docs: expand README with detailed instructions

Author: hqn21

README.md

@@ -1,3 +1,117 @@
 # Protocols.io MCP Server
 
-An MCP server that enables MCP clients like Claude Desktop to interact with data from protocols.io.
+A Model Context Protocol (MCP) server that enables MCP clients like Claude Desktop to interact with [protocols.io](https://www.protocols.io), a popular platform for sharing scientific protocols and methods.
+
+## Available Tools
+
+The server provides the following tools that can be used by MCP clients:
+
+### Search and Retrieval
+- `search_public_protocols` - Search for public protocols by keyword
+- `get_protocol` - Get basic protocol information by ID
+- `get_protocol_steps` - Get detailed steps for a specific protocol
+- `get_my_protocols` - Retrieve all protocols from your account
+
+### Protocol Creation and Management
+- `create_protocol` - Create a new protocol with title and description
+- `update_protocol_title` - Update the title of an existing protocol
+- `update_protocol_description` - Update the description of an existing protocol
+
+### Step Management
+- `set_protocol_steps` - Replace all steps in a protocol
+- `add_protocol_step` - Add a single step to the end of a protocol
+- `delete_protocol_step` - Delete a specific step from a protocol
+
+## Requirements
+
+- Python 3.10 or higher
+- protocols.io account with API access token
+- MCP client (such as Claude Desktop)
+
+## Installation
+
+Install the package using pip:
+
+```bash
+pip install protocols-io-mcp
+```
+
+## Configuration
+
+### Environment Variables
+
+Before running the server or tests, you must set your protocols.io API access token:
+
+```bash
+export PROTOCOLS_IO_CLIENT_ACCESS_TOKEN="your_client_access_token"
+```
+
+To obtain an API token:
+1. Visit [protocols.io/developer](https://www.protocols.io/developers)
+2. Sign in to your account
+3. Go to API clients section and add a new client
+4. Copy the generated client access token and set it in your environment
+
+## Usage
+
+### Command Line Interface
+
+Run the MCP server with various transport options:
+
+```bash
+# Default: stdio transport (recommended for MCP clients)
+protocols-io-mcp
+
+# HTTP transport
+protocols-io-mcp --transport http --host 127.0.0.1 --port 8000
+
+# Server-Sent Events transport
+protocols-io-mcp --transport sse --host 127.0.0.1 --port 8000
+```
+
+#### CLI Options
+
+```
+Usage: protocols-io-mcp [OPTIONS]
+
+  Run the protocols.io MCP server.
+    
+Options:
+  --transport [stdio|http|sse]  Transport protocol to use [default: stdio]
+  --host TEXT                   Host to bind to when using http and sse
+                                transport [default: 127.0.0.1]
+  --port INTEGER                Port to bind to when using http and sse
+                                transport [default: 8000]
+  --help                        Show this message and exit.
+```
+
+### Integration with Claude Desktop
+
+To use this server with Claude Desktop, add the following configuration to your `claude_desktop_config.json`:
+
+```json
+{
+  "mcpServers": {
+    "protocols-io": {
+      "command": "protocols-io-mcp",
+      "env": {
+        "PROTOCOLS_IO_CLIENT_ACCESS_TOKEN": "your_client_access_token"
+      }
+    }
+  }
+}
+```
+
+## Development
+
+### Running Tests
+
+Ensure you have set the `PROTOCOLS_IO_CLIENT_ACCESS_TOKEN` environment variable, then run:
+
+```bash
+pytest
+```
+
+## License
+
+This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.