Metadata-Version: 2.1
Name: pyvipr
Version: 1.0.4
Summary: Widget to visualize PySB models in Jupyter Notebook
Home-page: https://github.com/LoLab-VU/pyvipr
Author: Oscar Ortega
Author-email: oscar.ortega@vanderbilt.edu
License: UNKNOWN
Description: # <img alt="pyViPR" src="https://github.com/LoLab-VU/pyvipr/blob/master/pyvipr_logo.png" height="100">
        
        
        [![Documentation Status](https://readthedocs.org/projects/pyvipr/badge/?version=latest)](https://pyvipr.readthedocs.io/en/latest/?badge=latest)
        ![](https://github.com/Lolab-VU/pyvipr/workflows/build/badge.svg)
        [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LoLab-VU/pyvipr/master?filepath=binder) 
        
        [![Gitter](https://badges.gitter.im/LoLab-VU/pyvipr.svg)](https://gitter.im/LoLab-VU/pyvipr?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
        
        # PyViPR
        PyViPR is a Jupyter widget that generates network dynamic and static visualizations of [PySB](http://pysb.org/), [Tellurium](http://tellurium.analogmachine.org/),
        [BNGL](https://www.csb.pitt.edu/Faculty/Faeder/?page_id=409), [SBML](http://sbml.org/Main_Page), and [Ecell4](https://github.com/ecell/ecell4) 
         models using [Cytoscape.js](http://js.cytoscape.org/). Additionally, it can be used to visualize networks encoded in the graphml, 
         sif, sbgn xml, cytoscape json, gexf, gml and yaml formats.
         
         ## Trying it online
        
        To try out PyViPR interactively in your web browser, just click on the binder
        link below:
        
        [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LoLab-VU/pyvipr/master?filepath=binder)
        
        ## Installation
        
        ### From conda
        
        #### To use with Jupyter Notebooks:
        
        ```bash
        > conda install pyvipr -c ortegas
        ```
        
        #### To use with JupyterLab:
        
        ```bash
        > conda install pyvipr -c ortegas
        > jupyter labextension install @jupyter-widgets/jupyterlab-manager
        > jupyter labextension install pyvipr
        ```
        
        ### From PyPI
        
        #### To use with Jupyter Notebooks:
        
        ```bash
        > pip install pyvipr
        ```
        
        #### To use with JupyterLab:
        
        ```bash
        > pip install pyvipr
        > jupyter labextension install @jupyter-widgets/jupyterlab-manager
        > jupyter labextension install pyvipr
        ```
        
        ### From git (requires npm)
        ```bash
        $ git clone https://github.com/LoLab-VU/pyvipr.git
        $ cd pyvipr
        $ pip install .
        ```
        
        ## How to use the widget
        After installing the widget, it can be used by importing it in the Jupyter notebook. The widget is simple to use with PySB 
        models, [SimulationResult](https://pysb.readthedocs.io/en/stable/modules/simulator.html#pysb.simulator.SimulationResult) 
        objects, [Tellurium](http://tellurium.analogmachine.org/) models and BNGL & SBML files. 
        
        PyViPR has three main interfaces: Graph formats, PySB, and a Tellurium.
        
        ### Graph formats interface
        This interface leverages NetworkX and Cytoscape.js to generate network visualizations of graphs encoded in different 
        file formats.
        
        #### Graphml example:
        ```python
        import pyvipr.network_viz as nviz
        
        nviz.graphml_view('path_to_file/mygraph.graphml', layout_name='fcose')
        ```
        ![graphml_view](graphml.png)
        
        ### PySB interface
        
        PySB is needed to visualize PySB models and it is needed if you want to use the pyvipr.pysb_viz module:
        
        Installing PySB from pip:
        ```bash
        > pip install pysb
        ```
        
        When using pip the [installation of PySB](https://pysb.readthedocs.io/en/stable/installation.html#option-1-install-pysb-natively-on-your-computer)
        requires to manually install BioNetGen into the default path for your platform 
        (/usr/local/share/BioNetGen on Mac and Linux, c:\Program Files\BioNetGen on Windows), 
        or set the BNGPATH environment variable to the BioNetGen path on your machine.
        
        Installing PySB from conda:
        ```bash
        > conda install pysb -c alubbock
        ```
        
        #### PySB static example:
        ```python
        import pyvipr.pysb_viz as pviz
        from pyvipr.examples_models.lopez_embedded import model
        
        pviz.sp_comm_louvain_view(model, random_state=1, layout_name='klay')
        ```
        ![species_view_pysb](earm_communities.png)
        
        #### PySB Dynamic Example:
        ```python
        import pyvipr.pysb_viz as pviz
        from pyvipr.examples_models.mm_two_paths_model import model
        from pysb.simulator import ScipyOdeSimulator
        import numpy as np
        
        tspan = np.linspace(0, 1000, 100)
        sim = ScipyOdeSimulator(model, tspan).run()
        pviz.sp_dyn_view(sim)
        ```
        
        ![enzymatic_reaction](pyvipr_dynamic.gif)
        
        
        ### Tellurium interface
        
        Tellurium is needed to visualize Tellurium models and it is needed if you want to use the pyvipr.tellurium_viz module:
        
        Installing Tellurium from pip:
        ```bash
        > pip install tellurium
        ```
        
        ```python
        import tellurium as te
        import pyvipr.tellurium_viz as tviz
        
        model = te.loadSBMLModel("https://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000001")
        
        tviz.sp_view(model)
        ```
        ![species_view_tellurium](tellurium_example.png)
        
        ## Documentation
        
        To get started with using `PyViPR`, check out the full documentation
        
        https://pyvipr.readthedocs.io/
        
        ## Citation
        To cite PyViPR, please cite the iScience paper:
        
        [Interactive Multiresolution Visualization of Cellular Network Processes](https://www.cell.com/iscience/fulltext/S2589-0042(19)30493-6)
        
        Ortega O and Lopez C
        
        
        
        ## License
        
        [MIT](https://opensource.org/licenses/MIT)
        
Keywords: ipython,jupyter,widgets,pysb,systems biology,cytoscape,graph,visualization
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: IPython
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Multimedia :: Graphics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
