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Submitting, Managing, and Updating Submissions

4.1 Submitting

To submit your designs to SynBioHub, follow these steps:

  1. Navigate to SynBioHub's home page.

  2. Click on the Submit option, and it will direct you to the Submit page.

Now, there are two ways to make your submissions: creating a new collection and then submitting your resource, or submitting to an existing collection.

4.1.1 Creating a New Collection

  1. Select the New collection option.

  2. Fill in the following attributes:

  3. Name: This is the name string that will be assigned to the submission.

  4. Collection Description: This is the description string that briefly explains your submission.
  5. Collection ID: This is a user-defined string identifier for the submission and should contain alphanumeric and underscore characters only.
  6. Collection Version: This is the version string associated with the submission.
  7. Citations (optional): This is a list of comma-separated PubMed IDs of citations to store with the submission, just for reference. It is an optional attribute.

  8. SBOL/GENBANK/GFF3/FASTA/ZIP file (OPTIONAL): The file should be of the following types:

    Type Description
    SBOL The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology.
    GFF3 The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines.
    FASTA In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package but has now become a near-universal standard in the field of bioinformatics.
    zip ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed.

    To submit a file, you must have already submitted the collection. Once you do, you can click Submit, and it will submit to the collection just created.

  9. Handler: You also need to select a handler. By default, only one option is provided, but more handlers can be added via submit plugins.

  10. Finally, you have an option to overwrite the existing objects in that collection, i.e., removing all the existing objects in the collection and adding new ones, or keeping the old resources and adding the new ones.

  11. Finally, click on Submit.

4.1.2 Submitting to an Existing Collection

  1. Select the add to existing collection option.

  2. Then, select your desired collection to which you want to add your submission from the dropdown menu.

  3. Subsequently, upload the files you want to submit. The file should be of the following types:

Type Description
SBOL The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. To know more about SBOL, visit this page.
Annotated zip ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. To know more about zip, visit this page.
GFF3 The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. To know more about GFF3, click here.
FASTA In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package but has now become a near-universal standard in the field of bioinformatics. To know more about FASTA file format, click here.
Zip ZIP is an archive file format that supports lossless data compression. A ZIP file may contain one or more files or directories that may have been compressed. To know more about zip, visit this page.

  1. Finally, you have an option to overwrite the existing objects in that collection, i.e., removing all the existing objects in the collection and adding new ones, or keeping the old resources and adding the new ones.

  2. At last, click on submit.

4.2 Managing Submissions

  1. Navigate to SynBioHub's home page.

  2. Click on manage submissions. On this page, you will be able to see collections broadly divided into two categories. The first one is public collections, which you have created and only you have access to them, and the second one is private collections, to which all users have access.

  3. You can view your collection by clicking on the collection name.

  4. To make your collection public, click on the collections you want (using the checkboxes on the left-hand side), then click on Publish. This will enable other users to view your collection and its contents.

  5. To delete your collection, click on Remove. This will remove the collection as well as the resources contained in that specific collection, namely promoters, activators, modules, components, engineered regions, etc.

4.3 Updating Submissions

  1. On the submit page, select the collection you want to submit your design to.

  2. Select the design that you want to submit.

  3. You may choose to overwrite the existing objects in a collection.

  4. Then, click on Submit.

4.4 Editing a Submission

To edit your submissions, follow these steps:

  1. Go to the submissions page.

  2. Select the collection that you want to edit.

  3. First of all, you can edit the name and description of the record.

  4. Then, you can add a source for your record.

  5. Subsequently, you may add a brief description for your record. This may contain details that can be described briefly about that particular record.

  6. As you scroll down, you will find a clickable menu titled details. Under this section, you can find the following options which you can edit. They are as follows:

  7. Add Description: Here, you can provide a detailed description for your record.

  8. Add notes: In this section, you can provide additional notes for explaining your record.

    Here you can use basic text formatting options, such as bold, italic, and underlining. Also, you may include an image as well as links with the use of HTML tags.

  9. Source: Here, you can enter various links referring to the place from where your record has been generated.

  10. Citations: You just need to add PubMed IDs separated by commas, using which you can cite several research papers.

  11. Then, we have the section titled other properties. Under this section, you can add/edit various properties, other than Synbiohub#ownedBy and Synbiohub#topLevel.

  12. Finally, we have the attachments section. Herein, you can upload as well as look up an attachment. The process for both options is described in detail as follows:

  13. Upload attachments: To upload an attachment, you just need to click the select file(s) option, and a popup shall appear. Now you need to select the attachments from your machine based on your convenience.

  14. Lookup attachment: Under this option, you can search for attachments. For this, you need to provide a URL for the attachment as well as its name. Then you need to select the type of attachment for which you want to search. The types are as follows: .nib, 2bit, A2M, ABI, etc...

4.5 Add to an Existing Collection

On some record pages, you might find an option titled add to an existing collection. Using this option, you can add the record you are currently viewing to a collection that is already there. For that, simply follow these steps:

  • Click add to collection. This will direct you to a page consisting of a dropdown menu.
  • Then, click on that dropdown menu. This will contain a list of collections that are already existing, and the record which you are currently viewing can be added to it.
  • Then, select the collection as per your convenience from the dropdown menu.
  • Finally, click add to collection.

This shall add the record or the collection you are currently viewing to the collection you have selected.