The following article applies to academic users.
If you're an enterprise user, please contact Benchling directly.
The Benchling Bioregistry helps organizations track the entire life cycle of any biological entity across experiments, projects, and groups. Researchers can account for everything that has ever happened to any sample, run structured queries, and mine the data that’s important for their research.
We’ve modeled the process of creating and registering files in the Bioregistry around the physical process of creating a new strain in lab, and the journey it takes from a temporary fridge to a shared box the -80C freezer. In Benchling, a new strain is created in a project and then makes its way to your personal collection and finally the organization’s collection.
If you haven't already, start by Setting Up Your Bioregistry.
Projects → Temporary Lab Fridge: contains strains that you are still modifying.
Personal Collection → Personal box a -80C Freezer: contains “completed” strains that are in your personal freezer box, usually after sequence verification. Each lab member has their own Personal Collection.
Organization Collection → Lab box in the lab’s -80C Freezer: contains “completed” strains that are used by the whole lab, usually after someone leaves the lab or after publication.
As you register your strains into the Bioregistry, each new file will be given a unique ID.
- Schema Prefix: This helps identify data types (e.g. “b” for bacteria, “y” for yeast).
- Organization Initials: Your lab is assigned initials and files in your Org’s Collection will be assigned those initials upon registration (e.g. “DL” for Darwin’s Lab).
- Padded Number: Each newly registered sample will be given a number suffix. Numbering is based on the file type, so the third bacteria strain will be “bDL003” and the third yeast strain will be “yDL003”
- Personal Initials: Each lab member is assigned his or her own unique set of initials and files registered in Personal Collections will be assigned those initials. Files in both Org and Personal Collections will retain both IDs.
See Setting Up your Bioregistry to set up prefixes and initials.
Creating Data in Projects
In a typical experiment, a new bacterial strain may initially start in a local temporary fridge. In Benchling, the analogous location is a specific project.
- Open the project you’ll be working in. Click the plus sign, select Custom Inventory, and then Bacterial Strain.Note: Any custom inventory you set up in the Registry Settings will appear in this dropdown list (e.g. Bacterial Strain, Cell Line).
- Give your file a name and hit Next. Hit split workspace at the bottom right to collapse the description tab.
- In the metadata tab, fill in the appropriate values for your new strain by hovering over the row and clicking the pencil icon. You just created your first strain!
Tip - Link Plasmid Maps: Connect plasmid maps to your strains. You’ll first need to set the Scheme Field type for Plasmid to “Sequence Link” in the Bioregistry settings page. See the Setting Up your Bioregistry help document for more details.
Registering Files in your Personal Collection
You have now sequence verified your strain and to move it to your personal box in the -80C freezer. In Benchling, the analogous action involves registering this strain to My Collection in the Bioregistry.
To register an individual strain:
- Open the Meta Data tab and click Register.
- Select My Collection and leave Use existing file names as registry IDs unchecked.
- Click Register and Benchling will assign a registry ID number to your strain.Note: You’ll notice that the original name you gave your strain will be in the Alias section. You can search for files using the new Registry ID or the Alias.
To register multiple strains:
- Open the project that contains your strains and shift-select the files that need to be registered.
- Click the register button on the right and then select Register.
- In the next screen, select My Collection and leave Use existing file names as registry IDs unchecked. Benchling will assign a registry ID number to your strain.
Registering Files in your Organization’s Collection
It’s time to publish the research you conduced with your bacterial strain! Your whole lab needs access to your strain so it’s time to move it to a shared lab box.
In Benchling, you’ll now have to move this strain from My Collection to the Org Collection.
To move an individual strain:
- Select the strain in My Collection and open the metadata tab.
- Click the Change Collections button.
- Keep both Personal Collection and Organization Collection checked. Your strain will be given a new registry ID name using your organization’s initials.
To move multiple strains:
- Open My Collection and shift-select the strains that will be moved to the Org Collection.
- Click the Change Collections button on the top right and keep both Personal Collection and Organization Collection checked.
- Click Register. Your strain will be given a new registry ID name using your organization’s initials.