Foldy is a webtool for doing computational structural biology, centered around protein structure prediction with AlphaFold.
Foldy is a composable set of services which can be deployed lots of ways. We currently document three types of deployment: Development, Foldy-in-a-Box, and Helm. The development deployment is not fully featured - it cannot run jobs - but supports the frontend features and it can easily be run on a laptop for development purposes. Foldy-in-a-box is a quick deployment option - it can be run in under ten minutes - for creating a full featured Foldy instance on a Google Cloud machine. It could also be the starting point for a more bespoke deployment on a large local machine. Finally the Helm deployment is the horizontally scalable, cloud deployment, built on Kubernetes. The name comes from Helm Charts, which are a tool for specifying Kubernetes deployments. The Helm deployment is involved, but it is secure and can be scaled to hundreds of users and tens of thousands of folds.
You can find more information about employing the different deployment options in their respective deployment directories.
| Deployment Type | Features | Ease of setup | Setup |
|---|---|---|---|
| Development | No tools, just an interface | Extremely easy | Instructions |
| Foldy-in-a-Box | All tools can run | Easy | Instructions |
| Helm | Scalable to hundreds of users | Hard | Instructions |
See docs/interface.md.
See docs/architecture.md.
There is a rich ecosystem for running structural biology tools, and Foldy is not the right structural biology wrapper for everyone! Please review the Foldy paper for a comparison to other useful structural biology tool wrappers.
Foldy utilizes many separate libraries and packages including:
We thank all their contributors and maintainers!
Use of the third-party software, libraries or code Foldy may be governed by separate terms and conditions or license provisions. Your use of the third-party software, libraries or code is subject to any such terms and you should check that you can comply with any applicable restrictions or terms and conditions before use.
Foldy is distributed under a modified BSD license (see LICENSE).
Foldy Copyright (c) 2023, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and University of California, Berkeley. All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].
NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.