From fde3eed9f6dfb643fb7e88b5f04aff00d4e1457c Mon Sep 17 00:00:00 2001 From: "Dr. Alex M. Mawla, PhD" <8989493+ammawla@users.noreply.github.com> Date: Sun, 8 Mar 2026 17:34:27 -0700 Subject: [PATCH 1/2] Add encode-toolkit - ENCODE Project genomics MCP server MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ENCODE Toolkit — MCP server for the ENCODE Project (encodeproject.org) providing 20 tools and 47 skills for functional genomics research. Published on PyPI and npm. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d49b98db..1b8d9986 100644 --- a/README.md +++ b/README.md @@ -229,7 +229,7 @@ Design and visualize software architecture, system diagrams, and technical docum - [Narasimhaponnada/mermaid-mcp](https://github.com/Narasimhaponnada/mermaid-mcp) 📇 ☁️ 🍎 🪟 🐧 - AI-powered Mermaid diagram generation with 22+ diagram types including flowcharts, sequence diagrams, class diagrams, ER diagrams, architecture diagrams, state machines, and more. Features 50+ pre-built templates, advanced layout engines, SVG/PNG/PDF exports, and seamless integration with GitHub Copilot, Claude, and any MCP-compatible client. Install via NPM: `npm install -g @narasimhaponnada/mermaid-mcp-server` ### Biology, Medicine and Bioinformatics - +- [ammawla/encode-toolkit](https://github.com/ammawla/encode-toolkit) 🐧 - MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments. - [cafferychen777/ChatSpatial](https://github.com/cafferychen777/ChatSpatial) 🐍 🏠 - MCP server for spatial transcriptomics analysis with 60+ integrated methods covering cell annotation, deconvolution, spatial statistics, and visualization. - [dnaerys/onekgpd-mcp](https://github.com/dnaerys/onekgpd-mcp) ☕ ☁️ 🍎 🪟 🐧- real-time access to 1000 Genomes Project dataset - [genomoncology/biomcp](https://github.com/genomoncology/biomcp) 🐍 ☁️ - Biomedical research MCP server providing access to PubMed, ClinicalTrials.gov, and MyVariant.info. From 86340d7b9c51e37575a70a7dcaee08a01f39c633 Mon Sep 17 00:00:00 2001 From: "Dr. Alex M. Mawla, PhD" <8989493+ammawla@users.noreply.github.com> Date: Sun, 8 Mar 2026 18:26:38 -0700 Subject: [PATCH 2/2] Modify encode-toolkit entry in README Updated the encode-toolkit entry to include a link to Glama. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1b8d9986..10ba6b3c 100644 --- a/README.md +++ b/README.md @@ -229,7 +229,7 @@ Design and visualize software architecture, system diagrams, and technical docum - [Narasimhaponnada/mermaid-mcp](https://github.com/Narasimhaponnada/mermaid-mcp) 📇 ☁️ 🍎 🪟 🐧 - AI-powered Mermaid diagram generation with 22+ diagram types including flowcharts, sequence diagrams, class diagrams, ER diagrams, architecture diagrams, state machines, and more. Features 50+ pre-built templates, advanced layout engines, SVG/PNG/PDF exports, and seamless integration with GitHub Copilot, Claude, and any MCP-compatible client. Install via NPM: `npm install -g @narasimhaponnada/mermaid-mcp-server` ### Biology, Medicine and Bioinformatics -- [ammawla/encode-toolkit](https://github.com/ammawla/encode-toolkit) 🐧 - MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments. +- [ammawla/encode-toolkit](https://github.com/ammawla/encode-toolkit) [glama](https://glama.ai/mcp/servers/ammawla/encode-toolkit) 🐧 - MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments. - [cafferychen777/ChatSpatial](https://github.com/cafferychen777/ChatSpatial) 🐍 🏠 - MCP server for spatial transcriptomics analysis with 60+ integrated methods covering cell annotation, deconvolution, spatial statistics, and visualization. - [dnaerys/onekgpd-mcp](https://github.com/dnaerys/onekgpd-mcp) ☕ ☁️ 🍎 🪟 🐧- real-time access to 1000 Genomes Project dataset - [genomoncology/biomcp](https://github.com/genomoncology/biomcp) 🐍 ☁️ - Biomedical research MCP server providing access to PubMed, ClinicalTrials.gov, and MyVariant.info.