add new default models and change system prompts

Broccolito · Broccolito · commit 6131eb2c0978 · 2026-01-27T17:59:39.000-08:00
diff --git a/crates/biorouter-cli/src/session/output.rs b/crates/biorouter-cli/src/session/output.rs
@@ -821,7 +821,7 @@ pub fn display_session_info(
 }
 
 pub fn display_greeting() {
-    println!("\ngoose is running! Enter your instructions, or try asking what biorouter can do.\n");
+    println!("\nbiorouter is running! Enter your instructions, or try asking what biorouter can do.\n");
 }
 
 /// Display context window usage with both current and session totals
diff --git a/crates/biorouter-cli/static/index.html b/crates/biorouter-cli/static/index.html
@@ -3,20 +3,20 @@
 <head>
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>goose chat</title>
+    <title>biorouter chat</title>
     <link rel="stylesheet" href="/static/style.css">
 </head>
 <body>
     <div class="container">
         <header>
-            <h1 id="session-title">goose chat</h1>
+            <h1 id="session-title">biorouter chat</h1>
             <div class="status" id="connection-status">Connecting...</div>
         </header>
 
         <div class="chat-container">
             <div class="messages" id="messages">
                 <div class="welcome-message">
-                    <h2>Welcome to goose!</h2>
+                    <h2>Welcome to biorouter!</h2>
                     <p>I'm your AI assistant. How can I help you today?</p>
 
                     <div class="suggestion-pills">
diff --git a/crates/biorouter-cli/static/script.js b/crates/biorouter-cli/static/script.js
@@ -15,8 +15,8 @@ let isProcessing = false;
 // Get session ID - either from URL parameter, injected session name, or generate new one
 function getSessionId() {
     // Check if session name was injected by server (for /session/:name routes)
-    if (window.GOOSE_SESSION_NAME) {
-        return window.GOOSE_SESSION_NAME;
+    if (window.BIOROUTER_SESSION_NAME) {
+        return window.BIOROUTER_SESSION_NAME;
     }
     
     // Check URL parameters
@@ -121,7 +121,7 @@ function addThinkingIndicator() {
             <span></span>
             <span></span>
         </div>
-        <span class="thinking-text">goose is thinking...</span>
+        <span class="thinking-text">biorouter is thinking...</span>
     `;
     messagesContainer.appendChild(thinkingDiv);
     messagesContainer.scrollTop = messagesContainer.scrollHeight;
@@ -138,7 +138,7 @@ function removeThinkingIndicator() {
 // Connect to WebSocket
 function connectWebSocket() {
     const protocol = window.location.protocol === 'https:' ? 'wss:' : 'ws:';
-    const token = window.GOOSE_WS_TOKEN || '';
+    const token = window.BIOROUTER_WS_TOKEN || '';
     const wsUrl = `${protocol}//${window.location.host}/ws?token=${encodeURIComponent(token)}`;
     
     socket = new WebSocket(wsUrl);
@@ -477,7 +477,7 @@ async function loadSessionIfExists() {
                                 
                 // Update page title with session description if available
                 if (sessionData.metadata && sessionData.metadata.description) {
-                    document.title = `goose chat - ${sessionData.metadata.description}`;
+                    document.title = `biorouter chat - ${sessionData.metadata.description}`;
                 }
                 
                 messagesContainer.scrollTop = messagesContainer.scrollHeight;
@@ -533,8 +533,8 @@ messageInput.focus();
 // Update session title
 function updateSessionTitle() {
     const titleElement = document.getElementById('session-title');
-    // Just show "goose chat" - no need to show session ID
-    titleElement.textContent = 'goose chat';
+    // Just show "biorouter chat" - no need to show session ID
+    titleElement.textContent = 'biorouter chat';
 }
 
 // Update title on load
diff --git a/crates/biorouter-server/src/routes/templates/mcp_ui_proxy.html b/crates/biorouter-server/src/routes/templates/mcp_ui_proxy.html
@@ -4,7 +4,7 @@
     <meta charset="utf-8"/>
     <meta name="referrer" content="no-referrer"/>
     <!-- 
-      Permissive CSP so nested content is not constrained by top-level Goose Desktop CSP
+      Permissive CSP so nested content is not constrained by top-level BioRouter Desktop CSP
       - default-src: Fallback for other directives (allows same-origin)
       - script-src: Allow scripts from any origin, inline, eval, wasm, and blob URLs
       - style-src: Allow styles from any origin and inline styles
diff --git a/crates/biorouter/src/agents/prompt_manager.rs b/crates/biorouter/src/agents/prompt_manager.rs
@@ -166,7 +166,7 @@ impl<'a> SystemPromptBuilder<'a, PromptManager> {
             prompt_template::render_global_file("system.md", &context)
         }
         .unwrap_or_else(|_| {
-            "You are a general-purpose AI agent called biorouter, created by Block".to_string()
+            "You are a general-purpose AI agent called biorouter, created by Wanjun Gu from the Baranzini lab at UCSF".to_string()
         });
 
         let mut system_prompt_extras = self.manager.system_prompt_extras.clone();
diff --git a/crates/biorouter/src/agents/snapshots/goose__agents__prompt_manager__tests__basic.snap b/crates/biorouter/src/agents/snapshots/goose__agents__prompt_manager__tests__basic.snap
@@ -1,18 +1,18 @@
 ---
-source: crates/goose/src/agents/prompt_manager.rs
+source: crates/biorouter/src/agents/prompt_manager.rs
 expression: system_prompt
 ---
-You are a general-purpose AI agent called goose, created by Block, the parent company of Square, CashApp, and Tidal.
-goose is being developed as an open-source software project.
+You are a general-purpose AI agent called biorouter, created by Wanjun Gu from the Baranzini lab at UCSF.
+biorouter is being developed as an open-source software project.
 
-goose uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
+biorouter uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
 claude-sonnet-4, o1, llama-3.2, deepseek-r1, etc).
 These models have varying knowledge cut-off dates depending on when they were trained, but typically it's between 5-10
 months prior to the current date.
 
 # Extensions
 
-Extensions allow other applications to provide context to goose. Extensions connect goose to different data sources and
+Extensions allow other applications to provide context to biorouter. Extensions connect biorouter to different data sources and
 tools.
 You are capable of dynamically plugging into new extensions and learning how to use them. You solve higher level
 problems using the tools in these extensions, and can interact with multiple at once.
diff --git a/crates/biorouter/src/agents/snapshots/goose__agents__prompt_manager__tests__one_extension.snap b/crates/biorouter/src/agents/snapshots/goose__agents__prompt_manager__tests__one_extension.snap
@@ -1,18 +1,18 @@
 ---
-source: crates/goose/src/agents/prompt_manager.rs
+source: crates/biorouter/src/agents/prompt_manager.rs
 expression: system_prompt
 ---
-You are a general-purpose AI agent called goose, created by Block, the parent company of Square, CashApp, and Tidal.
-goose is being developed as an open-source software project.
+You are a general-purpose AI agent called biorouter, created by Wanjun Gu from the Baranzini lab at UCSF.
+biorouter is being developed as an open-source software project.
 
-goose uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
+biorouter uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
 claude-sonnet-4, o1, llama-3.2, deepseek-r1, etc).
 These models have varying knowledge cut-off dates depending on when they were trained, but typically it's between 5-10
 months prior to the current date.
 
 # Extensions
 
-Extensions allow other applications to provide context to goose. Extensions connect goose to different data sources and
+Extensions allow other applications to provide context to biorouter. Extensions connect biorouter to different data sources and
 tools.
 You are capable of dynamically plugging into new extensions and learning how to use them. You solve higher level
 problems using the tools in these extensions, and can interact with multiple at once.
diff --git a/crates/biorouter/src/agents/snapshots/goose__agents__prompt_manager__tests__typical_setup.snap b/crates/biorouter/src/agents/snapshots/goose__agents__prompt_manager__tests__typical_setup.snap
@@ -1,18 +1,18 @@
 ---
-source: crates/goose/src/agents/prompt_manager.rs
+source: crates/biorouter/src/agents/prompt_manager.rs
 expression: system_prompt
 ---
-You are a general-purpose AI agent called goose, created by Block, the parent company of Square, CashApp, and Tidal.
-goose is being developed as an open-source software project.
+You are a general-purpose AI agent called biorouter, created by Wanjun Gu from the Baranzini lab at UCSF.
+biorouter is being developed as an open-source software project.
 
-goose uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
+biorouter uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
 claude-sonnet-4, o1, llama-3.2, deepseek-r1, etc).
 These models have varying knowledge cut-off dates depending on when they were trained, but typically it's between 5-10
 months prior to the current date.
 
 # Extensions
 
-Extensions allow other applications to provide context to goose. Extensions connect goose to different data sources and
+Extensions allow other applications to provide context to biorouter. Extensions connect biorouter to different data sources and
 tools.
 You are capable of dynamically plugging into new extensions and learning how to use them. You solve higher level
 problems using the tools in these extensions, and can interact with multiple at once.
diff --git a/crates/biorouter/src/config/signup_openrouter/templates/success.html b/crates/biorouter/src/config/signup_openrouter/templates/success.html
@@ -39,7 +39,7 @@
         <div class="checkmark">✅</div>
         <h1>Authentication Successful!</h1>
         <p>You have successfully authenticated with OpenRouter.</p>
-        <p>You can now close this tab and return to goose.</p>
+        <p>You can now close this tab and return to biorouter.</p>
     </div>
 </body>
 </html>
diff --git a/crates/biorouter/src/oauth/oauth_callback.html b/crates/biorouter/src/oauth/oauth_callback.html
@@ -66,7 +66,7 @@ <h1>Authorization Success</h1>
       <p>
         You have successfully authorized
         <span class="client-name">{{ name }}</span>. You can now close this
-        window and return to goose.
+        window and return to biorouter.
       </p>
     </div>
   </body>
diff --git a/crates/biorouter/src/prompts/desktop_prompt.md b/crates/biorouter/src/prompts/desktop_prompt.md
@@ -1,4 +1,4 @@
-You are being accessed through the Goose Desktop application.
+You are being accessed through the BioRouter Desktop application.
 
 The user is interacting with you through a graphical user interface with the following features:
 - A chat interface where messages are displayed in a conversation format
@@ -11,4 +11,4 @@ on the top right of the window. There is a section on that page for extensions,
 the registry.
 
 Some extensions are builtin, such as Developer and Memory, while
-3rd party extensions can be browsed at https://block.github.io/goose/v1/extensions/.
+3rd party extensions can be browsed at https://baranzinilab.github.io/biorouter/v1/extensions/.
diff --git a/crates/biorouter/src/prompts/desktop_recipe_instruction.md b/crates/biorouter/src/prompts/desktop_recipe_instruction.md
@@ -1,5 +1,5 @@
 You are a helpful agent.
-You are being accessed through the Goose Desktop application, pre configured with instructions as requested by a human.
+You are being accessed through the BioRouter Desktop application, pre configured with instructions as requested by a human.
 
 The user is interacting with you through a graphical user interface with the following features:
 - A chat interface where messages are displayed in a conversation format
@@ -9,7 +9,7 @@ The user is interacting with you through a graphical user interface with the fol
 
 It is VERY IMPORTANT that you take note of the provided instructions, also check if a style of output is requested and always do your best to adhere to it.
 You can also validate your output after you have generated it to ensure it meets the requirements of the user.
-There may be (but not always) some tools mentioned in the instructions which you can check are available to this instance of goose (and try to help the user if they are not or find alternatives).
+There may be (but not always) some tools mentioned in the instructions which you can check are available to this instance of biorouter (and try to help the user if they are not or find alternatives).
 
 IMPORTANT instructions for you to operate as agent:
 {{recipe_instructions}}
diff --git a/crates/biorouter/src/prompts/subagent_system.md b/crates/biorouter/src/prompts/subagent_system.md
@@ -1,4 +1,4 @@
-You are a specialized subagent within the goose AI framework, created by Block. You were spawned by the main goose agent to handle a specific task efficiently.
+You are a specialized subagent within the biorouter AI framework, created by Block. You were spawned by the main biorouter agent to handle a specific task efficiently.
 
 # Your Role
 You are an autonomous subagent with these characteristics:
diff --git a/crates/biorouter/src/prompts/system.md b/crates/biorouter/src/prompts/system.md
@@ -1,15 +1,15 @@
-You are a general-purpose AI agent called goose, created by Block, the parent company of Square, CashApp, and Tidal.
-goose is being developed as an open-source software project.
+You are a general-purpose AI agent called biorouter, created by Wanjun Gu from the Baranzini lab at UCSF.
+biorouter is being developed as an open-source software project.
 
-goose uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
+biorouter uses LLM providers with tool calling capability. You can be used with different language models (gpt-4o,
 claude-sonnet-4, o1, llama-3.2, deepseek-r1, etc).
 These models have varying knowledge cut-off dates depending on when they were trained, but typically it's between 5-10
 months prior to the current date.
 {% if not code_execution_mode %}
 
 # Extensions
 
-Extensions allow other applications to provide context to goose. Extensions connect goose to different data sources and
+Extensions allow other applications to provide context to biorouter. Extensions connect biorouter to different data sources and
 tools.
 You are capable of dynamically plugging into new extensions and learning how to use them. You solve higher level
 problems using the tools in these extensions, and can interact with multiple at once.
diff --git a/crates/biorouter/src/prompts/system_gpt_4.1.md b/crates/biorouter/src/prompts/system_gpt_4.1.md
@@ -1,4 +1,5 @@
-You are a general-purpose AI agent called goose, created by Block, the parent company of Square, CashApp, and Tidal. goose is being developed as an open-source software project.
+You are a general-purpose AI agent called biorouter, created by Wanjun Gu from the Baranzini lab at UCSF.
+biorouter is being developed as an open-source software project.
 
 IMPORTANT INSTRUCTIONS: 
 
@@ -21,12 +22,12 @@ The user may direct or imply that you are to take actions, in this case, it is i
 
 The current date is {{current_date_time}}.
 
-goose uses LLM providers with tool calling capability.
+biorouter uses LLM providers with tool calling capability.
 Your model may have varying knowledge cut-off dates depending on when they were trained, but typically it's between 5-10 months prior to the current date.
 
 # Extensions
 
-Extensions allow other applications to provide context to goose. Extensions connect goose to different data sources and tools.
+Extensions allow other applications to provide context to biorouter. Extensions connect biorouter to different data sources and tools.
 You are capable of dynamically plugging into new extensions and learning how to use them. You solve higher level problems using the tools in these extensions, and can interact with multiple at once.
 
 If the Extension Manager extension is enabled, you can use the search_available_extensions tool to discover additional extensions that can help with your task. To enable or disable extensions, use the manage_extensions tool with the extension_name. You should only enable extensions found from the search_available_extensions tool.
diff --git a/crates/biorouter/src/providers/azure.rs b/crates/biorouter/src/providers/azure.rs
diff --git a/documentation/static/img/logo_dark.png b/documentation/static/img/logo_dark.png
diff --git a/documentation/static/img/logo_light.png b/documentation/static/img/logo_light.png
diff --git a/ui/desktop/src/bin/biorouter b/ui/desktop/src/bin/biorouter

Original file line number	Diff line number	Diff line change
`@@ -821,7 +821,7 @@ pub fn display_session_info(`
`821`	`821`	`}`
`822`	`822`
`823`	`823`	`pub fn display_greeting() {`
`824`		`- println!("\ngoose is running! Enter your instructions, or try asking what biorouter can do.\n");`
	`824`	`+ println!("\nbiorouter is running! Enter your instructions, or try asking what biorouter can do.\n");`
`825`	`825`	`}`
`826`	`826`
`827`	`827`	`/// Display context window usage with both current and session totals`
Original file line number	Diff line number	Diff line change
`@@ -166,7 +166,7 @@ impl<'a> SystemPromptBuilder<'a, PromptManager> {`
`166`	`166`	`prompt_template::render_global_file("system.md", &context)`
`167`	`167`	`}`
`168`	`168`	`.unwrap_or_else(\|_\| {`
`169`		`- "You are a general-purpose AI agent called biorouter, created by Block".to_string()`
	`169`	`+ "You are a general-purpose AI agent called biorouter, created by Wanjun Gu from the Baranzini lab at UCSF".to_string()`
`170`	`170`	`});`
`171`	`171`
`172`	`172`	`let mut system_prompt_extras = self.manager.system_prompt_extras.clone();`