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k-dense-ai avatar

Esm

k-dense-ai/scientific-agent-skills
1.1k installs33k stars
Summary

This connects you to EvolutionaryScale's protein language models for generative design and embedding tasks. ESM3 handles the generative side: you can design new protein sequences, predict structures, do inverse folding, or condition on functional properties using multimodal prompts. ESM C gives you embeddings for ML tasks. You can run small models locally with open weights (Python 3.12 required) or hit the Forge API for the bigger models like the 98B parameter ESM3. The API mirrors the local interface, which is nice. If you're working on protein engineering, variant design, or need quality protein representations without training your own model, this gets you current SOTA tools with minimal setup.

Install to Claude Code

npx -y skills add k-dense-ai/scientific-agent-skills --skill esm --agent claude-code

Installs into .claude/skills of the current project.

CodeRabbit
CodeRabbit
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inference shell
inference shell
create and run specialised agents in minutes
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Plug Mailtrap into your AI workflow and let it handle the email.
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Make your agent a DeFi expert
Make your agent a DeFi expert
Agent, run crypto. Access onchain data & trade routes via 1inch.
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Capacitor - Shared memory for your team’s coding agents.
Capacitor - Shared memory for your team’s coding agents.
Make coding agent sessions - Searchable, Shareable, Vendor-neutral & Scored.
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CodeScene MCP ServerCodeScene MCP Server
CodeScene MCP Server
Your agent targets a perfect 10 Code Health score. Deterministic. Every commit.
Try For Free →
Give your AI the whole web as clean markdownGive your AI the whole web as clean markdown
Give your AI the whole web as clean markdown
Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →
belt - the only tool your agent needs
belt - the only tool your agent needs
belt cli automatically finds the best tools and skills for your agent. image, video, music, tts...
one prompt install →
CodeRabbit
CodeRabbit
AI writes the code. CodeRabbit catches the slop.
Try For Free →
inference shell
inference shell
create and run specialised agents in minutes
build now →
MCP-ready Email SendingMCP-ready Email Sending
MCP-ready Email Sending
Plug Mailtrap into your AI workflow and let it handle the email.
Connect Mailtrap MCP →
Make your agent a DeFi expert
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Agent, run crypto. Access onchain data & trade routes via 1inch.
Install now →
Capacitor - Shared memory for your team’s coding agents.
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Make coding agent sessions - Searchable, Shareable, Vendor-neutral & Scored.
Try For Free →
CodeScene MCP ServerCodeScene MCP Server
CodeScene MCP Server
Your agent targets a perfect 10 Code Health score. Deterministic. Every commit.
Try For Free →
Give your AI the whole web as clean markdownGive your AI the whole web as clean markdown
Give your AI the whole web as clean markdown
Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →
belt - the only tool your agent needs
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belt cli automatically finds the best tools and skills for your agent. image, video, music, tts...
one prompt install →
Files
SKILL.md

Select a file.

Featured
CodeRabbit
CodeRabbit
AI writes the code. CodeRabbit catches the slop.
Try For Free →
inference shell
inference shell
create and run specialised agents in minutes
build now →
MCP-ready Email SendingMCP-ready Email Sending
MCP-ready Email Sending
Plug Mailtrap into your AI workflow and let it handle the email.
Connect Mailtrap MCP →
Make your agent a DeFi expert
Make your agent a DeFi expert
Agent, run crypto. Access onchain data & trade routes via 1inch.
Install now →
Capacitor - Shared memory for your team’s coding agents.
Capacitor - Shared memory for your team’s coding agents.
Make coding agent sessions - Searchable, Shareable, Vendor-neutral & Scored.
Try For Free →
CodeScene MCP ServerCodeScene MCP Server
CodeScene MCP Server
Your agent targets a perfect 10 Code Health score. Deterministic. Every commit.
Try For Free →
Give your AI the whole web as clean markdownGive your AI the whole web as clean markdown
Give your AI the whole web as clean markdown
Integrate web data into your AI product. One API to scrape website & brand data.
Get API Key Now →
belt - the only tool your agent needs
belt - the only tool your agent needs
belt cli automatically finds the best tools and skills for your agent. image, video, music, tts...
one prompt install →
Categories
AI & Agent BuildingPython
First SeenJun 3, 2026
View on GitHub

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k-dense-ai avatar
pathml

k-dense-ai/scientific-agent-skills

Use PathML for local, research-only computational pathology workflows: load and tile slides, build preprocessing and QC pipelines, manage h5path data, quantify multiplex images, construct spatial graphs, and plan bounded model inference.
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k-dense-ai avatar
pysam

k-dense-ai/scientific-agent-skills

Python/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
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pymatgen

k-dense-ai/scientific-agent-skills

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k-dense-ai avatar
depmap

k-dense-ai/scientific-agent-skills

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k-dense-ai avatar
phylogenetics

k-dense-ai/scientific-agent-skills

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
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k-dense-ai avatar
treatment-plans

k-dense-ai/scientific-agent-skills

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