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    "info": {
        "author": "JJTimmons",
        "author_email": "jtimmons@latticeautomation.com",
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        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# synbio\n\n`synbio` is a library for designing and assembling DNA. Users can design plasmids or libraries and export multi-step build protocols. Input SeqRecords. Output assembly SeqRecords, protocols, plate maps, and robotic picklists.\n\nDocumentation is available at [https://lattice-automation.github.io/synbio](https://lattice-automation.github.io/synbio)\n\n## Installation\n\n```bash\n# with pip\npip install synbio\n\n# OR with conda\nconda install -c jtimmons synbio\n```\n\n## Models\n\n`synbio` only expects the user to define their `Design` and `Protocol`. Several protocols are pre-defined.\n\n### Designs\n\nAll are in `synbio.designs`:\n\n- `Combinatorial` - list of SeqRecords to combinatorially anneal into all valid assemblies\n- `CombinatorialBins` - list of bins of SeqRecords for combinatorial assembly of records between bins\n- `Plasmid` - single list of SeqRecords to combine into a plasmid\n- `PlasmidLibrary` - list of list of SeqRecords to combine into plasmids\n\n### Protocols\n\nAll are in `synbio.protocols`:\n\n- `Gibson` - Gibson assembly based on [NEB's E5510](https://www.neb.com/protocols/2012/12/11/gibson-assembly-protocol-e5510)\n- `GoldenGate` - Golden Gate assembly based on [NEB's E1601](https://www.neb.com/products/e1601-neb-golden-gate-assembly-mix#Product%20Information)\n\n## Example\n\nIn the example below, the user specifies a combinatorial library design. All SeqRecords are tested for circularization with other SeqRecords. New and valid plasmids are assembled.\n\nBehind the scenes, `synbio` is filtering all combinations of SeqRecords from the design that will circularize into valid plasmids (via [circuits in a graph](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0544-x/figures/1)). After running the `protocol`, users can export plate maps (`to_csv()`), composite plasmids (`to_fasta()`, `to_genbank()`), and assembly instructions (`to_txt()`, `to_picklists()`).\n\n```python\n\"\"\"Example of a Combinatorial Golden Gate assembly with human and robot output protocols.\"\"\"\n\nimport os\nfrom Bio.SeqIO import parse\nfrom synbio.designs import Combinatorial\nfrom synbio.protocols import GoldenGate\n\ndef read_all_records():\n    gg_dir = os.path.join(\".\", \"data\", \"goldengate\")\n    records = []\n    for file in os.listdir(gg_dir):\n        if file.endswith(\".gb\"):\n            records.extend(parse(os.path.join(gg_dir, file), \"genbank\"))\n    return records\n\n# create a combinatorial library design from all valid combinations\ndesign = Combinatorial(read_all_records())\n\n# create a protocol using Golden Gate as the sole composite step and run\nprotocol = GoldenGate(\n    name=\"Combinatorial Golden Gate\",\n    design=design,\n    include=[\"KanR\"],  # only keep circularized plasmids with a KanR SeqFeature\n    min_count=5,  # only keep circularized plasmids from >=5 SeqRecords\n)\nprotocol.to_fasta(\"plasmids.fasta\")  # export multi-FASTA\nprotocol.to_csv(\"plates.csv\")  # export plate layouts\nprotocol.to_txt(\"protocol.txt\")  # export human protocol\nprotocol.to_picklists(\"picklist\", platform=\"hamilton\")  # export a hamilton picklist\n```\n\nplasmids.fasta:\n\n```txt\n>J23100_AB+B0032m_BC+C0012m_CD+B0015_DE+DVK_AE\nGGAGTTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGCTACTAGAGTCACACAGGAAAG\nTACTAAATGATGGTGAATGTGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGT\n...\n```\n\nplates.csv:\n\n```csv\nSetup Wells with volumes (uL) shown:\nPlate:1,1,2,3,4,5,6,7,8,9,10,11,12\nA,B0015_DE(4),C0080_CD(18),R0010_AB(54),water(36)\nB,B0015_DE(160),DVK_AE(160),cre_CD(18),water(156)\n...\n```\n\nprotocol.txt:\n\n```txt\nCombinatorial GoldenGate:\n1. Setup PCR plate with (volumes) shown:\n\t1.1. Dilute plasmid DNA to 75 ng/\u00b5L in 'water'\n\t1.2. Create 'assembly-mix' from 1:1 T4 Ligase Buffer (10X) and NEB Golden Gate Assembly Mix\n...\n```\n\npicklist.gwl:\n\n```txt\nA;Plate:2;;;15;;2.0;;;\nD;Plate:3;;;80;;2.0;;;\nW;;;;;;;;;\n...\n```\n\n## Annotation\n\nIn addition to DNA assembly, `synbio` exposes a plasmid annotation function in `synbio.features`. An example is below, where a new SeqRecord is created with additional SeqFeatures from a curated database of common plasmid features.\n\n```python\nfrom Bio.SeqIO import parse\nfrom synbio.features import annotate\n\nrecord = next(parse(\"plasmid.fa\", \"fasta\"))\n\nrecord_with_features = annotate(record, identity=0.96)\n```\n\n## Alternatives\n\nThis is a non-exhaustive list. Contact me for a comparison of these libraries/platforms and `synbio`.\n\n- [Aquarium](https://www.aquarium.bio/) is an extensive library/application for LIMS, protocol definition/execution, and workflow design. A lab operating system.\n- [Autoprotocol](https://github.com/autoprotocol/autoprotocol-python) is a specification standard for experiments in the life sciences.\n- [BioBricks](https://github.com/liaupm/BioBlocks) is a general focus, web-based editor for describing experiments in Biology.\n- [Biocoder](https://jbioleng.biomedcentral.com/articles/10.1186/1754-1611-4-13) is a C++ library with extensive protocol step definition capabilities.\n- [Plateo](https://github.com/Edinburgh-Genome-Foundry/Plateo) is a python library for planning, running and checking laboratory experiments. Great for parsing and exporting plates and picklists form multiple formats.\n- [pydna](https://github.com/BjornFJohansson/pydna) is a python DNA assembly simulation library with a human-readable description of clone and assembly strategies.\n\n\n",
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