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Timothy Kassis 1e5eeffbda
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Update version numbers and enhance skill documentation 
- Bumped version in plugin.json and pyproject.toml to 2.66.0.
- Updated skill metadata versions across multiple skills, reflecting improvements and new features.
- Added citation guidelines to various skill documentation to ensure proper referencing of the "Scientific Agent Skills" paper.
2026-09-02 09:25:16 -07:00
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adaptyv
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
aeon
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
analytical-method-validation
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
anndata
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
arbor
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
arboreto
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
astropy
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
autoskill
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
benchling-integration
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
bgpt-paper-search
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
bids
Update documentation and improve test structure for autoskill
2026-07-26 09:54:14 -07:00
biopython
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
bioservices
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
bulk-rnaseq
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
cellxgene-census
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
cirq
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
citation-management
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
clinical-decision-support
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
clinical-reports
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
cobrapy
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
consciousness-council
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
dask
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
database-lookup
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
datamol
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
deepchem
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
deepspot-m
deepspot-m: document the ~19k-gene panel limit, drop redundant eval calls, add diagram
2026-08-07 13:09:04 -07:00
deeptools
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
depmap
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
dhdna-profiler
Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.
2026-07-28 10:50:49 -07:00
diffdock
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
dnanexus-integration
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
docx
Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.
2026-07-28 10:50:49 -07:00
esm
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
etetoolkit
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
exa-search
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
experimental-design
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
exploratory-data-analysis
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
flowio
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
fluidsim
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
generate-image
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
geniml
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
genomic-coordinates
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
genomic-intelligence
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
geomaster
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
geopandas
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
get-available-resources
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
gget
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
ginkgo-cloud-lab
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
glycoengineering
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
gtars
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
histolab
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
hugging-science
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
hypogenic
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
hypothesis-generation
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
imaging-data-commons
Update imaging-data-commons skill from v1.4.0 to upstream v1.8.1
2026-08-10 17:06:22 -04:00
infographics
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
iso-standards-readiness
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
lab-hardware-cad
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
labarchive-integration
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
lamindb
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
latchbio-integration
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
latex-posters
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
liteparse
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
literature-review
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
markdown-mermaid-writing
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
market-research-reports
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
markitdown
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
matchms
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
matlab
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
matplotlib
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
medchem
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
modal
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
molecular-dynamics
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
molfeat
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
ncats-arax
Add bounded NCATS ARAX knowledge graph skill
2026-08-08 02:44:06 -04:00
networkx
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
neurokit2
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
neuropixels-analysis
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
nextflow
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
omero-integration
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
onekgpd
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
ontology-term-resolution
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
open-notebook
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
openpiv
Test every script-bearing skill, and enforce that it stays that way
2026-07-28 10:20:12 -07:00
opentrons-integration
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
optimize-for-gpu
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pacsomatic
Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.
2026-07-28 10:50:49 -07:00
paper-lookup
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
paperclip
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
paperzilla
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
parallel-web
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pathml
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pathogen-variant-surveillance
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pathway-enrichment
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pdf
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
peer-review
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pennylane
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
phylogenetics
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
pi-agent
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pkpd-modeling
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
polars
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
polars-bio
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pptx
Update skill versions and enhance security measures across multiple skills. Added a triage report to SECURITY.md, improved endpoint validation in autoskill, and updated various skills to version 1.1 or 1.2. Enhanced documentation for imaging-data-commons and other skills to clarify installation and usage instructions.
2026-07-28 10:50:49 -07:00
pptx-posters
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
primekg
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
protocolsio-integration
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pufferlib
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pydeseq2
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pydicom
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pyhealth
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pylabrobot
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pymatgen
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pymc
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pymoo
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pyopenms
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pysam
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pytdc
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pytorch-lightning
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
pyzotero
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
qiskit
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
qutip
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
rdkit
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
relsa-severity-assessment
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
research-grants
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
research-lookup
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
rowan
Fix Rowan examples for SDK 3.1.13 (#237)
2026-08-29 06:52:25 -07:00
scanpy
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scholar-evaluation
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scientific-brainstorming
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scientific-critical-thinking
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scientific-schematics
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scientific-slides
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scientific-visualization
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scientific-writing
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scikit-bio
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scikit-learn
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scikit-survival
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
scvelo
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
scvi-tools
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
seaborn
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
shap
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
simpy
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
stable-baselines3
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
statistical-analysis
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
statistical-power
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
statsmodels
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
sympy
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
tamarind
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
tiledbvcf
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
timesfm-forecasting
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
torch-geometric
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
torchdrug
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
transformers
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
treatment-plans
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
umap-learn
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
uncertainty-and-units
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
usfiscaldata
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
vaex
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
venue-templates
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
waypoint-bio
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00
what-if-oracle
Update skill metadata formatting and improve .gitignore entries
2026-07-26 09:29:16 -07:00
xlsx
Enforce use of uv for packagment installation whenever needed
2026-07-31 10:29:07 -07:00
zarr-python
Update version numbers and enhance skill documentation
2026-09-02 09:25:16 -07:00