AI Chat Tools

The Genome Studio AI Chat agent comes with 65 built-in tools across 13 categories. These tools allow the AI to interact with the filesystem, run code, search the web, query biological databases, manage tasks, and manipulate the workflow canvas.

How to Call Tools

Just ask the AI in plain English. The agent automatically picks the right tool based on your message. For example:

“Read the file at /app/data/counts.csv” → triggers read_file
“Search PubMed for CRISPR papers” → triggers query_entrez_database
“Add a Python node called Preprocess” → triggers canvas_add_node

Complete Tool Reference

File & Code (9)

run_commandExecutes a bash command and returns its output

read_fileReads a file with optional line range support

scan_fileGets a structural preview of a large file

edit_filePerforms exact string replacements in files

write_fileWrites content to a file on the filesystem

grep_searchSearches file contents using regex patterns

glob_findFinds files by glob pattern (e.g. **/*.py)

list_directoryLists directory contents with sizes and counts

notebook_editEdits or inserts cells in a Jupyter notebook

Web & Search (3)

web_fetchFetches content from a URL in text or HTML format

web_searchSearches the web and returns titles and URLs

web_browserBrowses a URL, extracts content, or screenshots

Knowledge & Memory (3)

generate_memory_contextStores important info for future reference

knowledge_searchSearches the persistent knowledge base

store_knowledgeStores information in the knowledge base

Bioinformatics (3)

query_entrez_databaseQueries NCBI databases via Bio.Entrez

query_bio_databaseQueries 35+ biological databases in natural language

autoresearchLogs experiment attempts to a structured TSV file

Task Management (7)

task_createCreates a background task with title and priority

task_getGets details of a specific task by ID

task_updateUpdates a task's status or priority

task_listLists all tasks, optionally filtered by status

task_outputGets output and status of a background task

task_stopStops or cancels a running background task

todo_writeCreates and manages a structured task list

Agent & Team (5)

spawn_agentSpawns a subagent with isolated context

team_createCreates a team of coordinating agents

team_deleteDeletes an agent team by ID

send_messageSends a message to a peer agent

list_peersLists available peer agents for communication

Planning (3)

enter_plan_modeEnters read-only plan mode for research

exit_plan_modeExits plan mode with an auto-approved plan

ask_user_questionAsks the user a question with options

Session & Persistence (4)

save_to_sessionSaves large data to the session temp folder

list_session_filesLists all files saved in the current session

read_session_fileReads content of a file saved in the session

search_session_filesSearches saved session files by tags

Workflow & Canvas (15)

workflow_executeExecutes a named workflow with parameters

canvas_create_flowCreates a new flow file on the canvas

canvas_add_nodeAdds a single node to the workflow canvas

canvas_add_edgeConnects two nodes with an edge

canvas_list_nodesLists all nodes on the current canvas

canvas_search_nodesSearches nodes by name or type

canvas_remove_nodeRemoves a single node from the canvas

canvas_remove_nodesRemoves multiple nodes from the canvas

canvas_clearClears all nodes and edges from the canvas

canvas_get_active_flowGets the active flow file path and metadata

canvas_get_flow_nodesGets all nodes from a specific flow file

canvas_get_node_detailsGets detailed information about a node

canvas_edit_nodeEdits a node's properties (code, title, language)

canvas_verify_flowVerifies a flow's structure and connectivity

canvas_readReads the full canvas state (nodes and edges)

Development (5)

lsp_toolLanguage Server Protocol for code intelligence

repl_evalEvaluates Python code in a REPL environment

enter_worktreeCreates a git worktree for isolated dev

exit_worktreeRemoves and cleans up a git worktree

powershellExecutes a PowerShell command (Windows only)

Scheduling & Monitoring (5)

cron_createCreates a scheduled task (cron job)

cron_deleteDeletes a scheduled task by ID

cron_listLists all scheduled tasks

remote_triggerTriggers a remote endpoint with a payload

monitor_toolMonitors a resource for changes

Utility (12)

config_getGets configuration value(s) for the AI agent

skill_executeExecutes a discovered skill by name

tool_searchSearches for tools by name or description

sleep_toolSleeps for a specified number of seconds

brief_toolGenerates a brief summary of a topic

send_user_fileSends a file to the user for download

push_notificationSends a push notification to the user

subscribe_prSubscribes to PR updates for notifications

snip_toolRemoves old conversation messages to free context

overflow_testTests context overflow handling

ctx_inspectInspects current context window usage

terminal_captureCaptures the current terminal state

MCP (2)

list_mcp_resourcesLists resources from MCP servers

read_mcp_resourceReads a resource from an MCP server by URI