Enter neutralization data (submit data)

This instruction describes the steps and methods for submitting neutralization data into the COVID-DRDB database. A pull request will be reviewed and accepted if it is created following this instruction.

A paper with neutralization tests against SARS-CoV-2 variants of following three types of "treatments" can be added to DRDB:

• monoclonal antibodies (mAbs)
• convalescent plasma / sera (CP)
• vaccinee plasma / sera (VP)

Step 0: get familiar with GitHub flow

We use GitHub flow to collaborate with inside and outside contributors. If you have not heard about the GitHub flow or unfamiliar with it, we strongly recommended you to read this article first: https://docs.github.com/en/get-started/quickstart/github-flow.

Step 1: create repository fork

To be able to edit our repository directly, you need to create a fork from it. By clicking the "Fork" button on the top right of this page, you can create a "forked" repository under your username space. Once a fork is created, you can clone the repository to your local directory.

git clone git@github.com:[your_username]/covid-drdb-payload.git

If this is not your first time submitting pull requests, don't forget to merge the upstream to your local repository:

cd covid-drdb-payload
git pull https://github.com/hivdb/covid-drdb-payload.git master

Step 2: Prepare all required data files and save them in the correct folders

If you're using Excel templates to format data, please save each spreadsheet into individual CSV files. For metadata tables, please append your data to the corresponding files. For neutralization data tables, please save the file to corresponding folders.

Step 3: finalizing and create pull request

Once you finished entering the potency data, you are good to commit your changes to your forked repository. You can do the following multiple times while you are still editing, this is like the "saving" button:

cd covid-drdb-payload
git add .
git commit -m "update file xxx21-pot.csv"  # don't forget to replace the message!
git push -u origin master

Once you have finished all editing, visit to the home page of your forked repository (github.com/your_username/covid-drdb-payload). You will be able to find the "contribute" dropdown and then click "open pull request". In the newly opened page, click the "create pull request" button.

In the "open a pull request" page, fill in the title and write some text to describe your changes. You can also attach the temporary files you created for entering the data for permanent record. Once you clicked "create pull request" button, we will start reviewing the changes you made and executing our data validation and auto-generation processes. If everything looks good to us, your changes will be merged.