}})
If you've used OneZoom in teaching or research and you want to cite the project please use
-OneZoom Core Team (2021). OneZoom Tree of Life Explorer Version 3.5 URL: {{=A('http://www.onezoom.org', _href="http://www.onezoom.org")}}
+OneZoom Core Team (2021). OneZoom Tree of Life Explorer Version 4.0 URL: {{=A('http://www.onezoom.org', _href="http://www.onezoom.org")}}
We also appreciate citations of our scientific publications about OneZoom development
diff --git a/views/default/how.load b/views/default/how.load index 5cb3e313..242626d3 100755 --- a/views/default/how.load +++ b/views/default/how.load @@ -36,11 +36,15 @@ 4.) Settings -->Many of the things we'll be referring to in this user guide are accessible from a settings menu at the bottom left of the tree view. You need to press the settings button to open the settings menu.
+Many of the things we'll be referring to in this user guide are accessible from a settings menu at the top right of the tree view. You need to press the settings button to open the settings menu.
The language setting is an easy one to explain to start with. It does what it says on the tin and enables you to change the language of the tree of life explorer itself. Unfortunately, it does not yet change the language on other pages of our website.
+The information section provides further information about the tree. For example, the present guide is accessible from the 'how to use' option. Another example is a detailed page listing all the data sources contributing to the tree.
+}})
+
+
+The language setting does what it says on the tin: it enables you to change the language of the tree of life explorer itself. Unfortunately, it does not yet change the language on other pages of our website.
The page content setting enables you to select between slightly different markups of extra information on the tree. So far the only alternative to our default is a markup to accompany The Ancestor's Tale (2016) book by Dawkins and Wong.
@@ -131,14 +135,14 @@ Note that the tabs of information on offer aren't always the same as not every rWhen exploring a large tree it can be easy to get lost. To help avoid this, when exploring with a mouse, the tree won't permit you to navigate to a place where no leaf or common ancestor is on the screen. It also won't let you zoom in to a useless extent (e.g. fill the whole screen with one letter. We've provided additional tools to help you know where you are in the tree.
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-The list of groups opened with the compass icon are all clickable and will zoom the tree out automatically to the ancestor node that you clicked on.
+The location icon on the left brings up a list of groups that are all clickable and will zoom the tree out automatically to the ancestor node that you clicked on.
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@@ -146,8 +150,8 @@ Note that the tabs of information on offer aren't always the same as not every r
The compass feature only lists named nodes that are ancestors to your current view of the tree. The grey shapes between named nodes on your list also give information. The group 'Lady beetles' with 12 species is a very tiny part of the much larger group that contains it. The shape connecting the two is therefore almost a triangle showing that 'lady beetles' are a very tiny part of the 'Lady beetles and ladybird beetles'.
+The location button on the bottom left lists named nodes that are ancestors to your current view of the tree. The grey shapes between named nodes on your list also give information. The group 'Lady beetles' with 12 species is a very tiny part of the much larger group that contains it. The shape connecting the two is therefore almost a triangle showing that 'lady beetles' are a very tiny part of the 'Lady beetles and ladybird beetles'.
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@@ -245,17 +249,6 @@ Note that the tabs of information on offer aren't always the same as not every r
The information button on the bottom left can be used to access further information about the tree.
-}})
-The present guide is accessible from the 'how to use' option. Another example is a detailed page listing all the data sources contributing to the tree.
-
-There have been 11 substantial upgrades to OneZoom over the last 9 years with versions spanning from version 1.0 (October 2012) to version 3.5 (October 2021). Some features from earlier versions have not been retained in the latest software, so versions 1.0 and 1.2 remain supported to provide access to these features - such as customisation of the view to accommodate a user's tree and the growth animation function for dated trees.
- - -}})
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- Includes all the features of version 3.4.1 but adds several improvements i) improved colour scheme for showing extinction risk of species ii) added colour scheme for showing the popularity index of species as a continuous colour gradient iii) main colour schemes now show randomly resolved polytomies in a different way on the tree for improved scientific accuracy and to avoid misunderstandings about the level of accuracy in the current tree. iv) colour blind friendly mode available for all colour schemes v) improved tabs for each species linking to other resources with better explanation around the IUCN resources and added links to GBIF vi) substantial improvements to the content and interpretation pages throughout the site vii) new resources explaining how to use the tree of life explorer viii) docker images for easier deployment by third parties ix) a range of minor bug fixes.
- +There have been 12 substantial upgrades to OneZoom over the last 9 years with versions spanning from version 1.0 (October 2012) to version 4.0 (April 2024). Some features from earlier versions have not been retained in the latest software, so versions 1.0 and 1.2 remain supported to provide access to these features - such as customisation of the view to accommodate a user's tree and the growth animation function for dated trees.
-Includes all the features of version 3.4 and adds new APIs to access vernacular names, ID mappings and representative images.
-}})
+ Includes all the features of version 3.5 but adds the concept of TreeTours: guided visits around the tree of life with accompanying video and audio. New tours can be created via a separate GitHub repository. The treeview UI has changed slightly (e.g. toolbars moved) after a combination of user and developer feedback. Under the hood, improvements have been made in pinpointing areas of the tree to display, and the code used to construct the underlying data behind the tree of life has been streamlined and also placed into its own GitHub repository. Various minor bugs have also been fixed, and testing of the OneZoom codebase has been substantially increased.
+Includes all the features of version 3.3.1 and adds a completely redesigned landing page together with improvements to the site content as a whole.
+
+ Includes all the features of version 3.4.1 but adds several improvements i) improved colour scheme for showing extinction risk of species ii) added colour scheme for showing the popularity index of species as a continuous colour gradient iii) main colour schemes now show randomly resolved polytomies in a different way on the tree for improved scientific accuracy and to avoid misunderstandings about the level of accuracy in the current tree. iv) colour blind friendly mode available for all colour schemes v) improved tabs for each species linking to other resources with better explanation around the IUCN resources and added links to GBIF vi) substantial improvements to the content and interpretation pages throughout the site vii) new resources explaining how to use the tree of life explorer viii) docker images for easier deployment by third parties ix) a range of minor bug fixes.
+Includes all the features of version 3.4 and adds new APIs to access vernacular names, ID mappings and representative images.
+Includes all the features of version 3.3.1 and adds a completely redesigned landing page together with improvements to the site content as a whole.
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+
Includes all the features of version 3.3 and adds code to build a museum tree of life display exhibit in seconds. In particular, i) the user interface has been customized for museum display use, ii) the display URL has been 'sandboxed' so that users can't break out and explore material outside the tree of life and taxa pages on Wikipedia, iii) a new tutorial has been added to the display, and iv) a 'screensaver' function ensures that unattended displays automatically reset and fly around the tree to attract potential users passing by. A new launch page enables customization of the museum display including the home taxa location, language, view type and other settings. Version 3.4 also features some updates to the menus and pages on the website outside of the tree of life explorer.
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- This is very different from the other version 1.2 variants in terms of functionality. This code provides an easy to deploy explorer for touch screen environments in public venues. It has been developed using feedback from surveys and observations made at venues hosting the display. Features include... embedded images, embedded animal sounds, dynamic zooming around the tree when not in use, full search functionality and a bespoke on screen keyboard so that the system keyboard need not be exposed to users.
Download OneZoom version 1.2 kiosk , note that to function properly this also requires raw data that is not included in the download. You will need to unzip the software, then contact us to request an example data set (we have tetrapods and plants). You can then use this to learn the file formats and layouts necessary to input your own data without needing to edit the code itself.
+
+ This is very different from the other version 1.2 variants in terms of functionality. This code provides an easy to deploy explorer for touch screen environments in public venues. It has been developed using feedback from surveys and observations made at venues hosting the display. Features include... embedded images, embedded animal sounds, dynamic zooming around the tree when not in use, full search functionality and a bespoke on screen keyboard so that the system keyboard need not be exposed to users.
Download OneZoom version 1.2 kiosk , note that to function properly this also requires raw data that is not included in the download. You will need to unzip the software, then contact us to request an example data set (we have tetrapods and plants). You can then use this to learn the file formats and layouts necessary to input your own data without needing to edit the code itself.
The most advanced OneZoom website that can be hosted simply by copying the files into your webspace. More recent versions of OneZoom from 2.0 onwards require running your own Python based webserver and SQL database server.
All downloads of OneZoom version 1.2 are released under an MIT license which is OSI approved. Please note that the zip files also contain Boot Strap and jQuery which are built by third parties and licensed for further use under those third party license rules (please open the source files for information). The zip files may also include icons for e.g. facebook and twitter which are should be used under the terms of those organisations but are provided here for convenience.
Download OneZoom 1.2, this is the complete OneZoom website fully functional as it was live online until April 2016 when version 2.0 was released. - -Without downloading or installing any software you can still use our embed and link tool if you want to embed custom versions of a tree that's already on OneZoom. After selecting the settings you want the page will generate a short piece of code that you can copy any paste into your website to give you a OneZoom visualisation. This can incorporate highlights of pairs of taxa and their common ancestors as well as zooming animations and user interaction. If you want to use your own tree data, however, you will need to download the code and edit the data sources.
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A cut down version 1.2 designed to be easier to edit and use to build your customised explorable tree pages. Download OneZoom 1.2 lite
-}})
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+
The first version of OneZoom with basic features released alongside a publication in PLoS Biology. This version of OneZoom will still be useful if you want to quickly explore a Newick formatted phylogeny online. It also has the advantage of comprising of a single easily portable file which includes all code and data, later versions of OneZoom all use complex directory structures containing a range of files. Download OneZoom version 1.0 licensed under an MIT license which is OSI approved. - - - -
Please note that compared the latest version of OneZoom, this version 1.0 visualisation may appear clunky, and there is no touch screen support. The feature to load your own data was dropped from version 2.0 and above so that we could focus our limited resources more effectively on providing an easily accessible explorer for the complete tree of life. It would be a relatively small package of development to make the latest version of OneZoom capable of displaying other trees.
- -If you do go ahead and use this feature as it stands now, your data is only stored on your personal computer for this visualisation and is not transmitted over the internet so it is safe to visualise unpublished data in this way. If you prefer, you can still download OneZoom version 1.0 and do everything locally and offline.
- +Please note that compared the latest version of OneZoom, this version 1.0 visualisation may appear clunky, and there is no touch screen support. The feature to load your own data was dropped from version 2.0 and above so that we could focus our limited resources more effectively on providing an easily accessible explorer for the complete tree of life. It would be a relatively small package of development to make the latest version of OneZoom capable of displaying other trees.
+If you do go ahead and use this feature as it stands now, your data is only stored on your personal computer for this visualisation and is not transmitted over the internet so it is safe to visualise unpublished data in this way. If you prefer, you can still download OneZoom version 1.0 and do everything locally and offline.