BioBuilder is a web-based biochemical kinetics editor and simulator! 🧪✨ Built specifically to run simulations quickly and easily.
Biochemical kinetics allows you to predict the future in biology. 🔮 It allows you to know exactly which chemicals and how much will be produced, given some set of initial conditions.
We believe that biochemists shouldn't need to be computer scientists to benefit from this technique. BioBuilder bridges the gap between biologists and computers, and allows you to start running simulations NOW! To understand what our project is trying to achieve, see VISION.md.
There are two repos: The frontend (this repo) to interface with scientists, and the backend (HERE) to run our simulations.
Go to BioBuilder.app to start using the software now!
Want to see a new feature on the site? Is there a small tweak that would make the site less frustrating? The best person to make the change is YOU! You don't need to be an expert computer scientist to make a meaningful impact. Whether you're a seasoned open-source veteran, or this is your first contribution, we always welcome any help we can get, and we've created a guide to help make it easy for you to get started.
See CONTRIBUTING.md for a guide on how to get started making your first contributions. For a general view of what we're trying to achieve, see VISION.md. For actionable steps on what needs to be done, view ROADMAP.md or at our pull requests!
Go to https://biobuilder.app to start using the software now!
The hardest part of biochemical kinetics isn't performing the simulation: it's finding the right parameters. While we plan on adding integrations with existing databases, for now, you will need to add your own biochemical kinetic parameters. The wikipedia page for Metabolic Network Modelling is a helpful guide if you're just getting started with biochemical kinetics.
Your model needs 3 outside components:
- Reaction Diagrams
- Rates & Parameters
- Initial conditions
Reaction Diagrams can be found from a number of free online databases, including:
Rates & Parameters are evaluated from real experiments scientists have performed. One of the most well-known databases to gather these kinetic rate parameters is Sabio-RK. Another helpful resource is BioNumbers.
Initial Conditions depend on YOUR experiment! If you plan on going into the lab to do some work, use plausible information about your system (BioNumbers is helpful for this). If you're doing some theoretical work, use numbers that closely resemble your system wherever possible, or run multiple simulations with different values to find the ones that are most realistic!
After you know your diagrams, parameters, and initial conditions, it's time to start putting them in the simulation! Here's a quick guide on how:
- Create the reaction diagram (add nodes, draw edges to represent reactions)
- Edit reaction parameters (click each edge to open the reaction drawer. Each edge needs to have a rate law.)
- Edit initial values (in the reaction editor, you can set the initial values of each reactant!)
Now you've set up your simulation, it's time to run it! Click "SIMULATE" in the top right corner, and voila! You just ran the simulation!
We LOVE feedback, and we're always looking for ways to improve the platform! Feel free to shoot me an email at mark@biobuilder.app with any suggestions or feedback, and I'd be happy to respond.
You can also fill out THIS feedback form!
For exhaustive instructions on how to run the code, see CONTRIBUTING.md. Here's a quick refresher:
Locally, run npm run dev
To deploy, run
npm run build
npm run deploy