Open-CoNtRol, an open source web Chemical Reaction Network visualizer.

Can use a simple way to input chemical reaction networks

Or use antimony to input them copy-paste style easier (or the simpler format from the placeholer in the image below: yes i know it's not centered leave me alone

You first get a numerical analysis of your system

From which you can graph your results in different shenanigans and schemes

The default basic one is the Time series representation, giving you a page from which you can select your initial values for species and reaction rates

and from there outcomes this beauty

A network diagram (DSR Graph) is similar, except you don't have to fill out the complaint form beforehand

The phase portrait is neat in that you can select either 2 or 3 species to represent and it plots a 2D and respectively 3D phase portrait

Installation

Please note pygraphviz has to be installed beforehad. So if you're not on unix (for some reason) meaning the bellow command doesn't work, please consult the installation guides here.

To run the flask web app:

Linux

git clone https://github.com/viktorashi/Open-CoNtRol.git
cd Open-CoNtRol
sudo apt-get install graphviz graphviz-dev
pip install pygraphviz
pip install -r requirements.txt

Then to run the server

chmod +x ./set_vars.sh 
chmod +x ./run_script.sh
./set_vars.sh 
./run_script.sh

If it doesn't find you a proper port try:

python -m flask run

MacOS / OS X

Make sure you have homebrew

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

git clone https://github.com/viktorashi/Open-CoNtRol.git
cd Open-CoNtRol
brew install graphviz
pip install pygraphviz
pip install -r requirements.txt

Note: if the pygraphviz installation fails, comment out the entry for pygraphviz in requirements.txt (example)

...
#pygraphviz==1.13
...

and run the following command:

pip install --config-settings="--global-option=build_ext" \
            --config-settings="--global-option=-I$(brew --prefix graphviz)/include/" \
            --config-settings="--global-option=-L$(brew --prefix graphviz)/lib/" \
            pygraphviz

Then to run the server

chmod +x ./set_vars.sh 
chmod +x ./run_script.sh
./set_vars.sh 
./run_script.sh

If it doesn't find you a proper port try:

python -m flask run

On Windows

i'm not really sure tbh, i just use WSL

It will inherit the app name and options from .flaskenv

Or simply, if you just want to run it without contributing, create a virtualenv however way you want ( virtualenvwrapper recommended by yours truly) and install it there as a package with:

pip install git+https://github.com/viktorashi/Open-CoNtRol.git
flask --app open_control --debug run

In the above case you can't really configure the host ip adress that the server will be running on like in the first example. In order to do that you'd need to download at least the script "run_script.sh" from the repo then give it execute permissions and run with

chmod +x ./run_script.sh
./run_script.sh