syssynbio/pyvipr

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

PyViPR

PyViPR is a Jupyter widget that generates network dynamic and static visualizations of PySB, Tellurium, BNGL, SBML, and Ecell4 models using Cytoscape.js. 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:

Installation

From conda

To use with Jupyter Notebooks:

> conda install pyvipr -c ortegas

To use with JupyterLab:

> conda install pyvipr -c ortegas
> jupyter labextension install @jupyter-widgets/jupyterlab-manager
> jupyter labextension install pyvipr

From PyPI

To use with Jupyter Notebooks:

> pip install pyvipr

To use with JupyterLab:

> pip install pyvipr
> jupyter labextension install @jupyter-widgets/jupyterlab-manager
> jupyter labextension install pyvipr

From git (requires npm)

$ 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 objects, Tellurium 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:

import pyvipr.network_viz as nviz

nviz.graphml_view('path_to_file/mygraph.graphml', layout_name='fcose')

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:

> pip install pysb

When using pip the installation of PySB 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:

> conda install pysb -c alubbock

PySB static example:

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')

PySB Dynamic Example:

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)

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:

> pip install tellurium

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)

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

Ortega O and Lopez C

License

MIT