borealBytes 7a3ce8fb18 fix(mermaid): replace \n with <br/> in all node labels ...

Mermaid renders literal \n as text on GitHub — line breaks inside
node labels require <br/> syntax. Fixed 12 occurrences across 4 files:

- SKILL.md: three-phase workflow (Phase 1/2/3 nodes)
- issue-00000001: three-phase workflow nodes
- pr-00000001: skill name node
- example-research-report.md: Stage 1-5 nodes in experimental workflow

2026-02-19 18:35:25 -05:00

..

adaptyv

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

aeon

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

alphafold-database

Merge pull request #30 from marovole/fix/shell-command-injection-docs

2026-01-08 08:53:35 -08:00

anndata

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

arboreto

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

astropy

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

benchling-integration

Clean description fields

2026-01-05 14:29:10 -08:00

biopython

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

biorxiv-database

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

bioservices

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

brenda-database

Clean description fields

2026-01-05 14:29:10 -08:00

cellxgene-census

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

chembl-database

Clean description fields

2026-01-05 14:29:10 -08:00

cirq

Clean description fields

2026-01-05 14:29:10 -08:00

citation-management

Enhance citation management and literature review guidelines

2026-01-05 13:01:10 -08:00

clinical-decision-support

Clean description fields

2026-01-05 14:29:10 -08:00

clinical-reports

Clean description fields

2026-01-05 14:29:10 -08:00

clinicaltrials-database

Clean description fields

2026-01-05 14:29:10 -08:00

clinpgx-database

Clean description fields

2026-01-05 14:29:10 -08:00

clinvar-database

Clean description fields

2026-01-05 14:29:10 -08:00

cobrapy

Clean description fields

2026-01-05 14:29:10 -08:00

cosmic-database

Clean description fields

2026-01-05 14:29:10 -08:00

dask

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

datacommons-client

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

datamol

Clean description fields

2026-01-05 14:29:10 -08:00

deepchem

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

deeptools

Clean description fields

2026-01-05 14:29:10 -08:00

denario

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

diffdock

Clean description fields

2026-01-05 14:29:10 -08:00

dnanexus-integration

Clean description fields

2026-01-05 14:29:10 -08:00

document-skills

Clean description fields

2026-01-05 14:29:10 -08:00

drugbank-database

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

ena-database

Clean description fields

2026-01-05 14:29:10 -08:00

ensembl-database

Clean description fields

2026-01-05 14:29:10 -08:00

esm

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

etetoolkit

Clean description fields

2026-01-05 14:29:10 -08:00

exploratory-data-analysis

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

fda-database

Clean description fields

2026-01-05 14:29:10 -08:00

flowio

Clean description fields

2026-01-05 14:29:10 -08:00

fluidsim

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

fred-economic-data

Add support for economic data form the Federal Reserve using FRED

2026-01-27 10:41:40 -08:00

gene-database

Clean description fields

2026-01-05 14:29:10 -08:00

generate-image

Clean description fields

2026-01-05 14:29:10 -08:00

geniml

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

geo-database

Clean description fields

2026-01-05 14:29:10 -08:00

geopandas

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

get-available-resources

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

gget

Fix description formatting in SKILL.md

2026-01-07 15:15:18 +08:00

gtars

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

gwas-database

Clean description fields

2026-01-05 14:29:10 -08:00

histolab

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

hmdb-database

Clean description fields

2026-01-05 14:29:10 -08:00

hypogenic

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

hypothesis-generation

Enhance literature search and research lookup documentation

2026-02-03 14:31:19 -08:00

imaging-data-commons

update to v1.3.1

2026-02-11 09:42:22 -05:00

infographics

Add infographics skill for creating visual data representations

2026-02-03 17:03:44 -08:00

iso-13485-certification

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

kegg-database

Clean description fields

2026-01-05 14:29:10 -08:00

labarchive-integration

Clean description fields

2026-01-05 14:29:10 -08:00

lamindb

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

latchbio-integration

Clean description fields

2026-01-05 14:29:10 -08:00

latex-posters

Enhance literature search and research lookup documentation

2026-02-03 14:31:19 -08:00

literature-review

Enhance literature search and research lookup documentation

2026-02-03 14:31:19 -08:00

markdown-mermaid-writing

fix(mermaid): replace \n with <br/> in all node labels

2026-02-19 18:35:25 -05:00

market-research-reports

Clean description fields

2026-01-05 14:29:10 -08:00

markitdown

Enhance literature search and research lookup documentation

2026-02-03 14:31:19 -08:00

matchms

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

matlab

Support for writing and executing MATLAB/Octave scripts

2026-01-05 10:15:22 -08:00

matplotlib

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

medchem

Clean description fields

2026-01-05 14:29:10 -08:00

metabolomics-workbench-database

Clean description fields

2026-01-05 14:29:10 -08:00

modal

fix(security): replace shell=True with safe subprocess patterns in documentation

2026-01-08 15:05:30 +08:00

molfeat

Clean description fields

2026-01-05 14:29:10 -08:00

networkx

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

neurokit2

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

neuropixels-analysis

Replace all instances of Sonnet to Opus

2026-01-21 09:16:34 -05:00

offer-k-dense-web

Add K-Dense Web skill

2026-01-05 18:20:10 -08:00

omero-integration

Clean description fields

2026-01-05 14:29:10 -08:00

openalex-database

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

opentargets-database

Clean description fields

2026-01-05 14:29:10 -08:00

opentrons-integration

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

paper-2-web

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

pathml

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

pdb-database

Clean description fields

2026-01-05 14:29:10 -08:00

peer-review

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

pennylane

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

perplexity-search

Clean description fields

2026-01-05 14:29:10 -08:00

plotly

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

polars

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

pptx-posters

Merge branch 'main' into fix-writing-skills

2026-01-05 15:46:55 -08:00

protocolsio-integration

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

pubchem-database

Clean description fields

2026-01-05 14:29:10 -08:00

pubmed-database

Clean description fields

2026-01-05 14:29:10 -08:00

pufferlib

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

pydeseq2

Clean description fields

2026-01-05 14:29:10 -08:00

pydicom

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

pyhealth

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

pylabrobot

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

pymatgen

Clean description fields

2026-01-05 14:29:10 -08:00

pymc

Clean description fields

2026-01-05 14:29:10 -08:00

pymoo

Clean description fields

2026-01-05 14:29:10 -08:00

pyopenms

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

pysam

Clean description fields

2026-01-05 14:29:10 -08:00

pytdc

Clean description fields

2026-01-05 14:29:10 -08:00

pytorch-lightning

Clean description fields

2026-01-05 14:29:10 -08:00

qiskit

Clean description fields

2026-01-05 14:29:10 -08:00

qutip

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

rdkit

refactor(rdkit): update fingerprint generation to use rdFingerprintGenerator API

2026-01-26 20:25:28 +08:00

reactome-database

Clean description fields

2026-01-05 14:29:10 -08:00

research-grants

Clean description fields

2026-01-05 14:29:10 -08:00

research-lookup

Enhance literature search and research lookup documentation

2026-02-03 14:31:19 -08:00

rowan

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

scanpy

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

scholar-evaluation

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

scientific-brainstorming

Clean description fields

2026-01-05 14:29:10 -08:00

scientific-critical-thinking

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

scientific-schematics

Enhance literature search and research lookup documentation

2026-02-03 14:31:19 -08:00

scientific-slides

Clean description fields

2026-01-05 14:29:10 -08:00

scientific-visualization

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

scientific-writing

Enhance literature search and research lookup documentation

2026-02-03 14:31:19 -08:00

scikit-bio

Clean description fields

2026-01-05 14:29:10 -08:00

scikit-learn

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

scikit-survival

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

scvi-tools

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

seaborn

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

shap

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

simpy

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

stable-baselines3

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

statistical-analysis

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

statsmodels

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

string-database

Clean description fields

2026-01-05 14:29:10 -08:00

sympy

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

torch_geometric

Clean description fields

2026-01-05 14:29:10 -08:00

torchdrug

Disambiguate descriptions

2026-01-05 14:25:22 -08:00

transformers

Add suggestion to use K-Dense Web for complicated workflows.

2026-01-02 13:27:48 -08:00

treatment-plans

Clean description fields

2026-01-05 14:29:10 -08:00

umap-learn

Clean description fields

2026-01-05 14:29:10 -08:00

uniprot-database

Clean description fields

2026-01-05 14:29:10 -08:00

uspto-database

Add patentsview api key for patent search api

2026-01-08 22:38:59 -08:00

vaex

Clean description fields

2026-01-05 14:29:10 -08:00

venue-templates

Enhance citation management and literature review guidelines

2026-01-05 13:01:10 -08:00

zarr-python

Clean description fields

2026-01-05 14:29:10 -08:00

zinc-database

Clean description fields

2026-01-05 14:29:10 -08:00