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Running the Cello UCF to SBOL script

With default configurations

Once you have installed all dependencies (listed in INSTALL.md, go to the folder where you have downloaded the source code. Then type the following in a terminal:

node ucfToSBOL.js

If you are using the default UCF file, this will create the following files:

  • cello.xml - in the /result/ folder.
  • circuitConstraints.json - in the /result/ folder.
  • 14 cytometry json files - in the /result/cytometry/ folder.
  • 14 toxicity json files - in the /result/toxicity/ folder.

Using custom files and configurations

The default UCF file used by the script is /ucf/Eco1C1G1T0.UCF.json. You can use the script for any Cello UCF file. Replace the value of the ucfFilepath variable in /ucfToSBOL.js.

You can also change the filepath of the folder where the result files are created by changing the value of the resultFolder variable of the main result folder, the cytometryFolder variable to change where the cytometry json files are created, the toxicityFolder to change where the toxicity json files are created and the resultSBOL variable to change the name and filepath of the resulting SBOL file.

Uploading the SBOL file to Synbiohub.

  • In a browser, type the address of the desired synbiohub instance.
  • Log in (or sign up if you do not have an account).
  • Click on the Submit button in the top right.
  • In the submission form, fill in the ID, VERSION, NAME, DESCRIPTION, CITATIONS (Pubmed IDs if any).
  • Upload the cello.xml (or the name of the xml file if you changed the output file) in the SBOL/GENBANK/FASTA FILE.
  • Click submit.

Once the file has been submitted, you can make the collection public by clicking the Make Public button.

Uploading attachments

  • Once the SBOL file has been submitted, click on the newly created Collection.
  • Upload the circuitConstraints.json as an attachment.
  • Search for each ComponentDefinition for the following gates (if you are using the default Cello UCF file):
  1. A1_AmtR
  2. B1_BM3R1
  3. B2_BM3R1
  4. B3_BM3R1
  5. E1_BetI
  6. F1_AmeR
  7. H1_HlyIIR
  8. P1_PhlF
  9. P2_PhlF
  10. P3_PhlF
  11. S1_SrpR
  12. S2_SrpR
  13. S3_SrpR
  14. S4_SrpR
  • For each such Component Definition, attach the corresponding cytometry and toxicity json file.