{ "info": { "author": "Rodrigo Santib\u00e1\u00f1ez", "author_email": "glucksfall@users.noreply.github.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Operating System :: Unix", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering" ], "description": "# pleione\n\nPleione is a python3 package that implement methods that are common to\ntraditional modeling frameworks, and apply them to analyze Rule-Based Models.\n\nHere you'll find the necessary documentation to install and use the methods in\nPleione. At the moment, Pleione parameterizes Rule-Based Models written either\nin *BioNetGen* (https://www.csb.pitt.edu/Faculty/Faeder/?page_id=409) or *kappa*\nlanguage (https://www.kappalanguage.org/). Models are simulated with BNG2\n(https://github.com/RuleWorld/bionetgen, PMID 27402907), NFsim\n(https://github.com/RuleWorld/nfsim, PMID 26556387), KaSim\n(https://github.com/Kappa-Dev/KaSim, PMID 29950016), or PISKaS\n(https://github.com/DLab/PISKaS, PMID 29175206). Please contact us or write an\nissue to include your favorite stochastic simulator to Pleione\n(https://github.com/glucksfall/pleione/issues).\n\nPleione implements a Genetic Algorithm with elitism, on the contrary to\nBioNetFit (https://github.com/RuleWorld/BioNetFit, PMID 26556387) that\nimplements a parents selection within a distribution probability that is inverse\nto the rank. Nonetheless, Pleione's methods to parameterize Rule-Based Models\ninclude both, a uniform or inverse to the rank probability to select models from\nwithin an elite or all models.\n\nExamples to run Pleione are located in https://github.com/glucksfall/pleione/tree/master/example\nand in the python distribution wheel. The table with the U-test critical values is\nlocated at the same folder and in subfolders.\n\nThe plan to add methods into Pleiades (https://github.com/glucksfall/pleiades)\nincludes a sensitivity analysis and a parameterization employing a Particle\nSwarm Optimization protocol. You could write us if you wish to add methods into\npleione or aid in the development of them.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/glucksfall/pleione", "keywords": "systems biology,stochastic modeling,parameter estimation", "license": "GPLv3+", "maintainer": "", "maintainer_email": "", "name": "pleione", "package_url": "https://pypi.org/project/pleione/", "platform": "", "project_url": "https://pypi.org/project/pleione/", "project_urls": { "Bug Reports": "https://github.com/glucksfall/pleione/issues", "Homepage": "https://github.com/glucksfall/pleione", "Manual": "https://pleione.readthedocs.io", "Source": "https://github.com/glucksfall/pleione" }, "release_url": "https://pypi.org/project/pleione/1.5.2/", "requires_dist": [ "numpy", "pandas", "statsmodels" ], "requires_python": "~=3.0", "summary": "Pleione: statistical and multi-objective 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