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
9827af22ad
Update readme
2026-01-02 19:09:54 -08:00
Timothy Kassis
58a32ff246
Update readme
2026-01-02 19:09:01 -08:00
Timothy Kassis
8f337f1574
Clarify licensing terms in README.md to specify that while the repository is MIT licensed, individual skills may have different licenses. Added a section on individual skill licenses to ensure users understand their compliance responsibilities.
2026-01-02 13:50:33 -08:00
Timothy Kassis
6de317a90c
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
Timothy Kassis
805b1e1e0b
Add compatibility field to some of the skills
2025-12-31 15:15:59 -08:00
Timothy Kassis
9a89e01aba
Update license metadata field
2025-12-31 15:10:41 -08:00
Timothy Kassis
2621ee329d
Add skill author
2025-12-31 13:57:51 -08:00
Timothy Kassis
57bde764fe
Added ISO 13485 certification prep skill
2025-12-29 11:12:50 -08:00
Timothy Kassis
4fc6ac7727
Merge pull request #18 from robotlearning123/feature/neuropixels-analysis
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Add neuropixels-analysis skill for extracellular electrophysiology
2025-12-18 11:31:11 -08:00
Robert
95a3b74b3b
Move Neuropixels-Analysis to new Neuroscience category
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Create new "🧠 Neuroscience & Electrophysiology" category for better
classification. Neuropixels is research neuroscience (animal models,
invasive recordings) rather than clinical healthcare AI.
- Remove from Healthcare AI section
- Add new Neuroscience & Electrophysiology section
- Keep NeuroKit2 in Healthcare AI (surface biosignals, clinical focus)
🤖 Generated with [Claude Code](https://claude.com/claude-code )
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com >
2025-12-17 11:20:00 -05:00
Robert
1e00b1536e
Fix SpikeInterface API compatibility in neuropixels_pipeline.py
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- Change stream_name to stream_id in read_spikeglx() call
- Change output_folder to folder in run_sorter() call
These parameters were renamed in SpikeInterface ≥0.100.
🤖 Generated with [Claude Code](https://claude.com/claude-code )
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com >
2025-12-17 11:13:09 -05:00
Robert
312f18ae60
Add neuropixels-analysis skill for extracellular electrophysiology
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Adds comprehensive toolkit for analyzing Neuropixels high-density neural
recordings using SpikeInterface, Allen Institute, and IBL best practices.
Features:
- Data loading from SpikeGLX, Open Ephys, and NWB formats
- Preprocessing pipelines (filtering, phase shift, CAR, bad channel detection)
- Motion/drift estimation and correction
- Spike sorting integration (Kilosort4, SpykingCircus2, Mountainsort5)
- Quality metrics computation (SNR, ISI violations, presence ratio)
- Automated curation using Allen/IBL criteria
- AI-assisted visual curation for uncertain units
- Export to Phy and NWB formats
Supports Neuropixels 1.0 and 2.0 probes.
🤖 Generated with [Claude Code](https://claude.com/claude-code )
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com >
2025-12-17 11:06:28 -05:00
Timothy Kassis
4fb9c053f7
Merge pull request #16 from K-Dense-AI/fix-skills
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Update writer skills with latest versions
2025-12-12 13:58:21 -08:00
Vinayak Agarwal
4515ca6268
Correct the versioning on marketplace.json
2025-12-12 11:46:28 -08:00
Vinayak Agarwal
09d9aa3bb2
Restore marketplace.json from main
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Keep the original marketplace.json unchanged - only add new skills files.
2025-12-12 11:45:36 -08:00
Vinayak Agarwal
cf1d4aac5d
Update all the latest writing skills
2025-12-12 11:42:41 -08:00
Timothy Kassis
d4ca5984ca
Bump version
2025-12-12 09:21:26 -08:00
Timothy Kassis
a643493a32
Merge pull request #15 from K-Dense-AI/add-writer-skills
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Added all updated deep research and writing skills
2025-12-12 09:19:38 -08:00
Vinayak Agarwal
c85faf039a
Update marketplace.json to version 2.10.0 and reorganize scientific skills, adding new skills for citation management, clinical decision support, and research documentation while restoring previously removed skills.
2025-12-11 20:00:59 -08:00
Vinayak Agarwal
ae60fcf620
Added all updated deep research and writing skills
2025-12-11 18:37:06 -08:00
Timothy Kassis
78331e1b37
Remove all writing skills for upcoming upgrade
2025-12-07 13:54:58 -08:00
Timothy Kassis
ab4aff4670
Update README.md to include a promotional note for k-dense.ai, enhancing visibility of advanced capabilities.
2025-12-07 13:41:35 -08:00
Timothy Kassis
6560f1d779
Change Flux.2-dev to flex since dev does not exist
2025-12-04 14:50:30 -08:00
Timothy Kassis
49567890a6
Add BRENDA enzyme database
2025-12-03 17:29:05 -08:00
Timothy Kassis
ec10daba7e
Merge pull request #12 from jxtse/add-brenda-database-skill
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Add BRENDA database skill for enzyme research and analysis
2025-12-02 20:47:18 -08:00
Jinxiang Xie
280a53f95e
Add BRENDA database skill for enzyme research and analysis
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- Add comprehensive BRENDA database skill with API integration
- Include enzyme data retrieval, pathway analysis, and visualization
- Support for enzyme queries, kinetic parameters, and taxonomy data
- Add visualization scripts for enzyme pathways and kinetics
2025-12-03 12:36:49 +08:00
Timothy Kassis
9347d99355
Improve generate-image description
2025-11-30 09:36:44 -05:00
Timothy Kassis
90de96a99b
Add support for generating scientific illustrations using Nano Banan Pro and Flux.2 Pro
2025-11-30 09:30:58 -05:00
Timothy Kassis
8d82c83a1a
Merge pull request #11 from aledlie/main
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refactor: replace manual argv parsing with argparse
2025-11-30 08:52:18 -05:00
Timothy Kassis
7e8deebf96
Add support for Qiskit from IBM: software stack for quantum computing and algorithms research. Build, optimize, and execute quantum workloads at scale.
2025-11-30 08:46:41 -05:00
Timothy Kassis
7763491813
Add support for PennyLane: a cross-platform library for quantum computing, quantum machine learning, and quantum chemistry.
2025-11-30 08:27:24 -05:00
Timothy Kassis
16e47a1755
Add support for Cirq: library for writing, manipulating, and optimizing quantum circuits, and then running them on quantum computers and quantum simulators.
2025-11-30 08:02:58 -05:00
Timothy Kassis
a077cee836
Add support for QuTiP: an open-source software for simulating the dynamics of open quantum systems.
2025-11-30 07:46:17 -05:00
Timothy Kassis
7caef7df68
Fix Reactome database nesting
2025-11-30 06:28:41 -05:00
Alyshia Ledlie
bf4267161f
refactor: replace manual argv parsing with argparse
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- Convert uniprot_client.py to use argparse module
- Convert peds_client.py to use argparse module
- Convert trademark_client.py to use argparse module
- Add mutually exclusive argument groups for better UX
- Implement comprehensive help text with examples
- Add short and long argument options for all commands
- Improve error handling with proper parser.error() calls
Replaces error-prone manual sys.argv parsing with robust
argparse implementation for better user experience and
input validation.
🤖 Generated with [Claude Code](https://claude.com/claude-code )
Co-Authored-By: Claude <noreply@anthropic.com >
2025-11-29 01:13:05 -05:00
Timothy Kassis
6ac2a15e39
Add support for GeoPandas
2025-11-27 18:57:26 -05:00
Timothy Kassis
41f272c2bd
Add Plotly support
2025-11-27 18:47:08 -05:00
Timothy Kassis
02574ba19d
Merge pull request #10 from K-Dense-AI/add_adaptyv_integration
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Add support for Adaptyv for protein design
2025-11-24 19:53:28 -05:00
Timothy Kassis
ea638c5618
Add support for Adaptyv for protein design
2025-11-24 19:52:45 -05:00
Timothy Kassis
8e7a791871
Merge pull request #8 from alperyilmaz/patch-1
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updated CHEMBL function calls
2025-11-23 04:54:15 -08:00
Alper Yilmaz
3bb0ee77be
updated CHEMBL function calls
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https://bioservices.readthedocs.io/en/latest/references.html#module-bioservices.chembl describes changes to functions after 1.6.0
also, get_compounds_by_chemblId fails when tested
2025-11-21 12:52:30 +03:00
Timothy Kassis
e5fc882746
Merge pull request #6 from K-Dense-AI:open_alex_integration
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Add support for OpenAlex
2025-11-19 13:39:08 -08:00
Timothy Kassis
65b39d45d6
Add support for OpenAlex
2025-11-19 13:38:32 -08:00
Timothy Kassis
c078c98ad2
Add Perplexity search
2025-11-16 16:16:21 -08:00
Timothy Kassis
2e80732340
Add uv installation instructions
2025-11-16 15:36:33 -08:00
Timothy Kassis
2fc3e6a88e
Updated installation instructions for all skills to always use uv pip install
2025-11-16 15:34:52 -08:00
Timothy Kassis
d94f21c51f
Add support for fluidsim for computational fluid dynamics
2025-11-13 19:46:29 -08:00
Timothy Kassis
19c0b390ee
Merge pull request #5 from K-Dense-AI/refactor_skills
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Refactor skills into a single installable plugin
2025-11-13 19:21:02 -08:00
Timothy Kassis
54cab8e4b5
Update readme to clarify refactoring
2025-11-13 19:20:09 -08:00
