Published October 23, 2021 | Version 3.5
Software Open

OneZoom tree of life explorer

  • 1. University of Oxford, Big Data Institute
  • 2. Imperial College London, Department of Life Sciences

Contributors

Description

The One Zoom tree of life explorer provides an easy way to navigate the evolutionary tree that connects all living things. It is a product of the OneZoom not for profit organisation registered in the UK. Our mission is to advance the education of the public in the subjects of evolution, biodiversity and conservation of the variety of life on earth.

The onezoom-complete.tpxz file is a compressed docker image containing everything necessary to run a stand-alone version of the One Zoom website (www.onezoom.org, see also our code repository at https://github.com/OneZoom/OZtree). Please note that the image contains both OneZoom software (use of which is subject to the open access One Zoom license https://www.onezoom.org/OZtree/static/downloads/OneZoom_License_V1.pdf) and third party data sources including images (please see https://www.onezoom.org/data_sources.html for more information).

Notes

You can use this docker image to run OneZoom for viewing on port 8080 (http://127.0.0.1:8080) using: `docker load --input oztree-complete.tpxz && docker run -p 8080:80 --name running_onezoom onezoom/oztree-complete` This may take a while (many minutes) to get going, because we are not allowed to package the IUCN data in this docker image (this would also risk packaging information which would become out of date). Therefore, when this image is run, it waits for the web server to be set up, then downloads the IUCN data from http://apiv3.iucnredlist.org/. This can take about 15 minutes and makes several large requests to the IUCN server (outputting console information as it does so). It can be tedious and unnecessary to have to re-download the IUCN data if you are regularly starting and stopping this image. To avoid this, once the IUCN processing has finished (when "IUCN DONE!" is output to the console), you can commit a new image using: `docker commit --change="CMD /sbin/my_init" running_onezoom onezoom/oztree-complete-with-iucn` then in future you can launch that image using `docker run -p 8080:80 onezoom/oztree-complete-with-iucn` which will run OneZoom on port 8080, without re-populating the IUCN data.

Files

OneZoom_License_V1.pdf

Files (1.7 GB)

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md5:2731e1eed709a4120af1de135d8f33ed
508 Bytes Download
md5:6317763380af83c7512db3b63744ecae
117.2 kB Preview Download
md5:318f7d840c9c115636dafa5131664c64
1.7 GB Download

Additional details

Related works

Is supplement to
Preprint: 10.1101/2020.10.14.323055 (DOI)

References

  • Wong, Y. and Rosindell, J. (2021) Dynamic visualisation of million-tip trees: the OneZoom project. BioRxiv 2020.10.14.323055;