NetworkPainter

Try It Here

NetworkPainter is a web-based program for visually analyzing data stored in Cytobank. NetworkPainter enables researchers to draw signaling network diagrams and animate them with time-lapsed experimental data such as flow and mass cytometry. NetworkPainter can be used to analyze any data contained within Cytobank.

Features

Hypothesis-driven data analysis — Describe prior knowledge about biological systems as network diagrams.
Animate experimental time courses — Animate signaling nodes with high-dimensional flow- and mass-cytometry data.
Cytobank integration — Easily visualize experiments stored in Cytobank.
Create stunning graphics — Create publication quality graphics in gif, jpg, png, and svg formats.
Computational simulation — Generate MATLAB code for Boolean network simulations.
Collaborate with colleagues — Manage user access to diagrams. Diagrams are stored on our server and accessible from any computer.
Open access — Share diagrams and animations with the world by making them public.
Export to common exchange formats — BioPax, CellML, and SBML.


Requirements

  • Cytobank account **
  • Web browser
  • Adobe Flash v10.0 or higher

** A free Cytobank account is required to analyze data stored in Cytobank and save signaling diagrams. In addition, researchers can use the free, stand-alone version of NetworkPainter at covert.stanford.edu/networkpainter without any registration or login.


Getting Started

Follow these steps to analyze your first data set:

  1. Login to Cytobank (Note: NetworkPainter is currently only available at http://beta.cytobank.org)
  2. From the experiments inbox, select an experiment, or create a new experiment and upload data
  3. From the experiment's page, select "View Signaling Network Diagrams" in the left-hand side "actions" menu
  4. Click the "Create a New Diagram" button in the left-hand side menu
  5. Draw an intracellular network
  6. Link network nodes to observed channels
  7. Play animation to paint nodes with observed data
  8. Display comparison heatmaps to explore data across experimental conditions, cell types, and individuals.
  9. Export network for use in papers and presentations


Demo experiments

A fully functional demonstration visualization is available. Please login, and select the experiments titled "NetworkPainter Demo -- Human PBMC mass cytometry {LPS, INF-α, ...} timecourse (Bodenmiller et al. 2012)" from the experiments inbox. This demonstration features a mass cytometry timecourse of immune signaling in human peripheral blood mononuclear cells (hPBMCs) reported by Bodenmiller et al., 2012.


Tutorials & Help

Three tutorials videos and extensive documentation are available.

Need more help? Please contact us at info@cytobank.org


About NetworkPainter

NetworkPainter was developed in collaboration with researchers in the Covert Lab at Stanford University

NetworkPainter was supported by an NIH Director's Pioneer Award (5DP1LM01150-05), a NIH K99/R00 grant (CA125994-01A1), and a Hellman Faculty Scholarship to MC; NDSEG, NSF, and Stanford Graduate Fellowships to JK; and NSF and Stanford Graduate Fellowships to HG.




The NetworkPainter source code is available under the MIT license at github.com

A stand-alone version of NetworkPainter is also available at covert.stanford.edu/networkpainter. This version is capable of analyzing any biological data but cannot directly access data stored in Cytobank.