Zenodo MCP Server for ClineGive Cline instant access to 14 tools to Create Deposition, Delete Deposition, Delete Deposition File, and more
GDPR Free for SubscribersCline is an autonomous AI coding agent inside VS Code that plans, executes, and iterates on tasks. Wire Zenodo through Vinkius and Cline gains direct access to every tool. from data retrieval to workflow automation. without leaving the terminal.
Ask AI about this MCP Server for Cline
The Zenodo MCP Server for Cline is a standout in the Knowledge Management category — giving your AI agent 14 tools to work with, ready to go from day one.
Vinkius delivers Streamable HTTP and SSE to any MCP client
Gemini{
"mcpServers": {
"zenodo": {
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
}
}
}Vinkius Desktop App
The modern way to manage MCP Servers — no config files, no terminal commands. Install Zenodo and 4,000+ MCP Servers from a single visual interface.
* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure
About Zenodo MCP Server
Connect your Zenodo account to any AI agent to streamline your scientific research workflows and data management through natural conversation.
Cline operates autonomously inside VS Code. it reads your codebase, plans a strategy, and executes multi-step tasks including Zenodo tool calls without waiting for prompts between steps. Connect 14 tools through Vinkius and Cline can fetch data, generate code, and commit changes in a single autonomous run.
What you can do
- Deposition Management — Create new unpublished depositions, update metadata, and manage your research drafts directly from the AI.
- Record Discovery — Search and list public records across the entire Zenodo database to find relevant research, software, or datasets.
- File Inspection — List all files attached to specific depositions to understand the contents of a research package.
- Metadata Control — Precisely update titles, creators, descriptions, licenses, and access rights for your unpublished work.
- Version Tracking — Retrieve specific deposition details using unique IDs to monitor the status of your submissions.
The Zenodo MCP Server exposes 14 tools through the Vinkius. Connect it to Cline in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.
All 14 Zenodo tools available for Cline
When Cline connects to Zenodo through Vinkius, your AI agent gets direct access to every tool listed below — spanning open-access, research-data, metadata-management, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.
Create deposition on Zenodo
You can optionally provide metadata. Create a new Zenodo deposition
Delete deposition on Zenodo
Note: Only unpublished depositions can be deleted. Delete an unpublished Zenodo deposition
Delete deposition file on Zenodo
Delete a file from a Zenodo deposition
Discard deposition on Zenodo
Discard edits on a Zenodo deposition
Edit deposition on Zenodo
Edit a published Zenodo deposition
Get deposition on Zenodo
Retrieve a Zenodo deposition by ID
Get record on Zenodo
Retrieve a published Zenodo record by ID
List deposition files on Zenodo
List files in a Zenodo deposition
List depositions on Zenodo
List Zenodo depositions
List records on Zenodo
Search published Zenodo records
New version deposition on Zenodo
Create a new version of a Zenodo deposition
Publish deposition on Zenodo
WARNING: Once published, a deposition cannot be deleted. Publish a Zenodo deposition
Update deposition on Zenodo
Update a Zenodo deposition
Upload deposition file on Zenodo
Upload a text file to a Zenodo deposition
Connect Zenodo to Cline via MCP
Follow these steps to wire Zenodo into Cline. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Open Cline MCP Settings
Add remote server
Enable the server
Start using Zenodo
Why Use Cline with the Zenodo MCP Server
Cline provides unique advantages when paired with Zenodo through the Model Context Protocol.
Cline operates autonomously. it reads your codebase, plans a strategy, and executes multi-step tasks including MCP tool calls without step-by-step prompts
Runs inside VS Code, so you get MCP tool access alongside your existing extensions, terminal, and version control in a single window
Cline can create, edit, and delete files based on MCP tool responses, enabling end-to-end automation from data retrieval to code generation
Transparent execution: every tool call and file change is shown in Cline's activity log for full visibility and approval before committing
Zenodo + Cline Use Cases
Practical scenarios where Cline combined with the Zenodo MCP Server delivers measurable value.
Autonomous feature building: tell Cline to fetch data from Zenodo and scaffold a complete module with types, handlers, and tests
Codebase refactoring: use Zenodo tools to validate live data while Cline restructures your code to match updated schemas
Automated testing: Cline fetches real responses from Zenodo and generates snapshot tests or mocks based on actual payloads
Incident response: query Zenodo for real-time status and let Cline generate hotfix patches based on the findings
Example Prompts for Zenodo in Cline
Ready-to-use prompts you can give your Cline agent to start working with Zenodo immediately.
"Search for public Zenodo records related to 'machine learning in healthcare'."
"Create a new Zenodo deposition for a dataset titled 'Global Temperature Trends 2023'."
"List all files currently attached to my deposition with ID 987654."
Troubleshooting Zenodo MCP Server with Cline
Common issues when connecting Zenodo to Cline through Vinkius, and how to resolve them.
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Zenodo + Cline FAQ
Common questions about integrating Zenodo MCP Server with Cline.
How does Cline connect to MCP servers?
Can Cline run MCP tools without approval?
Does Cline support multiple MCP servers at once?
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