{
    "info": {
        "author": "Justin Vrana",
        "author_email": "justin.vrana@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
        ],
        "description": "# Terrarium\n\nThis piece of software automatically plans scientific experiments in Aquarium using historical\nplanning data and current laboratory inventory. Data can be pulled from specific researchers\nto emulate how that particular researcher would plan experiments.\n\n## Requirements\n\n* development version of **trident (v0.1.0)**\n* Python >= 3.6\n* Aquarium login credentials\n\n## Usage\n\nInstalling a specific version\n\n```python\npip install terrarium-capp==0.1.2\n```\n\nNew models can be built as in the following:\n\n```python\nfrom pydent import AqSession\nfrom terrarium import AutoPlannerModel\nproduction = AqSession(\"login\", \"pass\", \"url\")\n\n# pull last 300 experimental to build model\nmodel = AutoPlannerModel(production, depth=300)\nmodel.build()\nmodels.save('terrarium.pkl')\n```\n\nSaved models can be open later:\n\n```python\nmodel = AutoPlannerModel.load('terrarium.pkl')\n```\n\nWhat protocols the model uses can be adjusted using filters:\n\n```python\nignore_ots = production.OperationType.where({\"category\": [\"Control Blocks\", \"Library Cloning\"], \"deployed\": True})\nignore_ots += production.OperationType.where({\"name\": \"Yeast Mating\"})\nignore_ots += production.OperationType.where({\"name\": \"Yeast Auxotrophic Plate Mating\"})\nignore = [ot.id for ot in ignore_ots]\nmodel.add_model_filter(\"AllowableFieldType\", lambda m: m.field_type.parent_id in ignore)\n```\n\nSample composition:\n\n```python\nsample_composition = nx.DiGraph()\n\n# build a new yeast strain from a plasmid, which is comprised of several fragments\nedges = [\n     ('DTBA_backboneA_splitAMP', 'pyMOD-URA-URA3.A.1-pGPD-yeVenus-tCYC1'),\n     ('T1MC_NatMX-Cassette_MCT2 (JV)', 'pyMOD-URA-URA3.A.1-pGPD-yeVenus-tCYC1'),\n     ('BBUT_URA3.A.0_homology1_UTP1 (from genome)', 'pyMOD-URA-URA3.A.1-pGPD-yeVenus-tCYC1'),\n     ('DH5alpha', 'pyMOD-URA-URA3.A.1-pGPD-yeVenus-tCYC1'),\n     ('TP-IRES-EGFP-TS', 'pyMOD-URA-URA3.A.1-pGPD-yeVenus-tCYC1' ),\n     ('pyMOD-URA-URA3.A.1-pGPD-yeVenus-tCYC1', 'CEN.PK2 - MAT alpha | his-pGRR-W5-W8-RGR-W36'),\n]\n\nfor n1, n2 in edges:\n    s1 = browser.find_by_name(n1)\n    s2 = browser.find_by_name(n2)\n    sample_composition.add_node(s1.id, sample=s1)\n    sample_composition.add_node(s2.id, sample=s2)\n    sample_composition.add_edge(s1.id, s2.id)\n```\n\n```python\nignore_items = []  # optional to not include certain items in the search.\ndesired_object_type = production.ObjectType.find_by_name('Fragment Stock')\ncost, paths, graph = network.run(desired_object_type, ignore=ignore_items)\n```\n\n```python\n# make a new plan\ncanvas = Planner(production)\n\n# add protocols from optimized network to plan\nnetwork.plan(paths, graph, canvas)\n\n# submit to Aquarium\ncanvas.create()\n```\n\n**Example of Planning Yeast Construction**\n\n![plan_example](assets/images/plan_example0.png)\n\n**Probability Matrix of Connecting Aquarium Protocols**\n\nThe autoplanner uses this type of data, in concert with the `sample_composition` network,\nto build an optimal experiment.\n\n![all_connections](assets/images/all_op_types.png)\n\n**Top 50 Connections**\n\n![top_50_connections](assets/images/top_50_optypes.png)\n\n## Model Factory\n\n```python\nfactory = ModelFactory(session)\n\n# make a model from a single user\nmodel1 = factory.emulate('user1').build()\n\n# make a model from a group of users\nuser_group = ['user2', 'user3']\nmodel2 = factory.emulate(user_group).build()\n\n# make a model from the last 100 plans\nmodel3 = factory.new(100).build()\n\n# compose a weighted model\nmodel = model1 + model2 * 3\n```\n\n## Future Version\n\n* estimate convidence for certain inventory items or operations based on\npast success rate\n* better api for\n* using 'ghost' plans to build model\n* emulating specific users / user groups\n** faster execution (currently ~45-60 seconds)\n\n## License\n\nFeb. 4, 2019 - This software is not currently licensed. The author (Justin D. Vrana of University of Washington) does not grant permission to copy or modify code base.\n",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://www.github.com/jvrana/Terrarium",
        "keywords": "",
        "license": "",
        "maintainer": "Justin Vrana",
        "maintainer_email": "justin.vrana@gmail.com",
        "name": "terrarium-capp",
        "package_url": "https://pypi.org/project/terrarium-capp/",
        "platform": "",
        "project_url": "https://pypi.org/project/terrarium-capp/",
        "project_urls": {
            "Documentation": "https://www.github.com/jvrana/Terrarium",
            "Homepage": "https://www.github.com/jvrana/Terrarium",
            "Repository": "https://www.github.com/jvrana/Terrarium"
        },
        "release_url": "https://pypi.org/project/terrarium-capp/0.1.5/",
        "requires_dist": [
            "dill (>=0.2.9,<0.3.0)",
            "pandas (>=0.24.2,<0.25.0)",
            "webcolors (>=1.9,<2.0)",
            "colorama (>=0.4.1,<0.5.0)",
            "arrow (>=0.14.2,<0.15.0)",
            "pydent (==0.1.5a1)",
            "fire (==0.1.3)",
            "validator.py (>=1.3,<2.0)"
        ],
        "requires_python": ">=3.6,<4.0",
        "summary": "Adaptive Computer Aided Process Planner",
        "version": "0.1.5"
    },
    "last_serial": 5594649,
    "releases": {
        "0.0.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "0037913aee56899f0afb4916bf8e8e6c",
                    "sha256": "25d00446b50a6426585b777677395512dacc0491e2767e3373ee56d8e1f40abc"
                },
                "downloads": -1,
                "filename": "terrarium_capp-0.0.0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "0037913aee56899f0afb4916bf8e8e6c",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.7,<4.0",
                "size": 34888,
                "upload_time": "2019-06-20T21:09:43",
                "url": "https://files.pythonhosted.org/packages/71/9a/400e444f1b86ce91c1fb3661ab06b21bfdf87a9b97db87abef67cee2a662/terrarium_capp-0.0.0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "7bbc644ecc11d9161ab9503d8b77a4e4",
                    "sha256": "50538ee94dc5e594be46ff9b563bb41bed310f58ea7e30ebcfbf65d7db8939cd"
                },
                "downloads": -1,
                "filename": "terrarium-capp-0.0.0.tar.gz",
                "has_sig": false,
                "md5_digest": "7bbc644ecc11d9161ab9503d8b77a4e4",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.7,<4.0",
                "size": 27355,
                "upload_time": "2019-06-20T21:09:41",
                "url": "https://files.pythonhosted.org/packages/2f/f3/f1e5f315ba061458396d2a608183138ef84d3b5109d98248f23838f301d9/terrarium-capp-0.0.0.tar.gz"
            }
        ],
        "0.0.1a0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "e00c5b3b574b464c0ab802010c6d2514",
                    "sha256": "9ef8e82aa964f64071a06fea58d7dd275cac61b4c3b651873f66b9ae6e37de23"
                },
                "downloads": -1,
                "filename": "terrarium_capp-0.0.1a0-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "e00c5b3b574b464c0ab802010c6d2514",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.7,<4.0",
                "size": 27183,
                "upload_time": "2019-06-22T03:39:36",
                "url": "https://files.pythonhosted.org/packages/a4/ad/2f382537cfc4546feab5cbbc818f2cdac43ea6690c5925ec146af4fef1b5/terrarium_capp-0.0.1a0-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "442da46f4d4d26fe574aa33778b354a5",
                    "sha256": "b71fe6b6d282d2c017c8bef8fc640f62c4ba173fbe979c36e4d9e4ca1db815bb"
                },
                "downloads": -1,
                "filename": "terrarium-capp-0.0.1a0.tar.gz",
                "has_sig": false,
                "md5_digest": "442da46f4d4d26fe574aa33778b354a5",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.7,<4.0",
                "size": 20166,
                "upload_time": "2019-06-22T03:39:34",
                "url": "https://files.pythonhosted.org/packages/99/6b/43dd9b33a2494019a8cd482cccc22ac3639e13b436408943109a27dc924e/terrarium-capp-0.0.1a0.tar.gz"
            }
        ],
        "0.1.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "d022c76e6fc597fdf9cdf61dc9378f25",
                    "sha256": "a664916bdd7d46fbf4e33a4e4e47b5ff460e099bfa114f6d7199105314f9b699"
                },
                "downloads": -1,
                "filename": "terrarium_capp-0.1.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "d022c76e6fc597fdf9cdf61dc9378f25",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6,<4.0",
                "size": 25521,
                "upload_time": "2019-07-26T16:01:03",
                "url": "https://files.pythonhosted.org/packages/98/b7/edf4a4f62cb9f701f770fdc6453f5259072084bad325113f8e7badeee908/terrarium_capp-0.1.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "5852b8799c1e934895a6cd7ae55d3894",
                    "sha256": "bf024763e24cc28523e724f086c5f14583d1606236f7cf262aa35b56e19f0dad"
                },
                "downloads": -1,
                "filename": "terrarium-capp-0.1.2.tar.gz",
                "has_sig": false,
                "md5_digest": "5852b8799c1e934895a6cd7ae55d3894",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6,<4.0",
                "size": 24461,
                "upload_time": "2019-07-26T16:01:01",
                "url": "https://files.pythonhosted.org/packages/ac/21/056921c83a58503f09cc4c9426abcb5120392d5bd4f2e795d52e030507da/terrarium-capp-0.1.2.tar.gz"
            }
        ],
        "0.1.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "8d9f49f11e2ef3d7e211f3e692823e1e",
                    "sha256": "ef42bb50266dd0a30f0fe9cfdea4593e6e9f04d3b37dd1705632d957887f4b27"
                },
                "downloads": -1,
                "filename": "terrarium_capp-0.1.3-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "8d9f49f11e2ef3d7e211f3e692823e1e",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6,<4.0",
                "size": 28340,
                "upload_time": "2019-07-26T19:59:52",
                "url": "https://files.pythonhosted.org/packages/d9/e9/75ae01ccb26d278f027a57b8347a15dbd531ee0d346392f3269d7587519d/terrarium_capp-0.1.3-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "e622d80191edc729e0d3b2849bd2e2f5",
                    "sha256": "6c992607f2c24a2d5aa9a04f7117535850a37e9338762f585339ccbf5a698306"
                },
                "downloads": -1,
                "filename": "terrarium-capp-0.1.3.tar.gz",
                "has_sig": false,
                "md5_digest": "e622d80191edc729e0d3b2849bd2e2f5",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6,<4.0",
                "size": 26542,
                "upload_time": "2019-07-26T19:59:50",
                "url": "https://files.pythonhosted.org/packages/0e/7a/8d1f09120785911ff1a6c2de733ee8bf165f5036b93bb5e3896742bbf1a7/terrarium-capp-0.1.3.tar.gz"
            }
        ],
        "0.1.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b96ed17db31cd425ade8c1bc71e1a620",
                    "sha256": "fbb397dd29c5359dd971a29ec28f8720fb9bcbe6a4f8463aa642a36405136f25"
                },
                "downloads": -1,
                "filename": "terrarium_capp-0.1.4-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "b96ed17db31cd425ade8c1bc71e1a620",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6,<4.0",
                "size": 30218,
                "upload_time": "2019-07-28T00:40:13",
                "url": "https://files.pythonhosted.org/packages/f8/6a/7287069ab2f99df7e7e5d04f2eea7f789d3e75629e3e62b507106cbeeda3/terrarium_capp-0.1.4-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "6ada19ea932008c49c0be3d956a28c79",
                    "sha256": "f5b44fc953cb736d90ef9f77c77743fadd7b2a09e5b6671d6feb4c72edf30dff"
                },
                "downloads": -1,
                "filename": "terrarium-capp-0.1.4.tar.gz",
                "has_sig": false,
                "md5_digest": "6ada19ea932008c49c0be3d956a28c79",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6,<4.0",
                "size": 28179,
                "upload_time": "2019-07-28T00:40:11",
                "url": "https://files.pythonhosted.org/packages/31/e1/6373af5b90bb63c0ff20625a9459368d741223b6ce07d3966415d20e4748/terrarium-capp-0.1.4.tar.gz"
            }
        ],
        "0.1.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "51724e835becbeaa340086839d8c845f",
                    "sha256": "0af1be9767d018acd352ef2a38141e1b636d07b8e493b3bea87a840e2293089c"
                },
                "downloads": -1,
                "filename": "terrarium_capp-0.1.5-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "51724e835becbeaa340086839d8c845f",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": ">=3.6,<4.0",
                "size": 30611,
                "upload_time": "2019-07-28T03:23:46",
                "url": "https://files.pythonhosted.org/packages/30/fa/490eb2e51e13d0b97186154132889cb1634589c884da2063a77740fada80/terrarium_capp-0.1.5-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "ddc9fcf2b0e1525bcfa2b2d334638ded",
                    "sha256": "fa1b9e1cf3534ab446946efe8539bd9cb6f9ba7cc7561a368b619a4ebe2957c7"
                },
                "downloads": -1,
                "filename": "terrarium-capp-0.1.5.tar.gz",
                "has_sig": false,
                "md5_digest": "ddc9fcf2b0e1525bcfa2b2d334638ded",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6,<4.0",
                "size": 28465,
                "upload_time": "2019-07-28T03:23:45",
                "url": "https://files.pythonhosted.org/packages/06/61/b874e6921df2ff27c86c01ffb54a1167418507d5b0d46d92b0869ba942ed/terrarium-capp-0.1.5.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "51724e835becbeaa340086839d8c845f",
                "sha256": "0af1be9767d018acd352ef2a38141e1b636d07b8e493b3bea87a840e2293089c"
            },
            "downloads": -1,
            "filename": "terrarium_capp-0.1.5-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "51724e835becbeaa340086839d8c845f",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=3.6,<4.0",
            "size": 30611,
            "upload_time": "2019-07-28T03:23:46",
            "url": "https://files.pythonhosted.org/packages/30/fa/490eb2e51e13d0b97186154132889cb1634589c884da2063a77740fada80/terrarium_capp-0.1.5-py3-none-any.whl"
        },
        {
            "comment_text": "",
            "digests": {
                "md5": "ddc9fcf2b0e1525bcfa2b2d334638ded",
                "sha256": "fa1b9e1cf3534ab446946efe8539bd9cb6f9ba7cc7561a368b619a4ebe2957c7"
            },
            "downloads": -1,
            "filename": "terrarium-capp-0.1.5.tar.gz",
            "has_sig": false,
            "md5_digest": "ddc9fcf2b0e1525bcfa2b2d334638ded",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.6,<4.0",
            "size": 28465,
            "upload_time": "2019-07-28T03:23:45",
            "url": "https://files.pythonhosted.org/packages/06/61/b874e6921df2ff27c86c01ffb54a1167418507d5b0d46d92b0869ba942ed/terrarium-capp-0.1.5.tar.gz"
        }
    ]
}