AI ChatTools
AI Chat Tools
The Bioinformatics Studio AI Chat agent comes with 73 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
File & Code
9 toolsrun_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 & Knowledge
Web & Search
3 toolsweb_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 toolsgenerate_memory_contextStores important info for future reference
knowledge_searchSearches the persistent knowledge base
store_knowledgeStores information in the knowledge base
Bioinformatics
Bioinformatics
11 toolsquery_entrez_databaseQueries NCBI databases (PubMed, Gene, Protein)
bio_queryQueries 41 biological databases with structured or natural language
bio_list_databasesLists available databases and their operations
bio_translate_idsTranslates gene/protein IDs between database formats
bio_build_graphBuilds biological knowledge graphs (KEGG, GO, Reactome, STRING)
bio_graph_queryQueries knowledge graphs for neighbors, paths, and subgraphs
bio_enrichmentGene set enrichment analysis (GO, KEGG, Reactome)
bio_research_workflowSuggests multi-database research workflows
bio_evidence_trailShows provenance trail for all database queries
bio_cache_statsShows local cache statistics for bio queries
autoresearchLogs experiment attempts to a structured TSV file
Workflow & Tasks
Task Management
7 toolstask_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
Workflow & Canvas
15 toolsworkflow_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)
Agents & Planning
Agent & Team
5 toolsspawn_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 toolsenter_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 & System
Session & Persistence
4 toolssave_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
Development
5 toolslsp_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 toolscron_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 toolsconfig_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 toolslist_mcp_resourcesLists resources from MCP servers
read_mcp_resourceReads a resource from an MCP server by URI
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