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Information for Contributors

Lucie Contamin edited this page Feb 19, 2020 · 21 revisions
Contents
Create GitHub account and fork this repository
Contributing information
- Contributing data
- Contributing parameter estimates
- Contributing documents
Collaboration platforms

Contributing to this GitHub Repository

Contributions can be made by submitting information to the MIDAS Coordination Center, which will then upload the information to the repository, or by making changes to your forked repository and submitting a pull request. Submitting information to the MIDAS Coordination Center can be done by creating an issue in this repository or by email to questions@midasnetwork.us.

Create GitHub account and fork this repository

  1. Create a GitHub account and log in through https://github.com
  2. Go to Midas Network repository: https:://github.com/midasnetwork/COVID-19
  3. On the upper right corner, click on Fork.
    You have now forked the MIDAS COVID-19 repository into your GitHub account.

Contributing information

To contribute to the COVID-19 repository with GitHub:

  1. Create or update new files or sub-directory in YOUR fork repository, in the folder and in the sub-folder corresponding to your contribution:
    • To create a sub-directory within the repo, you must create a New File and add the sub-directory name before the file name: i.e. /SUB-DIR/FILE-NAME.ext
    • To upload local files to your created sub-directory, click the "Upload Files" button, uploaded files can be edited within GitHub by clicking on each file and the edit button.
    • "Commit" all your changes
  2. To merge changes into the original repo, a Pull Request must be initiated by you from your fork.
    • This request will be reviewed and merged by owner.
    • Note: All changes must be made from YOUR repo fork.
    • Click on the green Pull Request button.
    • Owners of the MIDAS COVID-19 repo will verify and merge your changes to the original repo

Instructions adapted from Michael Johansson's zika repository: DOI

Contributing data

  1. Add your collection of files into the corresponding folder in YOUR fork repository
  2. Add a collection_metadata.csv file describing the content of your collection, a template is available here.
  3. Add a date_guide.csv file, if necessary, describing the variables used in your data-set, a template is available here.
  4. Create a pull-request to update your collection into the repository, a MIDAS staff member will review it before adding it to the repository.

Contributing parameter estimates

  1. Read the Data Guide for Parameter Estimates to ensure your data contains most of the necessary information to contribute to the repository.
  2. Create an issue to have a MIDAS staff member add an estimate, or create a pull request to the estimates.csv file to directly append your estimate to the main repository.
  3. A MIDAS staff member can add the new estimate to the estimate readme.md file, or create a pull request to the readme.md file to update the listing.

Contributing documents

  • To add a paper or report, create an issue containing the information related to the documents (Citation, link, ...) or the documents you want to add to the repository, and a MIDAS staff member will update the information in the Wiki and in the folder corresponding if necessary.
  • For pre-prints or peer-reviewed papers, we will link to the external file, since these are stored in well-established repositories.
  • For reports, you can also add files yourself into the corresponding folder or create a folder if necessary in the documents folder, in YOUR fork repository. Documents are organized by geography (global or country) and collection.
    • If the report uploaded concerns more than one country, it should be upload into the global folder.
    • The report file uploaded should be named following the convention "DATE_short_title" (Date in the ISO Format YYYY-MM-DD)
    • Don't forget to update the collection_metadata.csv files, if a new collection is created, you will need to add a collection_metadata.csv file describing the content of your collection, a template is available here
    • Create a pull-request to update your collection into the repository, a MIDAS staff member will review it before adding it to the repository.
  • For papers or reports, a MIDAS staff member will add the document ciration to the Mendeley reference library. The XML file for the reference library will be updated weekly.

Contributing software tools

  1. Read the Data Guide for Software tools to ensure your data contains most of the necessary information to contribute to the repository.
  2. Create an issue to have a MIDAS staff member add a software tool, or create a pull request to the software_catalog.csv file to directly append your listing to the main repository. MIDAS staff will then list the tool on the software tools readme file.

Collaboration platforms

Outbreak Science Rapid PREreview Platform

This rapid pre-review platoform enables the community to give feedback on pre-prints coming out with modeling and other analyses of the COVID-19 and other outbreaks.

2019 Novel Coronavirus section on virological.org

Virological.org is an online discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.

Slack modeling_ncov channel

A Slack workspace maintained by Caitlin Rivers (caitlin.rivers@gmail.com) for discussion on COVID-19 research. The workspace includes various channels: general, importation, news, random, publications, forecasting, data, announcements-welcomes

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