{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "\n",
    "sys.path.append(\"<REMOTE_USER_HOME>/BioAgentOS/biomni_release\")\n",
    "\n",
    "from biomni.agent import A1\n",
    "\n",
    "agent = A1(path=\"/dfs/project/bioagentos/biomni_data\", llm=\"claude-sonnet-4-20250514\")\n",
    "\n",
    "agent.go(\n",
    "    \"I have a plasmid plentiCRISPR v2 (sequence is at ./data/plentiCRISPR.txt). \"\n",
    "    \"I hope to clone a CRISPR sgRNA targeting human B2M into this plasmid. \"\n",
    "    \"Could you save the final assembied plasmid map into *.fasta and show step-by-step guidance\"\n",
    "    \" on how should I perform the cloning?\"\n",
    ")"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "biomni_env",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.11"
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 "nbformat": 4,
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