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Cracking Shells @crackingshells.bsky.social · 20/02/2026

It came out prettier than I thought! 😊 Just released Hatch v0.8.0. This update is all about UX: clean tables, helpful colors, outputs that actually make sense. 🐣 `pip install hatch-xclam` #MCP #AIForScience

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Cracking Shells @crackingshells.bsky.social · 22/12/2025

*Hatch!* v0.7.1 is out! 🐣 github.com/CrackingShel... It adds support for managing #MCP servers in - Codex - Kiro #AIForScience

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Cracking Shells @crackingshells.bsky.social · 21/11/2025

Name tags for our #MCP hackathon next week! Embracing Japan's 紅葉 season🍁🍂 for the theme 🐣 #AIForScience

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Cracking Shells @crackingshells.bsky.social · 12/11/2025

Just stumbled upon Augmented Nature's #MCP server collection for #LifeSciences. UniProt, AlphaFold, KEGG, PDB (and so many more!), all exposed via MCP: 🔗 github.com/Augmented-Na... #AIForScience #Biology

github.com

Augmented Nature

Augmented Nature has 25 repositories available. Follow their code on GitHub.

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Cracking Shells @crackingshells.bsky.social · 05/11/2025

Solid #MCP design patterns in @anthropic.com ’s latest: "Code execution with MCP: Building more efficient agents" 🔗 www.anthropic.com/engineering/... Exactly the kind of resource to share with your coding agent before tackling a server. I appreciate the didactic effort. 🐣 #AIForScience

anthropic.com

Code execution with MCP: building more efficient AI agents

Learn how code execution with the Model Context Protocol enables agents to handle more tools while using fewer tokens, reducing context overhead by up to 98.7%.

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Cracking Shells @crackingshells.bsky.social · 24/10/2025

Announcing our 2nd #MCP Hackathon – Nov 25-26 @ #RIKEN Kobe, Japan! After a closed first edition in August, we’re back open to all! Join up to 50 researchers/engineers to build MCP servers for scientific applications. 🔗 Sign up: forms.gle/vhTcV4uGDK9f... Details⬇️ #AIForScience #OpenScience

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Cracking Shells @crackingshells.bsky.social · 11/10/2025

Last week at #ICSB2025, we shared how #MCP can make LLM-based agents reliable for #SystemsBiology. MCP was barely known there. All the more reason for Cracking Shells to exist: simplifying onboarding for researchers. #AIForScience

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Cracking Shells @crackingshells.bsky.social · 01/10/2025

Two #MCP servers on Docker Hub for scientific papers 📚 🔗 paper-search: hub.docker.com/r/mcp/paper-search 🔗 arxiv-mcp-server: hub.docker.com/r/mcp/arxiv-mcp-server Useful for automating literature discovery in #AIForScience workflows. Have you tried them yet? #MCP #OpenScience

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Cracking Shells @crackingshells.bsky.social · 30/09/2025

Really excited to see what the async boost is about! 🐥 #MCP #AIForScience

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Cracking Shells @crackingshells.bsky.social · 30/09/2025

BioMCP: 24 #MCP tools for #biology 🧬 Shoutout to @genomoncology.bsky.social ! Search PubMed, ClinicalTrials, cBioPortal...Fetch genes/variants, expand disease synonyms, match trials to biomarkers, analyze OpenFDA safety data... 🔗 biomcp.org (Had forgotten about that one🤦) #AIForScience

biomcp.org

BioMCP

Biomedical Model Context Protocol Server

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Cracking Shells @crackingshells.bsky.social · 27/09/2025

Last week's #DevLog Hatch! 0.7.0 now lets you add MCP packages with one command—It's multi-dependencies and multi-host. Finally some versatility for #MCP setup 🐣 Still a pre-release, bug fixes & docs in progress! #AIForScience

A screen shot describing the CLI command to run to enbale installing and deploying MCP servers packaged as *Hatch!* packages. Supported dependency types are Python, System (apt), Docker, and other *Hatch!* packages. Supported MCP hosts are Claude Code, Claude Desktop, Cursor, VS Code, LM Studio, and Gemini

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Cracking Shells @crackingshells.bsky.social · 22/09/2025

AI Jam incoming in Japan! trip.riken.jp/en/aijam/ind... A hands-on event where scientists collaborate with LLMs from AWS, Anthropic, Google, and OpenAI to tackle challenging #research problems. 📆Dec 16-18: Main Session (Tokyo/Kobe) with on-site support from AI experts. #AIForScience

trip.riken.jp

Japan Scientist AI Jam Session 2025 | TRIP | Transformative Research Innovation Platform of RIKEN platforms

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Cracking Shells @crackingshells.bsky.social · 18/09/2025

For #AIForScience stack, #MCP servers for databases are crucial. A couple more of well-documented ones to explore: 🔗 Graph-based (for knowledge graphs): ArangoDB github.com/PCfVW/mcp-ar... 🔗 Document-based (for descriptive data): MongoDB github.com/mcp/mongodb-...

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Reposted by Cracking Shells

Model Context Protocol (MCP) @mcp-community.bsky.social · 17/09/2025

GitHub just launched the MCP Registry! It's the new place to find MCP Servers for any AI tool that speaks MCP, including GitHub Copilot and agents. Find what you need faster at: github.blog/ai-and-ml/gi... #GitHub #MCP #Developer #AI #OpenSource

github.blog

Home

Updates, ideas, and inspiration from GitHub to help developers build and design software.

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Cracking Shells @crackingshells.bsky.social · 18/09/2025

Great to see the MCP tool scalability problem getting attention! As the article notes, it’s a critical bottleneck, but solutions are coming. We’re tackling this too at Cracking Shells (ETA: December). The more minds on it, the faster we’ll crack it. 🐣 #MCP #AIForScience

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Cracking Shells @crackingshells.bsky.social · 17/09/2025

Using the server itself as a layer helping to manage the tools is indeed within the benefit of #MCP we'd cite. But the top one for us remains the encapsulation and being able to (almost) drop it anywhere. This is so convenient to decouple dev work from actual agent systems, particularly in #science

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Cracking Shells @crackingshells.bsky.social · 09/09/2025

After reading the MCP Registry docs, a few thoughts: 1. Not a perfect fit for #MCP for #science (yet), but that’s okay because 👇 2. Recommend filtering of existing registries AND 3. Support for custom package registries: the whole point of Cracking Shells 🤩—MCP servers for scientific applications

github.com

registry/docs at main · modelcontextprotocol/registry

A community driven registry service for Model Context Protocol (MCP) servers. - modelcontextprotocol/registry

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Cracking Shells @crackingshells.bsky.social · 09/09/2025

The MCP Registry is live! 🎉 Huge for tool discovery—especially if it works well for #MCP in #science. At Cracking Shells, we’ve built our own solutions, but we’re all for interoperability. Excited to test, compare, and adapt to what serves the community best. #AIForScience

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Cracking Shells @crackingshells.bsky.social · 08/09/2025

Here is nome inspiration from real-world MCP workflows (Slack → Notion/HubSpot). That could transfer to #LabAutomation e.g., routing logs from robotic systems or equipment notifications to research trackers. That could work today with systems we already have. #MCP #AIForScience

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Model Context Protocol (MCP) @mcp-community.bsky.social · 04/09/2025

For the open-source and decentralization folks: This session at the MCP Dev Summit is for you. Tadas Antanavicius and Toby Padilla are discussing the creation of an MCP Registry. A key step for the ecosystem. London, Oct 2. Register at mcpdevsummit.ai #OpenSource #Decentralization #AI #TechTalks

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Model Context Protocol (MCP) @mcp-community.bsky.social · 02/09/2025

For the tech and AI folks on Bluesky: Check out this talk from Andrew Culberson at the MCP Dev Summit. He's covering how MCP is the backbone for multi-agent, multi-user workspaces. A key topic for anyone building collaborative tools. See you in London on Oct 2. #TechTalks #AIagents #LondonTech #MCP

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Cracking Shells @crackingshells.bsky.social · 02/09/2025

Last week, we hosted our first #MCP hackathon for science with 22 #researchers (computational physics, chemistry, biology). None had used MCP or LLMs APIs before. By the end, they’d created their own MCP servers. This was invite-only, but more events are coming! 🐣 #AIForScience

The name tag of one of the staff of a hackathon entitled "Hatch! - MCP servers for scientific applications". The hackathon was hosted bu RIKEN from the 28th to 29th of August 2025. The staff's name is JACOPIN Eliott and is affiliated with RIKEN BDR.

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Model Context Protocol (MCP) @mcp-community.bsky.social · 02/09/2025

Security is non-negotiable. At the MCP Dev Summit in London, Vitor Balocco will present "MCP Security: The Exploit Playbook." A crucial session covering real-world exploits and defensive strategies for the age of autonomous agents. 🗓️ Oct 2|London mcpdevsummit.ai #MCPDevSummit #AISecurity #MCP #Ai

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Cracking Shells @crackingshells.bsky.social · 27/08/2025

#MCP isn’t the only way to connect LLMs to tools, but it won us over for #research: Small: the decorator pattern of the Python SDK is a killer to wrap existing API Decoupled: Devs build tools; users install them like packages (almost). Fits the ‘publish once, use anywhere’ model scientists like.

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Cracking Shells @crackingshells.bsky.social · 25/08/2025

Cracking Shells is an open-source project to help #researchers integrate their scientific software with LLMs using the Model Context Protocol #MCP. We are building it because we need it, and maybe you do too 😉 We'll be sharing more about it. In the meantime, take a look: github.com/CrackingShells

github.com

Cracking Shells

Gathering and servicing MCP servers as packages for Science - Cracking Shells

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