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MIDAS 2019 Novel Coronavirus Repository




We will be transitioning this GitHub repository to an online repository on the MIDAS website in the next months. We will not be accepting GitHub Pull requests or other contributions to this repository. If you'd like to point us to datasets, software, or other useful information, please post an issue and we'll aim to include the resource in the forthcoming MIDAS data portal.

New MIDAS Online Portal for COVID-19 Modeling Research

The MIDAS Coordination Center released an online portal for COVID-19 modeling research. The portal improves navigation and search of COVID-19 information. Moving forward we will use the online portal as landing page for COVID-19 data and information and the COVID-19 GitHub repository for sharing of computable (CSV) files with data, parameter estimates, software, and metadata. All community contribution functionality of this repository will be maintained, so continue to send pull requests or issues for questions or contributions!

Introduction

This repository serves as a central platform to share computable information (in CSV format) relevant for modeling of the COVID-19 outbreak. The MIDAS Coordination Center (MCC) has created and will maintain it in collaboration with the broader modeling community. Community members are encouraged to contribute resources to the repository and thus support the overall COVID-19 research effort. See Information for Contributors for guidance on how to contribute material. Contact questions@midasnetwork.us for any questions or ideas for improvements, or to send/request any material to be included.

MIDAS 2019 Novel Coronavirus Mailing List

The MIDAS Coordination Center maintains a dedicated mailing list for updates and news about COVID-19 modeling research. To join the mailing list, complete the online request form.

Community contributions

We highly encourage community member to contribute to COVID-19 repository. Community contributions are acknowledged here.

Name Affiliation Contribution
Matt Biggerstaff Centers for Disease Control Parameter estimates
Cécile Viboud Fogarty International Center Parameter estimates
John Drake University of Georgia Data resources used by the CEID Coronavirus Working Group
Sang Woo Park Princeton University Line listing on South Korean data sets
Caitlin Rivers Johns Hopkins University Parameter estimates
Matthew Malishev Emory University Parameter estimates
Srini Venkatramanan University of Virginia Biocomplexity Institute & Initiative Surveillance and imported cases dashboards
Matteo Chinazzi MOBS Lab Parameter estimates
Shi Chen University of North Carolina Parameter estimates
Mauricio Santillana Harvard University Parameter estimates and data associated
Kaiyuan Sun National Institutes of Health Data resources
Shifu Chen HaploX Biotechnology Software resources

Data

Data Catalog

All data published in the repository are uploaded/found here. Data are uploaded by the MCC and by community members. Sets of related data files are presented as "collections". For example, a collection can be a set of related outbreak situation updates from a country, a set of time-stamped backup files, or another set of related files. Each collection has its own metadata, data guide, and location dictionary that maps geographic locations listed in the collection to international standards. Given the amount of information available globally, we will concentrate our efforts on listing computable datasets created by community members, instead of country-specific situation updates.

Parameter Estimates

Parameter estimates are stored in one CSV file with estimates for epidemiological parameters relevant for COVID-19 modeling. Estimates are extracted from a variety of sources including preliminary model reports, pre-prints, and peer-reviewed publications. For each parameter, metadata are also extracted. Parameter estimates are extracted by a team of curators from the MIDAS Coordination Center and community members. Parameter information is reviewed by corresponding authors before being posted. New parameter estimates can also be added by appending to the CSV file (see Information for Contributors).

Software Tools

Software tools for data-processing, modeling, and visualizations will be included in this section together with relevant metadata. One CSV catalog file includes all tools, each on a separate row. New tools can be added by appending to the CSV file or by submitting an issue.

Documents

All documents relevant to COVID-19 are posted in this section. Documents are mostly organized by country or by topic. Pre-prints and peer-reviewd manuscripts are posted with links to external webpages only while all other documents are also stored in this repository as collections in the documents folder. Add new documents by submitting an issue with the document information. *Given the large number of COVID-19 papers being published, we will continue to update COVID-19 modeling papers only.

Information for Users

Many people have contributed to the creation of this repository and of its content. Please cite the creators of data or other content listed in the respective metadata if you use any of their contributions. Also cite this repository as the source for those contributions as per the following suggested citation: "Creators of object, name of object, Retrieved from: MIDAS 2019 Novel Coronavirus GitHub Repository, URL. Accessed date"

Contact Information

For any questions or comments related to this repository, submit an issue or contact the MIDAS Coordination Center.

MIDAS Coordination Center
University of Pittsburgh
A737 Public Health
130 DeSoto Street
Pittsburgh PA 15261
United States
Tel: +1 412-624-7693
Email: questions@midasnetwork.us

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