{ "info": { "author": "Adam Hughes", "author_email": "hughesadam87@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "Natural Language :: English", "Programming Language :: Python :: 2", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Medical Science Apps.", "Topic :: Scientific/Engineering :: Physics", "Topic :: Scientific/Engineering :: Visualization" ], "description": ".. image:: https://github.com/hugadams/PAME/blob/master/screenshots/gui.png\n :height: 100px\n :width: 200 px\n :scale: 50 %\n\n==========================================\nPAME: Plasmonic Assay Modeling Environment\n==========================================\n\nGraphical Python application for simulating plasmonic biosensors, particularly fiberoptic biosensors with nanoparticles.\n\nCheck out the `PAME preprint`_.\n\n .. _PAME preprint : https://linktonowhere\n\nTutorials\n=========\n\nIPython Notebooks\n-----------------\nSome of these are traditional tutorials, others are examples of analyzed data from our lab.\n\n - `Simultation Parsing Tutorial `_\n - `Gold Nanoparticle Self-Assembly Compared to Experimental Data `_\n - Experimental datasets are preloaded in `scikit-spectra library `_\n - `Simulating a Refractometer `_\n - `Protein binding to gold nanoparticle film `_\n - `Gold and Silver Nanoparticle Combined Layer 1 `_\n - `Gold and Silver Nanoparticle Combined Layer 2 `_\n\nScreencasts\n-----------\nTutorials are cumulative (eg screencast 2 picks up where 1 ends).\n\nPAME's tutorials are a series of screencasts. \n - Screencast 1: `Introduction to PAME- Anti-reflective coatings `_\n - Screencast 2: `Introduction to Nanoparticles `_\n - Screencast 3: `Nanoparticle film with silica shell `_\n - Screencast 4: `Nanoparticle film with protein shell `_\n - Screencast 5: `Intro to Fiberoptic Dip Sesnosr `_\n - Screencast 6: `Multiplexed Dip Sensor with Gold and Silver Nanoparticles `_\n - Screencast 7: `Gold Nanoparticle Fiber Dip Sensor Simulation `_ \n - Screencast 8: `Dip Sensor with Organosilane Layer `_ \n\nInstallation\n============\n\nBinaries (ie .exe one-click use files) are `under development `_, but for now, PAME must be installed as a python library and launched through the command line. Anyone interested in helping to develop binaries, please contact. \n\nPAME makes heavy use of the `SciPy Stack (numpy, ipython etc...) `_, and so it has a lot of dependencies. Instead of using a bare python distribution, I'd recommend using a scientific python distribution that comes pre-loaded with the SciPy Stack (eg `canopy `_ or `conda `_) or want to install PAME into a clean environment (this is suggested), see the `Conda` installation directions. Otherwise, you can use `pip install` as usual.\n\n\nPyPI\n----\n\nSince PAME requires many dependencies, this may upgrade numpy, scipy, ipython and other core scipy libraries.\n\nTo install from pip\n\n pip install PAME\n\nIf this gives you an error `(maybe for this reason) `_, do the following.\n\nDownload the `PAME sourcecode `_ as a zipfile and unzip. `cd` into the unzipped directory\n\n cd /path/to/PAME\n\nInstall from source\n\n python setup.py install\n\nInstall the dependencies from pip\n\n pip install -r requirements.txt\n\nYou also may need to `install the QT backend ` if it's not already configured.\n\n\n\nConda\n-----\nI use `anaconda` because it has an excellent virtual environment manager. The advantage is here you can installed a clean working environment only for PAME without altering any of your other packages. For a tutorial on conda virtual environments, `check this out `_. To configure a PAME environment in anaconda, first install anaconda and then do the following:\n\n\n1. Create a clean virtual environment (mine is named PAMEvenv)\n\n conda create -n PAMEvenv anaconda\n\nThis installs several required scientific packages including `numpy`, `pandas` and `ipython`.\n\n2. Activate the environment\n\n source activate PAMEvenv\n\n3. Install pame (download pame source code and unzip, then navigate into directory)\n\n cd /path/to/PAMEdirectory\n python setup.py install\n\n4. Conda install/upgrade dependencies\n\n conda install traits traitsui mayavi chaco mpmath PIL\n\n5. To deactivate the virtual environment\n\n source deactivate\n\nDependencies\n------------\n\nThe full list of PAME's dependencies is in the `requirements.txt `_ file. You also may need to `install the QT backend `.\n\n\nSupport\n=======\n\nQuestions? Interested in developing? Message: pame_env@googlegroups.com, or contact me directly (hughesadam87@gmail.com, @hughesadam87)\n\n\n\nWeb Utilitiles\n==============\n\nPAME doesn't run in the browser. Check out these related tools that do!\n\n - `Mie-coefficients `_\n\n - `Film Metrics (Thin Film Solver) `_\n\n - `Mie with shells and other tools `_\n\nLicense\n=======\n\n3-Clause Revised BSD_\n\n .. _BSD : https://github.com/hugadams/PAME/blob/master/LICENSE.txt\n\n", "description_content_type": null, "docs_url": null, "download_url": "https://github.com/hugadams/fibersim", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "UNKNOWN", "keywords": null, "license": "LICENSE.txt", "maintainer": null, "maintainer_email": null, "name": "PAME", "package_url": "https://pypi.org/project/PAME/", "platform": "UNKNOWN", "project_url": "https://pypi.org/project/PAME/", "project_urls": { "Download": "https://github.com/hugadams/fibersim", "Homepage": "UNKNOWN" }, "release_url": "https://pypi.org/project/PAME/0.3.2/", "requires_dist": null, "requires_python": null, "summary": "GUI for modeling nanoparticles on optical fiber with mixing/shell-filling models", "version": "0.3.2" }, "last_serial": 1546041, "releases": { "0.1": [ { "comment_text": "", "digests": { "md5": "9f5061c89dabb39d634b48729a4da672", "sha256": "3ad3962dc4c38417aa1556a3ae95476c27aa70b91973f341d49d57f550e65ffc" }, "downloads": -1, "filename": "PAME-0.1.tar.gz", "has_sig": false, "md5_digest": "9f5061c89dabb39d634b48729a4da672", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 119062, "upload_time": "2015-05-12T21:44:48", "url": "https://files.pythonhosted.org/packages/7c/a4/e911c0100d8978cd0b4389c3692b9f031a872d10ac9c301a8a6220c46c28/PAME-0.1.tar.gz" } ], "0.3": [ { "comment_text": "", "digests": { "md5": "3e906ffc0373e1e4b5dcda053bc2b7a8", "sha256": "c257c3b186e9c41b1e053f0df635a90ad455e81f881d722f0068d718cb45cc49" }, "downloads": -1, "filename": "PAME-0.3.tar.gz", "has_sig": false, "md5_digest": "3e906ffc0373e1e4b5dcda053bc2b7a8", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 119053, "upload_time": "2015-05-12T21:45:54", "url": "https://files.pythonhosted.org/packages/06/cb/88635f096f3e23c246713dfab5fabc9320bb8920896853cebe8bb005d534/PAME-0.3.tar.gz" } ], "0.3.2": [ { "comment_text": "", "digests": { "md5": "9cb7d110117004923e7bcc7695ccb180", "sha256": "62694227accc623b2ca480955feb981c46aebe71166d135b7ef8a965195e8dc4" }, "downloads": -1, "filename": "PAME-0.3.2.tar.gz", "has_sig": false, "md5_digest": "9cb7d110117004923e7bcc7695ccb180", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 121622, "upload_time": "2015-05-13T19:59:41", "url": "https://files.pythonhosted.org/packages/42/0c/2666296accdb0bbd163d594d493bef2f6773e2f4ab8cbc80d5718087420c/PAME-0.3.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "9cb7d110117004923e7bcc7695ccb180", "sha256": "62694227accc623b2ca480955feb981c46aebe71166d135b7ef8a965195e8dc4" }, "downloads": -1, "filename": "PAME-0.3.2.tar.gz", "has_sig": false, "md5_digest": "9cb7d110117004923e7bcc7695ccb180", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 121622, "upload_time": "2015-05-13T19:59:41", "url": "https://files.pythonhosted.org/packages/42/0c/2666296accdb0bbd163d594d493bef2f6773e2f4ab8cbc80d5718087420c/PAME-0.3.2.tar.gz" } ] }