md description
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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
2026-01-05 18:21:49 -08:00
Timothy Kassis
87497a3c60
Add K-Dense Web skill
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
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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
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
2026-01-05 13:33:11 -08:00
