Uploading structures
Any researcher who would like to deposit a structure into Nanobase is welcome to create an account. To begin, click the "Sign in" button in the upper right corner and select "Create an account". Once you fill in the form and verify your email, you are ready to upload a structure.
Uploading process
Begin by clicking the "Upload Structure" link in the navbar. This will take you to a form where you enter structure information. Make sure to include applications and keywords to make the structure easily searchable by users in the future. You can also enter publication information, including any patents and licensing information if applicable. Finally, on the file upload page you can include any files associated with an entry. At a minimum, we highly suggest uploading the following files:
- An original design file (for example, a Cadnano json file)
- At least one image (idealized, simulated or experimental) to be shown as the entry photo. If you do not have one available, you can use the oxView tool to produce such an image from the oxDNA files.
- If you also want the 3D structure viewer window to interactively display your structure, you will also need to convert your design file to oxDNA format. Note that providing oxDNA files is not necessary to upload structure, only recommended. The file converted to oxDNA format (using tacoxdna if your design tool of choice does not have a built-in exporter) should then be included in the list of the files that you upload. The following video demonstrates conversion from cadnano using oxView and how to relax structures. If you are having trouble converting into oxDNA format or relaxing the structure, please do not hesitate to contact us.
On this page you can also upload additional image files which will be shown in a gallery on the entry page, as well as experimental and simulation protocols and results which you would like to share with the wider community.
Private structures
If you do not want your structure to be publicly available, you can make it private by marking the checkbox in the last step of the upload process. This will prevent your structure from being searchable and appearing in the home page. Once uploaded, you will be taken your structure page. You may view your private structure by using the link for it or clicking "Profile" on the top navbar. The structure will only be visible to anyone who has a link to it.
Contact us
For any requests or queries please contact us at oxdna.help@gmail.com