From ccd61e0d630228dd1c66bd52f78d68a80e351890 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Mon, 26 Oct 2026 16:30:43 +0000 Subject: [PATCH] [upstream-sync] README.md from GoekeLab/awesome-genomic-skills@281f0b83 [catalogue] --- .../catalogue/README.md | 30 +++++++++++-------- 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/upstream/GoekeLab-awesome-genomic-skills/catalogue/README.md b/upstream/GoekeLab-awesome-genomic-skills/catalogue/README.md index a1b729f..0d8ca23 100644 --- a/upstream/GoekeLab-awesome-genomic-skills/catalogue/README.md +++ b/upstream/GoekeLab-awesome-genomic-skills/catalogue/README.md @@ -2,9 +2,9 @@ title: "Awesome Genomic Skills [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)" task: "" lineage_type: import -upstream_source: https://github.com/GoekeLab/awesome-genomic-skills/blob/8cf42e1d/README.md -upstream_sha: 8cf42e1d -imported_at: 2026-08-08 +upstream_source: https://github.com/GoekeLab/awesome-genomic-skills/blob/281f0b83/README.md +upstream_sha: 281f0b83 +imported_at: 2026-10-26 prompt_class: catalogue upstream_changes: accepted author: upstream @@ -23,15 +23,12 @@ A curated list of skills and MCP servers for working with AI coding agents (Clau ## Contents -- [Awesome Genomic Skills ](#awesome-genomic-skills-) - - [What is a Skill and what is an MCP?](#what-is-a-skill-and-what-is-an-mcp) - - [Contents](#contents) - - [Bioinformatics and Genomics Agent Skills](#bioinformatics-and-genomics-agent-skills) - - [MCP Servers for Life Sciences](#mcp-servers-for-life-sciences) - - [Benchmarks](#benchmarks) - - [General AI Coding Agent Skill Collections](#general-ai-coding-agent-skill-collections) - - [Other Notable Awesome Lists!](#other-notable-awesome-lists) - - [Contributing](#contributing) +- [Bioinformatics and Genomics Agent Skills](#bioinformatics-and-genomics-agent-skills) +- [MCP Servers for Life Sciences](#mcp-servers-for-life-sciences) +- [AI Scientist and Research Agent Systems](#ai-scientist-and-research-agent-systems) +- [Benchmarks](#benchmarks) +- [General AI Coding Agent Skill Collections](#general-ai-coding-agent-skill-collections) +- [Other Notable Awesome Lists!](#other-notable-awesome-lists) ## Bioinformatics and Genomics Agent Skills @@ -93,8 +90,17 @@ Existing registries and lists of MCP servers: - [awesome-mcp-servers](https://github.com/punkpeye/awesome-mcp-servers#bio) - General-purpose MCP server list with a Biology, Medicine, and Bioinformatics subsection. MCP related tools: +- [Paper2Agent](https://github.com/jmiao24/Paper2Agent) - A multi-agent system that auto-generates an MCP server from a paper's codebase by executing its tutorials and extracting the workflows as validated, parameterised tools. [Nature paper](https://doi.org/10.1038/s41586-026-11044-y) - [BioinfoMCP](https://github.com/florensiawidjaja/BioinfoMCP) - Not strictly an MCP, a converter that auto-generates MCP servers from existing tool documentation, plus a benchmark of the converted tools. Preprint available [here](https://arxiv.org/abs/2510.02139) +## AI Scientist and Research Agent Systems + +Standalone multi-agent applications that run end-to-end research workflows (e.g. hypothesis generation), rather than components you plug into your own agent. + +- [Co-Scientist](https://github.com/Kaimen-Inc/Co-Scientist) + - **Description:** Independent implementation of Google DeepMind's AI co-scientist; takes a natural-language research goal and returns a tournament-ranked overview of novel hypotheses via six agents (Generation, Reflection, Elo-tournament Ranking, Evolution, Proximity, Meta-review) under a Supervisor. Grounds hypotheses with PubMed, arXiv, Europe PMC, and web search (with URL provenance logging), and uses a pinned copy of DeepMind's [science-skills](https://github.com/google-deepmind/science-skills). Runs on an LLM API key (OpenRouter, Anthropic, OpenAI, Gemini) or a Claude Code / Codex subscription; includes a cross-model benchmarking harness. General-science rather than genomics-specific. Apache-2.0. + - **Developers:** Kaimen Inc, co-founded by Kuan-Lin Huang ([Huang Lab | Precision Omics](https://labs.icahn.mssm.edu/kuanhuanglab/), Icahn School of Medicine at Mount Sinai); not affiliated with Google or the AI co-scientist paper's authors. + ## Benchmarks Benchmarks, evaluations, and other helpful resources at the intersection of AI and genomics/bioinformatics. -- 2.54.0