Plasmid Database

Quartzy

The shared lab plasmid database is hosted on Quartzy. Each item is assigned a five-digit pKG number, in order.

Tip

To make sure you add new plasmids with the correct next number, click the “Item Name” column header to sort by this field. (It should now have a downward arrow icon.) Alternatively, use the following URL: https://app.quartzy.com/groups/190392/inventory?sort=-name

To add a new plasmid to the database, click the the “Add Item” button in the top left corner of the Quartzy page. Then, click “Skip Lookup” in the top right of the pop-up that appears.

Fill out fields as follows:

Field	Instructions
Vendor	Company that the plasmid was purchased from (e.g., Addgene)
Catalog #	Addgene number OR secondary plasmid name/ID (e.g., pGEEC100)
Item Name	`pKGNNNNN`, where `NNNNN` is the unique five-digit `pKG` number
Upload File	Upload the plasmid map
Type	Bacterial Stock
Date Stored	Date glycerol stock made
Plasmid	Short description of construct (e.g., pLentiX1-EF1a-mGL-bGH)
pKG#	`NNNNN`
Plasmid type	Select from options
Resistance markers	Select from options
Species	Bacterial cell type (e.g., NEB Stable)

Then, click the “Add Item” button in the lower left corner to add the item to the database.

Important

Double check that all the fields are correct, especially “Item Name”, “pKG#”, and “Upload File”! These are the most common sources of entry errors, particularly when adding a many plasmids at the same time.

Plasmid website

In addition to hosting the database on Quartzy, we also export plasmid information to a separate website. This way, we can group plasmids by alternate names, search plasmid names more easily, and add error/warning flags to improperly formatted entries.

The website displays plasmids with errors/warnings by pKG number, but it is often useful to group these entries by user so that the errors/warnings can be fixed. This list can be generated from the same project that builds the website: https://github.com/GallowayLabMIT/plasmids

Clone the git repo, then create and activate a virtual environment. See Startup checklist when working with repositories for instructions.
Create a file called credentials.json in the main directory of the repo. This should contain Quartzy login information in the following format:
```
{
    "username": "your-username",
    "password": "your-password"
}
```
In the terminal, run python -m quartzy_parser to print a list of pKG numbers with errors and warnings by user.
- To print only errors or only warnings, add the flag --only-errors or --only-warnings, respectively.
- To print only for a subset of users, add the flag --users followed by the list of users (full names).
- The numbers printed are the values in the pKG field, not the “Item Name” field.

Note

This code takes a while (~5 min) to run, since it has to scrape thousands of items from Quartzy.