Human instructions

.github/workflows/python-package.yml

@@ -0,0 +1,37 @@
+name: Python package
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  build:
+
+    runs-on: [ubuntu-latest]
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+
+    - name: Install pudu package in development mode with test dependencies
+      run: |
+        pip install -e .[test]
+
+    - name: Test scripts with opentrons_simulate
+      run: |
+        pytest -s -v

README.md

@@ -2,8 +2,8 @@
 Welcome to the PUDU (Protocol Unified Design Unit) repository, our Python package for liquid handling robot control on Synthetic Biology workflows.
 
 
-<img src="https://github.com/RudgeLab/PUDU/blob/main/images/PUDU_Logo.png#gh-light-mode-only" alt="PUDU logo" width="250"/>
-<img src="https://github.com/RudgeLab/PUDU/blob/main/images/PUDU_Logo.png#gh-dark-mode-only" alt="PUDU night logo" width="250"/>
+<img src="https://github.com/MyersResearchGroup/PUDU/blob/main/images/PUDU_Logo.png#gh-light-mode-only" alt="PUDU logo" width="250"/>
+<img src="https://github.com/MyersResearchGroup/PUDU/blob/main/images/PUDU_Logo_dark.png#gh-dark-mode-only" alt="PUDU night logo" width="250"/>
 
 ## *The art of automated liquid handling*
 
@@ -67,3 +67,19 @@ then in the OT-2 terminal run:
 ## Tutorials
 
 TODO
+
+## Manual Golden Gate protocol generation
+
+PUDU now supports generating a **human-readable manual Golden Gate protocol** from SBOL-style JSON input using `ManualAssembly`.
+
+- The class builds structured per-reaction records (product, backbone, ordered parts, enzyme, and calculated reagent volumes).
+- It renders a Markdown protocol suitable for lab use and future PDF conversion.
+- It does **not** generate OT-2 commands.
+
+Example script:
+
+```bash
+PYTHONPATH=src python scripts/generate_manual_assembly_protocol.py
+```
+
+This writes a protocol document to `scripts/manual_assembly_protocol.md`.

documentation/docs.md

@@ -0,0 +1 @@
+docs

documentation/manual_assembly_protocol_example.md

@@ -0,0 +1,63 @@
+# Golden Gate Manual Assembly Protocol
+
+## Overview
+Golden Gate assembly is a one-pot DNA cloning method that uses a Type IIS restriction enzyme, such as BsaI, together with DNA ligase to assemble multiple DNA fragments in a predefined order.
+Because Type IIS enzymes cut outside their recognition sites, they generate custom overhangs that direct fragment assembly and allow the recognition sites to be removed from the final construct.
+In this protocol, plasmids containing DNA parts and a destination backbone are combined with the restriction enzyme and ligase in a single tube, then cycled in a thermocycler between digestion and ligation temperatures. Repetition of these cycles enriches for the correctly assembled composite plasmid, after which the enzymes are heat-inactivated and the reaction is held at 4 °C until collection.
+
+## Inputs
+- Number of target products: 2
+- `composite_1` (https://SBOL2Build.org/composite_1/1)
+- `composite_2` (https://SBOL2Build.org/composite_2/1)
+
+## Reaction summary
+| Product | Backbone | Parts | Restriction Enzyme | # DNA Components | DNA each (µL) | Enzyme (µL) | Ligase (µL) | Buffer (µL) | Water (µL) | Total (µL) |
+| --- | --- | --- | --- | ---: | ---: | ---: | ---: | ---: | ---: | ---: |
+| composite_1 | pSB1C3 | J23101, B0034, GFP, B0015 | BsaI | 5 | 2 | 2 | 4 | 2 | 2 | 20 |
+| composite_2 | pSB1C3 | J23106, B0034, RFP, B0015 | BsaI | 5 | 2 | 2 | 4 | 2 | 2 | 20 |
+
+## Per-reaction instructions
+
+### Product: composite_1
+URI: https://SBOL2Build.org/composite_1/1
+
+1. Label one tube as `composite_1`.
+2. Add 2 µL nuclease-free water.
+3. Add 2 µL 10X T4 DNA Ligase Buffer.
+4. Add 4 µL T4 DNA Ligase.
+5. Add 2 µL BsaI (URI: https://SBOL2Build.org/BsaI/1).
+6. Add 2 µL backbone `pSB1C3` (URI: https://sbolcanvas.org/pSB1C3/1).
+7. Add 2 µL part `J23101` (URI: https://sbolcanvas.org/J23101/1).
+8. Add 2 µL part `B0034` (URI: https://sbolcanvas.org/B0034/1).
+9. Add 2 µL part `GFP` (URI: https://sbolcanvas.org/GFP/1).
+10. Add 2 µL part `B0015` (URI: https://sbolcanvas.org/B0015/1).
+11. Mix gently by pipetting. Do not vortex unless explicitly intended.
+12. Briefly spin down if appropriate.
+
+### Product: composite_2
+URI: https://SBOL2Build.org/composite_2/1
+
+1. Label one tube as `composite_2`.
+2. Add 2 µL nuclease-free water.
+3. Add 2 µL 10X T4 DNA Ligase Buffer.
+4. Add 4 µL T4 DNA Ligase.
+5. Add 2 µL BsaI (URI: https://SBOL2Build.org/BsaI/1).
+6. Add 2 µL backbone `pSB1C3` (URI: https://sbolcanvas.org/pSB1C3/1).
+7. Add 2 µL part `J23106` (URI: https://sbolcanvas.org/J23106/1).
+8. Add 2 µL part `B0034` (URI: https://sbolcanvas.org/B0034/1).
+9. Add 2 µL part `RFP` (URI: https://sbolcanvas.org/RFP/1).
+10. Add 2 µL part `B0015` (URI: https://sbolcanvas.org/B0015/1).
+11. Mix gently by pipetting. Do not vortex unless explicitly intended.
+12. Briefly spin down if appropriate.
+
+## Thermocycling
+- Use a cycling profile that holds 42°C for 2 minutes and 16°C for 5 minutes; repeat this profile 75 times.
+- Denature/inactivate proteins by holding 60°C for 10 minutes followed by 80°C for 10 minutes.
+- Hold at 4°C until samples are collected.
+
+## Notes
+- If the assembly was designed correctly, the final product should lack the Type IIS recognition sites used during assembly.
+- This generated document is a manual instruction sheet and not an automated OT-2 protocol.
+- Assumes all DNA parts are available at suitable concentrations and added at equal per-part volume.
+- Store the assembly product at 4 °C for better stability until used for downstream applications.
+- Validate assembled plasmids by restriction digest and gel electrophoresis, Sanger sequencing, or whole-plasmid sequencing.

notebooks/Assembly_to_OT2sim.ipynb

@@ -0,0 +1,208 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "f62bc338",
+   "metadata": {},
+   "source": [
+    "# SBOL to robot simulation"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "id": "7c2e1157",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Collecting git+https://github.com/MyersResearchGroup/SBOL2Build.git@roles-for-RE-and-Ligases\n",
+      "  Cloning https://github.com/MyersResearchGroup/SBOL2Build.git (to revision roles-for-RE-and-Ligases) to c:\\users\\lukef\\appdata\\local\\temp\\pip-req-build-jomazih6\n",
+      "  Resolved https://github.com/MyersResearchGroup/SBOL2Build.git to commit 2c0a53abada3731e81e0b04ac7c391f882c74a70\n",
+      "  Installing build dependencies: started\n",
+      "  Installing build dependencies: finished with status 'done'\n",
+      "  Getting requirements to build wheel: started\n",
+      "  Getting requirements to build wheel: finished with status 'done'\n",
+      "  Installing backend dependencies: started\n",
+      "  Installing backend dependencies: finished with status 'done'\n",
+      "  Preparing metadata (pyproject.toml): started\n",
+      "  Preparing metadata (pyproject.toml): finished with status 'done'\n",
+      "Requirement already satisfied: biopython in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2build==0.0b1) (1.81)\n",
+      "Requirement already satisfied: pydna in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2build==0.0b1) (5.0.0)\n",
+      "Requirement already satisfied: sbol2 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2build==0.0b1) (1.4.1)\n",
+      "Requirement already satisfied: numpy in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from biopython->sbol2build==0.0b1) (1.21.6)\n",
+      "Requirement already satisfied: networkx in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from pydna->sbol2build==0.0b1) (2.6.3)\n",
+      "Requirement already satisfied: prettytable in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from pydna->sbol2build==0.0b1) (3.7.0)\n",
+      "Requirement already satisfied: appdirs in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from pydna->sbol2build==0.0b1) (1.4.4)\n",
+      "Requirement already satisfied: requests in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2->sbol2build==0.0b1) (2.31.0)\n",
+      "Requirement already satisfied: urllib3 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2->sbol2build==0.0b1) (2.0.7)\n",
+      "Requirement already satisfied: rdflib>=5.0 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2->sbol2build==0.0b1) (6.3.2)\n",
+      "Requirement already satisfied: packaging>=20.0 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2->sbol2build==0.0b1) (24.0)\n",
+      "Requirement already satisfied: lxml in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2->sbol2build==0.0b1) (5.3.1)\n",
+      "Requirement already satisfied: deprecated in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2->sbol2build==0.0b1) (1.2.18)\n",
+      "Requirement already satisfied: python-dateutil in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from sbol2->sbol2build==0.0b1) (2.9.0)\n",
+      "Requirement already satisfied: pyparsing<4,>=2.1.0 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from rdflib>=5.0->sbol2->sbol2build==0.0b1) (2.4.7)\n",
+      "Requirement already satisfied: isodate<0.7.0,>=0.6.0 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from rdflib>=5.0->sbol2->sbol2build==0.0b1) (0.6.1)\n",
+      "Requirement already satisfied: importlib-metadata<5.0.0,>=4.0.0 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from rdflib>=5.0->sbol2->sbol2build==0.0b1) (4.13.0)\n",
+      "Requirement already satisfied: wrapt<2,>=1.10 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from deprecated->sbol2->sbol2build==0.0b1) (1.16.0)\n",
+      "Requirement already satisfied: wcwidth in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from prettytable->pydna->sbol2build==0.0b1) (0.2.10)\n",
+      "Requirement already satisfied: six>=1.5 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from python-dateutil->sbol2->sbol2build==0.0b1) (1.17.0)\n",
+      "Requirement already satisfied: certifi>=2017.4.17 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from requests->sbol2->sbol2build==0.0b1) (2024.8.30)\n",
+      "Requirement already satisfied: idna<4,>=2.5 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from requests->sbol2->sbol2build==0.0b1) (3.10)\n",
+      "Requirement already satisfied: charset-normalizer<4,>=2 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from requests->sbol2->sbol2build==0.0b1) (3.4.1)\n",
+      "Requirement already satisfied: zipp>=0.5 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from importlib-metadata<5.0.0,>=4.0.0->rdflib>=5.0->sbol2->sbol2build==0.0b1) (3.15.0)\n",
+      "Requirement already satisfied: typing-extensions>=3.6.4 in c:\\users\\lukef\\.conda\\envs\\test\\lib\\site-packages (from importlib-metadata<5.0.0,>=4.0.0->rdflib>=5.0->sbol2->sbol2build==0.0b1) (4.7.1)\n",
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "  Running command git clone --filter=blob:none --quiet https://github.com/MyersResearchGroup/SBOL2Build.git 'C:\\Users\\lukef\\AppData\\Local\\Temp\\pip-req-build-jomazih6'\n",
+      "  Running command git checkout -b roles-for-RE-and-Ligases --track origin/roles-for-RE-and-Ligases\n",
+      "  branch 'roles-for-RE-and-Ligases' set up to track 'origin/roles-for-RE-and-Ligases'.\n",
+      "  Switched to a new branch 'roles-for-RE-and-Ligases'\n"
+     ]
+    }
+   ],
+   "source": [
+    "pip install git+https://github.com/MyersResearchGroup/SBOL2Build.git@roles-for-RE-and-Ligases"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "id": "69c8a583",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sbol2build as sb2b"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 42,
+   "id": "e86cb15c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sbol2 as sb2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 43,
+   "id": "4f19b39f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def test_golden_gate():\n",
+    "        pro_doc = sb2.Document()\n",
+    "\n",
+    "        pro_doc.read('../tests/pro_in_bb.xml')\n",
+    "\n",
+    "        #where I am working adding 2 and 3\n",
+    "        pro2_doc = sb2.Document()\n",
+    "        pro2_doc.read('../tests/pro2_in_bb.xml') #add document\n",
+    "\n",
+    "        pro3_doc = sb2.Document()\n",
+    "        pro3_doc.read('../tests/pro3_in_bb.xml') #add document\n",
+    "    \n",
+    "        rbs_doc = sb2.Document()\n",
+    "        rbs_doc.read('../tests/rbs_in_bb.xml')\n",
+    "\n",
+    "        cds_doc = sb2.Document()\n",
+    "        cds_doc.read('../tests/cds_in_bb.xml')\n",
+    "        \n",
+    "        ter_doc = sb2.Document()\n",
+    "        ter_doc.read('../tests/terminator_in_bb.xml')\n",
+    "\n",
+    "        bb_doc = sb2.Document()\n",
+    "        bb_doc.read('../tests/backbone.xml')\n",
+    "\n",
+    "        part_docs = [pro_doc, rbs_doc, cds_doc, ter_doc]\n",
+    "\n",
+    "        assembly_doc = sb2.Document()\n",
+    "        assembly_obj = sb2b.golden_gate_assembly_plan('testassem', part_docs, bb_doc, 'BsaI', assembly_doc)\n",
+    "\n",
+    "        composites = assembly_obj.run()\n",
+    "\n",
+    "        assembly_doc.write('validation_assembly1.xml')\n",
+    "\n",
+    "        sbol_validation_result = assembly_doc.validate()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 44,
+   "id": "5bf7f217",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "adding: UJHDBOTD_70_extracted_part\n",
+      "adding: UJHDBOTD_70_three_prime_oh\n",
+      "adding: Scar_B\n",
+      "adding: J23101\n",
+      "adding: UJHDBOTD_70_five_prime_oh\n",
+      "adding: Scar_A\n",
+      "adding: UJHDBOTD_45_extracted_part\n",
+      "adding: UJHDBOTD_45_five_prime_oh\n",
+      "adding: Scar_B\n",
+      "adding: UJHDBOTD_45_three_prime_oh\n",
+      "adding: Scar_C\n",
+      "adding: B0034\n",
+      "adding: UJHDBOTD_106_extracted_part\n",
+      "adding: GFP\n",
+      "adding: UJHDBOTD_106_five_prime_oh\n",
+      "adding: Scar_C\n",
+      "adding: UJHDBOTD_106_three_prime_oh\n",
+      "adding: Scar_D\n",
+      "adding: UJHDBOTD_134_extracted_part\n",
+      "adding: B0015\n",
+      "adding: UJHDBOTD_134_three_prime_oh\n",
+      "adding: Scar_F\n",
+      "adding: UJHDBOTD_134_five_prime_oh\n",
+      "adding: Scar_D\n",
+      "adding: UJHDBOTD_extracted_backbone\n",
+      "adding: UJHDBOTD_159_five_prime_oh\n",
+      "adding: Scar_F\n",
+      "adding: Cir_qxow\n",
+      "adding: UJHDBOTD_159_three_prime_oh\n",
+      "adding: Scar_A\n",
+      "adding: composite_1\n"
+     ]
+    }
+   ],
+   "source": [
+    "test_golden_gate()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "test",
+   "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": "3.7.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}