Clayton Young
21f8536cef
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
2026-02-23 07:43:04 -05:00
Clayton Young
0607ad9cf8
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
2026-02-23 07:43:04 -05:00
Timothy Kassis
d17d74dc5d
Add support for economic data form the Federal Reserve using FRED
2026-01-27 10:41:40 -08:00
Timothy Kassis
c5413a6b5c
Remove Biomni due to incompatibilities
2026-01-21 09:11:38 -05:00
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
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
Haoxuan "Orion" Li
7232cf73a9
docs: add K-Dense Web GIF
2026-01-07 17:13:23 -08:00
Timothy Kassis
15d9e4699a
Update examples
2026-01-05 13:49:00 -08:00
Timothy Kassis
70375367d6
Support for writing and executing MATLAB/Octave scripts
2026-01-05 10:15:22 -08:00
Timothy Kassis
57bde764fe
Added ISO 13485 certification prep skill
2025-12-29 11:12:50 -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
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
78331e1b37
Remove all writing skills for upcoming upgrade
2025-12-07 13:54:58 -08:00
Timothy Kassis
49567890a6
Add BRENDA enzyme database
2025-12-03 17:29:05 -08:00
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
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
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
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
ea638c5618
Add support for Adaptyv for protein design
2025-11-24 19:52:45 -05:00
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
d94f21c51f
Add support for fluidsim for computational fluid dynamics
2025-11-13 19:46:29 -08:00
Timothy Kassis
ad2dfc3446
Update readme
2025-11-13 19:17:42 -08:00
Timothy Kassis
cc99fdb57d
Add support for Modal so researchers can scale compute on demand for heavy computational tasks beyond running locally
2025-11-10 10:57:05 -08:00
Timothy Kassis
5b7081cbff
Add examples
2025-11-06 17:04:04 -08:00
Timothy Kassis
1225ddecf1
Add support for both geniml and gtars
2025-11-04 10:22:03 -08:00
Timothy Kassis
4ad4f9970f
Improve the scikit-learn skill
2025-11-04 10:11:46 -08:00
Timothy Kassis
63a4293f1a
Add support for the Denario AI scientist
2025-11-03 17:04:20 -08:00
Timothy Kassis
86d8878eeb
Improve the astropy skill
2025-11-03 16:34:14 -08:00
Timothy Kassis
094d5aa9f1
Improve the aeon skill
2025-11-03 15:59:29 -08:00
Timothy Kassis
862445f531
Add support for Stable-Baselines3, a PyTorch-based library providing reliable, well-tested implementations of popular deep reinforcement learning algorithms with a simple and consistent API for research and training.
2025-11-02 14:54:16 -08:00
Timothy Kassis
b8c4d2bae1
Add support for PufferLib which is a high-performance, open-source Python toolkit that wraps complex RL environments to look like standard Gym/PettingZoo interfaces and supports massively parallel simulation (1M+ steps/sec) to accelerate deep reinforcement learning.
2025-11-02 14:52:06 -08:00
Timothy Kassis
27d6ee387f
Add support for Vaex for fast, memory-efficient exploration and visualization of large tabular datasets using lazy, out-of-core computation.
2025-11-02 14:43:20 -08:00
Timothy Kassis
f32b3f8b42
Add support for SymPY for symbolic mathematics that enables algebraic manipulation, equation solving, calculus, and symbolic computation directly in Python.
2025-11-02 14:30:20 -08:00
Timothy Kassis
ed2d1c4aeb
Add support for NetworkX for creating, analyzing, and visualizing complex networks and graphs.
2025-11-02 14:19:20 -08:00
Timothy Kassis
7e3fae3ad1
Add support to LaminDB
2025-10-31 11:39:54 -07:00
Timothy Kassis
346010a1bf
Add Markitdown skill to read all sorts of documents
2025-10-28 16:31:01 -07:00
Timothy Kassis
82901e9fbe
Add hypothesis generation using HypoGeniC and HypoRefine
2025-10-28 12:53:43 -07:00
Timothy Kassis
1f03feda5c
Add protocols.io integration
2025-10-26 11:09:03 -07:00
Timothy Kassis
04d528c4bc
Added support for NeuroKit2
2025-10-25 21:38:31 -07:00
Timothy Kassis
a5c2ed9bb6
Add literature review skill
2025-10-25 10:55:36 -07:00
Timothy Kassis
564bd39835
Add support for HistoLab
2025-10-24 13:41:06 -07:00
Timothy Kassis
ca6fd369d7
Add DrugBank access
2025-10-24 09:04:43 -07:00
Timothy Kassis
808fa11206
Add DataCommons which enables scientists to programmatically access nodes in the Data Commons knowledge graph.
2025-10-24 09:04:27 -07:00
Timothy Kassis
ee73143b53
Add scikit-survival for survival analysis allowing users to establish connections between covariates and time of an event
2025-10-23 10:02:16 -07:00
Timothy Kassis
b1df506eba
Add support for PyHealth making healthcare AI simpler and more powerful
2025-10-23 09:50:07 -07:00
Timothy Kassis
bb1c9f4573
Add support for PyDicom
2025-10-23 09:35:46 -07:00
