Modes

Co-Scientist includes build mode, plan mode, and goal mode so you can choose the right level of autonomy for each task.

Build mode

Build mode is the default interactive mode. Co-Scientist can:

• Read and search files
• Execute commands
• Edit or create files
• Carry out workflow changes directly in your workspace

Use build mode for implementation work, debugging, code generation, and file edits.

Plan mode

Plan mode is optimized for analysis and implementation planning.

In plan mode, Co-Scientist focuses on:

• Understanding the problem
• Comparing approaches and trade-offs
• Producing a step-by-step implementation plan
• Reading files and searching code for context

Plan mode blocks write and execution tools, including:

• execute_bash_local
• write_file_local
• edit_file_local
• create_directory_local

If the assistant tries to use one of these tools, the request is rejected and the assistant is told to switch back to build mode.

Switch between build mode and plan mode

Toggle modes during a session with Shift+Tab.

You can also:

• Check the current mode in the composer footer.
• Run /status to view the current mode alongside session and LSP status.
• Use /help to see mode-aware command guidance.

Goal mode

Goal mode is a persistent workflow for longer tasks. Set a goal with:

/goal <task description>

When goal mode is active, Co-Scientist:

• Keeps working toward the same objective over multiple model attempts.
• Automatically continues if more work is needed.
• Stops when the goal is complete or the goal attempt limit is reached.
• Switches approval mode to full so work can continue without repeated prompts.

Goal mode commands:

/goal
/goal off

Run /goal without arguments to inspect the current goal. Run /goal off to disable goal mode.

Co-Scientist currently gives goal mode up to 3 model attempts before it stops and asks you to start a new goal.

Keyboard shortcuts

Shortcut	Action
Shift+Tab	Toggle between build mode and plan mode.
Ctrl+Enter	If your terminal supports it, interrupt the current response and send a queued follow-up immediately.
Esc	Clear a queued follow-up or interrupt the current response.

Examples

Plan mode

Compare whether I should add FastQC or fastp as the first QC step in this RNA-seq pipeline, including the workflow changes each option would require

Inspect this repository and outline the changes needed for Seqera Platform deployment

Goal mode

/goal migrate this pipeline to DSL2 and add nf-tests

/goal update this workflow for AWS Batch and verify the config

Learn more

• Skills: Discover, create, and install skills
• Command approval: Control which commands run automatically
• Use cases: Co-Scientist CLI use cases
• Credits: Co-Scientist credits and how to request more