NanoFrame nanoframe.org is a web based tool for designing and synthesizing 3D wireframe polyhedra. NanoFrame's synthesizer generates polyhedra from single-origami scaffold of any length, which then can be used as building block for designing larger multi-origami structure in NanoFrame's playground. Save your work to the cloud by creating account at nanoframe.org.
Consider citing the associated paper if you find the project useful.
NanoFrame: A web-based DNA wireframe design tool for 3D structures.
Samson Petrosyan, Grigory Tikhomirov
paper | arXiv
- Control Flow
- Home
- Synthesizer
- Playground
- Guides
- Suggestions and Reporting Issues
- Working Locally
- Contributing
The application is broken down into three parts, each can be navigated to with the ribbon at the top of the page.
The entry point of nanoframe.org is the Home tab, where users are taken to a sign in/up page or their profile homepage (depending on cookie sessions); see Home for more info. Any user -- whether signed-in or not -- can synthesize polyhedra, the difference lies in saving the work to the cloud. Generated work can be saved as both private and public, further, once users login they can discover what other creators have been synthesizing with NanoFrame.
The NanoBot tab is where all the magic happens. Users can select one of the predefined shapes, or create their own (upcoming feature). After selecting a shape, users can interact with the shape dynamically by adjusting its attributes.
NanoFrame relies on several API which were developed on par with the project. These are completely free, but to make API calls clients need to register and obtain an API key. In playground tab, user would work with an active canvas and build shapes by dragging and dropping elements on it. Both a graphical user interface (GUI) and a scriptable interface exist for ease of use. As in synthesizer tab, uers will need to be registered to save work from playground, otherwise the service is open to all users.
The guides folder has documentation on all aspects of nanoframe.org, including video tutorials, file format description, methods and materials, and API docs.
All NanoFrame's features are available to any user, but only authenticated users can save their work. Authentication can be done either through signing up with NanoFrame and claiming a username, or through Google/Facebook authentication. Other third-party authentications will be added on demand. In addition, users can also view work of peers that are made public. This will be a feed type of page where users can view, share, and comment on designs generated by others. We also provide the option of saving work in private mode (that is - not visible to anyone but creator).
In Nanobot tab the user gets to choose a shape from given selection or make their own through custom shape to syntheszie a DNA object. We provide interactive display such that the user can have an approximate idea of what the final object will look like. In following pages, more detail is added until the most granual oxdna or pdb version is generated. Currently only cuboids are supported, but there is active work in regards to other general shapes. Nanobot will give a warning if the selected shape has greater than 200 leftover base pairs and will propt the user to either continue with the current design or check out dimension generator page.
Once you have selected the shape, filled out the parameters, and clicked synthesize, after a brief wait your structure will appear.
When your structure appears, you can change its orientation, zoom in and out, view the staple strands, and view the open form.
One of the features of NanoFrame is the level fine grain detail. After selecting and editing DNA routing, atomic level visualization is made available through oxView which uses the oxview file format. To view the atomic level visualization, navigate to your synthesized object, select the download files option then select the oxDNA files. Extract the files. Navigate to oxView click the black file button (third from left on top) add the 2 extracted files, and view your structure!
Please refer to our Guides
To suggestion or reporting issues in NanoFrame, simply go to Issues and click on New Issue. Provide a title and description. Please write as much detail in description as possible, including the browser and it's version. While NanoFrame is architecture independent, often broswers lag behind in JavaScript and WebGL updates, so simply changing the broswer may resolve the issue. Regardless, still open an issue so the authors are aware of possible bugs.
Working locally can speed up the process of certain queries. To get started clone this repo to your workspace. You will need to have ruby insatlled for running the next commands. chruby, rvm, and rbenv are all great ruby package managers. You will need to have ruby 3.3.3 to run the app locally.
You need to have cbc installed for ruby-cbc to work. On a mac, you can execute brew install cbc . On Debian and Ubuntu, use apt-get install coinor-libcbc-dev . On Archlinux, use pacman -S coin-or-cbc .
Once you have installed ruby and cbc successfully, run bundle install in NanoFrame's root directory to install all project dependencies (this might take some time). Then, run rails s to boot up the server. Now, navigate to http://localhost:3000 in your broswer and you should see NanoFrame get activated. Note, that none of you work on production mode (i.e. nanoframe.org) will be avaiable, however you can download the files from the website and upload locally through your homepage.
If you would like to contribute to this project, please fork this repository first and make a pull request with the branch name of the feature you would like to add. Be sure to check out the contributions page for further details. We made this project open-source so builders like you can help us provide best quality software to scientists interested in work with DNA nanotechnology. Thank YOU for taking the time to read this far!