# The Research Workbench: How the Tools Connect URL: https://research-memex.org/docs/implementation/research-workbench Description: One drawing of how the host, its connections, the models and your own records fit together, with what each part does and where to set it up. *See where each tool sits before you install any of them.* The research workbench is the set of tools that lets an AI work on your own research material while you stay in control of it. Your library, notes and papers stay in files you own. The AI reaches them only through the connections you add, and you decide what each connection can see. This page draws the configuration the systematic-review module ran. Cherry Studio is the host because most participants arrive from a chatbot, and it lets them compare models side by side before an agent touches their files ([Tools & budget](/docs/case-studies/systematic-reviews/systematic-review-syllabus#tools--budget)). Claude Code or another agent host can take the same position, with the same connections beneath it. ```text title="diagram:research-workbench" +---------------------------------------------+ | Researcher | | question / judgment / checks | +----------------------+----------------------+ | v +----------------------+----------------------+ | Host: Cherry Studio | | chat / agents / knowledge base | +---------+-----------------------+-----------+ ^ ^ | | v v +---------+----------+ +---------+----------+ | Tools through MCP | | Models through API | | Zotero MCP | | gateways: | | filesystem MCP | | OpenRouter | | (vault only) | | Haimaker | | Research Memex | | local model | | MCP server | | (optional) | +---------+----------+ +--------------------+ ^ | v +---------+----------+ +--------------------+ | Durable record | | Discovery | | Zotero library |<-+ Research Rabbit | | Obsidian vault | | OpenAlex | | papers as Markdown | +--------------------+ +--------------------+ ``` Read it from the top. You direct the host; the host calls the tools and the models, and each call returns a result, so those arrows run both ways. The models never open your files. They see what the tools hand the host, and what the model writes back reaches your records only through a tool. Discovery tools feed the record from outside, as papers you decide to keep. ## What each part does [#what-each-part-does] | Component | What it does | Why it matters | Guide | | ------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------- | | Researcher | Brings the question, makes the judgments, checks the output | The only part that knows what the review is for | [Session 1](/docs/case-studies/systematic-reviews/session-1-review-by-hand) | | Cherry Studio | Holds the conversation and the agents, and calls the tools and models below it | One window to compare models before an agent touches your files | [Cherry Studio](/docs/implementation/agentic-ai-tools/cherry-studio-setup-guide) | | Zotero MCP | Lets the model search and read your Zotero library | Citations come from your library, not from the model's memory | [Zotero MCP](/docs/toolkit/zotero-mcp) | | Filesystem MCP | Lets the model read and write files in the folders you allow | Scope it to the vault folder only, so the rest of your disk stays out of reach | [MCP Explorer](/docs/implementation/ai-environment-setup/mcp-explorer-guide#part-1-built-in-servers-for-cherry-studio) | | Research Memex MCP server | Serves this site's pages and its three roles to the model, at `research-memex.org/mcp` | The model can look up a method or run a role without you pasting pages in; the roles run on your own model | [How AI reads this site](/docs/introduction/llms) | | OpenRouter, Haimaker | Gateways: one account reaches models from several providers. The course buys credits once on OpenRouter and issues each participant a named key with its own spend cap. Haimaker describes itself as an AI API gateway to many providers' models through one OpenAI-compatible endpoint; the second run used it too | Everyone can run the same task through different frontier models without opening accounts | [API Keys](/docs/implementation/ai-environment-setup/api-keys-setup-guide) | | Local model | Runs a model on your own machine | Optional, free and private, and weaker than frontier models | [Free and low-cost options](/docs/implementation/core-references/ai-model-reference-guide#free-and-low-cost-options) | | Zotero library | Holds your sources and their bibliographic records | The citation record that outlasts any conversation | [Zotero](/docs/implementation/foundational-setup/zotero-setup-guide) | | Obsidian vault | Holds your notes, protocol and the AI's output as Markdown files | The place decisions are written down and can be found again | [Obsidian](/docs/implementation/foundational-setup/obsidian-setup-guide) | | Papers as Markdown | Converted text of each PDF | A model reads and quotes Markdown more reliably than a PDF | [PDF to Markdown](/docs/implementation/ai-environment-setup/ocr-pdf-conversion-guide) | | Research Rabbit | Finds related papers through citation networks | Widens the search from the papers you already trust | [Research Rabbit](/docs/implementation/foundational-setup/research-rabbit-setup-guide) | | OpenAlex | An open index of the literature with an API and a CLI | A search an agent can run and you can rerun | [OpenAlex](/docs/implementation/foundational-setup/openalex-setup-guide) | ## A round trip [#a-round-trip] 1. You ask. Paste your protocol into the host with the question, so the model works to your criteria rather than its own. 2. The model reads. It searches your library through Zotero MCP and opens the Markdown papers through the filesystem MCP. 3. It writes. The output goes into your vault as a note, with a locator, a page or a section, for every claim it takes from a paper. 4. You check. Hold each locator against the paper. If the output reads generic, run the [Output Mirror](/docs/implementation/roles/output-mirror) on it. Then record the decision in the vault, including the ones where you overrule the model. ## Minimum, recommended, full [#minimum-recommended-full] * Minimum: Zotero, Cherry Studio and one model provider. Enough to ask about papers you paste in and to compare models. * Recommended: add the filesystem MCP, Zotero MCP, Obsidian and PDF-to-Markdown conversion, so the model reads your library and papers and writes into your vault. * Full: add a local model, a second gateway, the Research Memex server and agent teams, as [Session 4](/docs/case-studies/systematic-reviews/session-4-agentic-workflows) runs them. For a guided setup, [Carrel](/docs/toolkit/carrel) configures the machine with you; for the order to install things in, follow [Quick Start](/docs/implementation/foundational-setup/quick-start-checklist).