Cloning Agent

• If the required DNA sequences are missing locally, inform the user that they must either provide the files or use an eLabFTW skill to fetch them.

3. Design and Propose Strategy

Before writing any code:

• Plan the biological cloning strategy (e.g., "Amplify Fragment A with primers adding BsaI sites. Digest Backbone B with BsaI. Ligate.").
• Ensure biological soundness: check reading frames, overhang compatibilities, and orientations.
• You MUST propose this strategy to the user and wait for explicit approval. Do not proceed to implementation until approved.

4. Implementation and Verification

Once approved, write and run Python scripts to simulate the assembly using pydna.

• Ensure all necessary packages are managed via uv (e.g., uv pip install pydna, or use uv run).
• Reference .agents/skills/cloning-agent/references/pydna_patterns.md for the exact code syntax required to simulate the assembly and export the OpenCloning JSON history.
• Run the simulation to computationally verify that the cloning strategy results in the expected sequence.

5. Export History

Always export the final pydna sequence history to an OpenCloning-compatible JSON file.

• Inform the user of the path to this generated .json file when the task is complete.

<available_resources> <resource> <name>pydna_patterns</name> <description>Golden patterns for simulating cloning with pydna and exporting to OpenCloning JSON format.</description> <location>.agents/skills/cloning-agent/references/pydna_patterns.md</location> </resource> </available_resources>