Our philosophy: Facilitating open-science & sharing of results

From the beginning, Nextstrain has had a focus on open, real-time, pre-publication sharing of results. Every situation is different and over time we’ve tried to develop a range of different approaches to make steps in this direction.

We are always excited to help you contribute to nextstrain, no matter what shape this takes. Please get in touch with us with any specific questions and we’ll be happy to help.

Centrally maintained, regularly updated datasets

There are a number of datasets which are run by the nextstrain team or close collaborators, for instance zika, influenza and West Nile Virus. Each individual dataset contains links to the scientists who maintain the different datasets.

We’re exited to collaborate with more groups and expand these datasets — please get in touch with us if this is something you’d like to be involved in.

Community maintained datasets

To make supporting this philosophy as easy as possible, we have created a “community builds” functionality, whereby GitHub is used to store the results of your analyses and the results are available for everyone via nextstrain.org. This is behind the community builds which you can see on the main page.

See this page for more information, including a step-by-step on how you can get your datasets up as a community build.

Bespoke auspice deployments

Auspice can be run on your own server, including customizations to the appearance and functionality. We have developed implementations of this using authentication for certain datasets where it’s inappropriate to share the data publicly. Tutorials and documentation about this are currently being written, but email us and we can discuss your use case.

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots etc may be used as long as a link to nextstrain.org is provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, Allison Black, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Garten, Dylan George, Ian Goodfellow, Nathan Grubaugh, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Louise Moncla, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Nathan Yozwiak for comments, suggestions and data sharing.

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© 2015-2019 Trevor Bedford and Richard Neher