Legacy agents will be deprecated in the future. All capabilities of the legacy agents are integrated with the Chat tool. For more information about Chat and how to use it, see the linked help article.
Compose accelerates Notebook entry and template creation using natural language prompt inputs and attached files. Use Compose to:
- Organize experimental data
- Extract information from uploaded notes
- Draft an entry for your experiment and insert structured tables
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Create a Notebook template from an image of a protocol
This is a Benchling AI capability. See the AI at Benchling page for information on how to ensure that this and other AI-based capabilities are provisioned to the appropriate users on your tenant.
Create a new Compose Agent chat
Each time you want to create a new document, you will need to create a new chat where you will enter your prompt. To create a new chat, follow the steps below:
- Click the sparkle icon in the navigation bar to access Benchling agents
- In the chat box, click Compose
- In the textbox, type your prompt in natural language, and attach necessary supporting files such as PDFs
- Send the chat to run the prompt
Once you send the chat, the side panel will expand with your document draft.
Note: Compose performs best when your prompt is clear and specific.
If the entry that you are making is intended to be part of a Template Collection, you can open the Compose chat directly from the Create dropdown in your collection. Selecting Entry template from Compose will bring you directly to the Compose chat box.
You can also access the Compose agent from the global create menu:
Use skills
Skills teach Benchling AI how to handle specific tasks reliably. Use skills in Benchling to extend the default capabilities of the Benchling AI Chat. Benchling Skills conform to the open Agent Skills standard.
There are two types of skills:
- Benchling-authored skills that are written by Benchling and made available for use in your tenant
- Custom skills written by you or your organization
Benchling-authored skills
Benchling-authored skills are auto installed by Benchling. Benchling-authored skills cannot be edited or deleted by users, Benchling will control all content and updates for these skills.
The list of available Benchling-authored skills are below:
Access skills
- Open AI in the main sidebar
- Click the gear icon in the top right corner of the AI panel
- Select the Skills tab
Manage your active skills
Each user controls which skills are available to Benchling AI during their sessions. Active skills can be pulled into context by the agent when relevant, while inactive skills are ignored.
Toggle skills on or off from either:
- AI Settings → Skills tab
- The + button inside AI Chat
Archive skills you authored if you no longer need them:
- Open AI Settings
- Navigate to Skills tab
- Click the Archive button in the top right corner of the skill
Using skills
Once a skill is active, the AI will pull it in automatically when it's relevant to your request. You can also invoke a skill directly from the + button in AI Chat if you want to use it explicitly.
Create a new skill
Describe the task you want Benchling AI to handle - what should trigger it, what steps it should follow, and any details specific to your workflow. Benchling AI will draft a skill you can review and refine.
Edit an existing skill
Mention your existing skill and tell Benchling AI what isn't working. It can fix outdated steps, add missing edge cases, or improve when the skill fires.
Upload an existing skill
If you've built a skill outside of Benchling or want to bring one in from another project, you can upload the skill file directly to make it available in your workspace. Benchling accepts .zip or .skill files for upload as skills. Simply click + Add in the top right corner of the Skills page to upload a skill file.
A few tips:
- Base your request on a real task: the more concrete, the better the result
- Include any templates, data sources, or sample outputs the AI should follow or reference. The more concrete your inputs, the more reliably the skill will perform.
- If the skill isn't triggering when you expect, ask Benchling AI to revisit its description - that's usually where the issue is
Edit and adjust your draft
In the event that you need to modify the document generated by the agent, you can do so either manually directly in the draft or by follow ups with a clarifying prompt in the same chat interface.
Save your draft
In order to finalize the output, you must save the draft. To do this, follow the steps below:
- Click Save as on the top right corner of your draft document
- Choose whether your draft should be saved as:
- A new entry
- A new template
View previous chats
- To open your chat history, click the sparkle icon in the navigation bar
- Click the History icon at the top left
- Click into each past chat to see more
Common use cases
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Transcribe uploaded SOP or Protocol files into Benching template with structured tables
- Example: "Create a notebook template based on the attached protocol. Include any appropriate result tables."
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Create a template based on one or more entries
- Example: "Templatize the experiments conducted in EXPXXX and EXPXXX."
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Transcribe an externally documented experiment and import structured data (PDF of a different ELN export, Word doc, etc.)
- Example: "Transcribe the attached lab notebook file into a Benchling entry. Import any data into structured result tables."
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Extract protocol steps from an external PDF or file to append to an existing entry
- Example: "Transcribe the attached lab notebook file into a Benchling entry."
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Extract methods from a scientific publication
- Example: "Based on the attached publication, draft an experiment protocol entry that captures the methods described. Include reagents, equipment, and step-by-step procedures. Format it as an actionable lab protocol that our team can follow to reproduce the experiment."
Limitations
- Larger operations can take longer to run. You can close the side panel and return later to review the results
Risks from AI mistakes
As with any AI tool, Compose may make mistakes, so it is critical to verify the results to ensure the data is properly entered into the system.
Data protection and security
For more information about data protection and security for AI-powered features, see Data protection and security for AI at Benchling.