Netflux is a user-friendly software for developing dynamic computational models of biological networks. Models are created in Excel format and then simulated using the Netflux graphical interface. No computer programming is required. Netflux is written in MATLAB, but binary versions are available for Windows and MacOS for those that do not have MATLAB installed.
Netflux can export network structures and simulation results for visualization in Cytoscape or other software packages. Netflux can also export MATLAB or Python code for more advanced network simulations. Netflux can import network structures based on SIF or SBML-QUAL formats.
Netflux simulates networks using a modeling approach called logic-based differential equations. These methods are described in detail here: Kraeutler MJ, Soltis AR, Saucerman JJ. Modeling cardiac β-adrenergic signaling with normalized-Hill differential equations: comparison with a biochemical model. BMC Syst Biol. 2010 Nov 18;4:157. https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-157 (open access)
Netflux has been used to develop large-scale computational models of signaling networks for cardiomyocyte hypertrophy, fibroblasts, and mechano-signaling. Netflux has also been used in educational settings from high school (simulations of social networks) through graduate school levels.
Click on the button labeled "Clone or download" and then "Download ZIP". This ZIP file contains the MATLAB version of Netflux as well as binary versions for Windows or MacOS users that do not have MATLAB installed.
Users with MATLAB version 2009b or higher Extract the “Netflux” folder from within the ZIP file and move it to your desired location.
Windows users that do not have MATLAB Open the “Netflux Compiled” folder and run “Netflux Installer Windows.exe”. This installer will automatically download and install the MATLAB Compiler Runtime, which will take some time as that file is about 800 MB. Netflux will be installed to the C:\Program Files\Netflux folder. Note installation may require administrator privileges on your computer. An exception to Windows firewall may also be needed, but we are checking on this.
MacOS users that do not have MATLAB Open the “Netflux Compiled” folder, extract “Netflux_Installer_MacOS”, and install “Netflux_Installer_MacOS.app”. This installer will automatically download and install the MATLAB Compiler Runtime, which will take some time as that file is about 800 MB. Netflux will be installed to the Applications\Netflux folder.
"Netflux Documentation.docx" is in the Netflux directory.
Video tutorials are available on Youtube at: https://www.youtube.com/watch?v=tU2gU8d5hvQ&list=PLTbDE7ZQfKy-ijd5ZrCQJ7eB-NSCQKIBi