Tree of life explorer

03.09.202203.09.2022 admin 0 Comments

Tree of life explorer

Tree of Life

The MinuteLabs Tree of Life Explorer was created by Jasper Palfree and Ever Salazar at MinuteLabs.io. Many excellent tools exist for looking at the evolutionary tree, like The Open Tree of Life and One Zoom, but we wanted to create a tool that would let us easily see the relationships between distant species.

The Data

We are getting our data from a few places, but the bulk of the data comes from The Open Tree of Life API.

Images come from a combination of Wikimedia Commons and Wikidata. We didn’t curate these images (that would take eons). So there may be some strange images because we’re effectively searching these image banks by the taxonomy label and pulling whatever images we find.

Support Us!

We do this because we love it, but it wouldn’t be possible without your support. The best way to support us is through patreon. Every bit helps. Thank you!

minutelabsio / Tree-of-Life-Explorer Goto Github PK

Explore Earth’s species and the relationships between them easily.

License: GNU General Public License v3.0

JavaScript 12.00% HTML 59.82% Vue 16.78% CSS 11.30% Shell 0.11% minutelabs

Tree-of-Life-Explorer’s Introduction

Tree of Life Explorer

Built by the MinuteLabs.io team

For a detailed explanation on how things work, check out the vuejs guide.

Tree-of-Life-Explorer’s People

Contributors

Stargazers

Watchers

Forkers

Tree-of-Life-Explorer’s Issues

Populous Children Box issue

If you click on something with a lot of children, the text extends way below the box.

I have also noticed this from time to time, not only on children list but on branches list. It seems that with the changes to scrolling, you broke something on the lists since they don’t scroll anymore and the full list is displayed on top of everything. For example, click on 34 here

Name display feature

Make cards display images only (without darkening) and put the scientific name below the card

The Chimpanzee Conundrum

If you search for «chimpanzee», it will give you the option to add «Pan Troglodytes» to the tree. But you will get an error. This is where things get confusing:

I posted this as a bug here. but turns out it’s not a bug in the app, it’s a bug in human classification.
OpenTreeOfLife/feedback#401

Even though «Pan Troglodytes» refer to the species classification of «Chimpanzees», it doesn’t represent a specific node in the tree. There are many different species of chimpanzee, so they get classified with affixes.

So we can search for «Western chimpanzee» or «Central chimpanzee» but searching for just «Chimpanzee» doesn’t work. I’m not sure how to deal with this.

It seems that chimpanzees don’t like trees 😉

Position of species in the tree

Right now, the position of the species in the tree seems to be determined automatically. What’s the pattern? Is it possible for the user to select the position of the branches? (For example, that lion appear on the left rather than on the right of the tiger)

Sometimes cards disappear from the tree

Undo/Redo options

I know that in order to undo, you can go to previous page in the browser, but is it possible to assign «ctrl+Z» and «ctrl+shift+z» to previous page and next page, respectively?

«More information» button/tab/link

We need to display at least a link to the database we’re pulling the information from and a link to the Wikipedia page and the identifier of the card. I think the easiest way to do this would be to add an information icon that brings an information screen with all of this and a enlarged picture, etc.

Highlight children already on display

Would be nice that on the children drop down menu, there was some visual cue for the children already on display. Maybe a text color change (such as light grey for the ones in display) or a little icon next to them. This, with the corresponding highlight when clicking on the child (even when is already on display) will help navigation.

Recover parent cards

Sometimes you hide a parent card, leaving plain text behind and then you can’t easily bring the card again. Would be good that clicking on the text gives the option to bring back the card.

The Search Engine Problem

So, it seems we need to figure out the search engine thing. I will be putting some ideas here:

This is not an issue, just to keep track of some FAQ we get. Here are some from Alex:

[NBD] Names of MRCA taxons on lists of parent nodes

Seems like the names of the MRCA taxons are now correctly displayed on their cards (fixing this issue), but not always on the lists of parent nodes. This isn’t a big problem for now, in my opinion, since the amount of mrca codes seem to be less than before?

Building tree issue

Sometimes the tree will not be constructed correctly. For example, the children for Theria are Eutheria and Metatheria, but when trying to display them the tree is not built correctly.

And the outcome is this:

Exit Fullscreen button

Scrolling over fullscreen button at bottom says “Exit Fullscreen” when it should say “enter fullscreen”

Lazuli Bunting not appearing in common names

scientific name: Passerina amoena

GBIF scientific name search doesn’t work

Searching for scientific names on GBIF database doesn’t work

Disabling Images and Expand buttons when in Zoomed In view

Since these buttons do nothing (visually) on the zoomed in view, maybe they should be disabled (and a hover text over them should say something like «This button only works in zoomed out view».

Notes from Henry

Some tree comments from my wildlife-biologist girlfriend:
1. Is there any way of capturing cases where phylogenies are being debated? Perhaps not, given that the tool is drawing from one database.
2. Is there some way to indicate the degree/extent of divergence on the branches to better understand how long ago two species diverged? I have no idea whether this is at all realistic.
3. I also had trouble finding a species by common name (Lazuli Bunting) which I found by its scientific name (Passerina amoena), which then populated my tree with Lazuli Bunting. So, I’m not sure what is up with that glitch. I tried it several times to make sure I was spelling correctly!
4. I like the zoom-in/zoom-out features.
I showed it to some lab mates and they thought it was cool and that they would use it to think about the species they work on.

Scrolling

Henry finds confusing that «I scroll vertically and click and drag horizontally. I would prefer either scrolling in both directions, or click and drag in both directions, or better yet, both/either!».

Search bar visible at all times

The search bar should be visible at all times, to avoid users having to pan up in order to search for something. Not sure where on the screen it should be, but maybe in a transparent layer on top of everything? (so that it doesn’t take too much space)

Subspecies aren’t always found

Try searching «snake» and now most results aren’t found.

Maybe i should try filtering autocomplete results by what is possible to find on OTL

Blurry text on Chrome Desktop

Not sure if it’s me or my computer or what, but the text looks blurry (and weirdly, it looks less blurry at different page zooming). I had this mentioned before to me but it wasn’t like this before.

I think this might be caused because the text is somehow scaled or the rendering is not being correctly displayed. It only happens on Chrome Desktop for me. (I have tried Firefox Desktop, Opera Desktop and Chrome Android and all of them have normal sharp text)

GBIF Duplicates

When using the search bar with the GBIF Database, many duplicates appear

Tool for finding the MRCA between two species

We should have a tool that allows to easily find the most recent common ancestor of two species selected. In a tree with a few species is easy and if we only search for two species, it’s also evident. However, in a big tree, it would be nice to have some sort of tool that allows to quickly see the MRCA of any two species selected (either by highlighting the paths or the mrca OR by removing everything else from the tree except for the two species selected (however, this would be kind of destructive)

I’m not sure what exactly needs to happen, but I’m throwing it on the air. Any ideas?

Common names are not always displayed on the info panel

For example, the Western Pine Beetle (ott1017378) appears with both common and scientific name in the search results, but the common name is not displayed in the info panel.

Tour Search Dialog in incorrect place for UltraWide Screen

The dialog looks out of place when the window is full screen in my Ultrawide screen monitor:

splash image alignment is off

Expand card button position

Right now, the position of the button to expand cards causes visual clutter when there are too many. Could you move it down to the inside of the phantom card? (to the red circle in the picture below)

Incorporate wikidata descriptions

eg: «infraphylum of jawed vertebrates»

«Clear all» and «Home»

So, right now the «Clear all» button is taking you to the homepage (and it’s also clearing things out). So, it miiiight be a bit confusing. Clicking on the logo should bring you back to home, too. And if we do this, maybe the «clear all» is not necessary? Or maybe we should move it closer to the undo/redo buttons and make it a «home» icon, rather than a «garbage» icon? Also, having it red draws too much attention to it.

Related comment from David: «“Clear All” button seems different than home button should be (Could solve this simply by making “Tree of Life” icon link back to home as well)»

Children of MRCA cards doesn’t work

When trying to display the children of MRCA cards, nothing happens and no error code is shown.

Children button disabled or absent when there aren’t children

Can we disable (visually make it fainter or something) or remove the children button if the card doesn’t have children?

Images on Parent Cards

Right now, «Felidae» displays the same image as «Panthera Tigris», which can be confusing. Not sure what to do in these cases, but it feels right that Felidae has some sort of picture when it’s not displaying any children, but maybe when it is displaying children, then remove the image? (maybe that would make things inconsistent or less smooth). Or maybe find a way to indicate that the picture displayed is from a children? The Carnivora card seems to diplay several animals at the same time, which might be a good solution too, even if they’re not individually recognizable. It seems that this is happening since the image pulled is actually a collage of images, but not sure where it is pulling it from, since the Wikipedia page for Felidae is also a collage.

Remove branch option

It would be nice to have both a «hide» card and also a «cut» entire branch option. Right now it is possible to hide each individual card, but in order to remove an entire branch, each card must be hidden individually.

Some examples of Curated Trees

This is not an issue, just meant to add suggestions for curated trees. One of the comments from people is that they want to see more curated trees (maybe even be able to submit them) and we should put our favorite ones there.

Henry pitched the Broccoli one

Giant logo in the middle

The giant logo on top pushes the good stuff below the fold; and since it’s already in the left corner, I think we can ditch it.

I also remember you and Henry suggesting something on this regard, however I didn’t understood what you meant:

Henry: I think that the issue is when you first go to the site, there’s nothing “tree of life-y” about it. Maybe even just including something tree of life-esque with the images for each curated tree somewhere? Or some sort of greyed-out tree in the background of the “start your own tree” blue box?
Jasper: ohh. maybe ever could mock up a little watermark i can put behind. Something that looks like a bigger riff on the icon
Henry: Yes! Exactly this
Ever: I don’t understand this. What does a «bigger riff on the icon» mean?

Overlapping drop down menus on Horizontal mode

When clicking on drop down menus (either children or parent branches) they’re displayed behind cards (and/or in weird positions). Maybe the solution is just to display the menus on top of every card, make sure the menus are displayed next to the button that originated them, AND make some indication that the button was pressed (having it a different color, for example)

A possibility to improve readability is that the color that the button changes to when pressed is somehow also displayed in the menu itself (maybe the outline of the menu is the same color as the highlight or something like that.

This is how it looks now:

Using https on Minutelabs

It seems Chrome is sending a «Not Secure» warning, which I’m guessing it’s because the site is not https

Expand branch

Sometimes, I want to be able to expand al the children and children’s children with one click, so I can explore a particular branch more easily. The OTL does this automatically, it seems, always showing «two generations» for every taxon. would it be possible that on the drop down menu there is an option to show all children and grandchildren?

«Children» and «Parent» navigation

It would be good that cards with children are immediately identifiable and that you can expand them with one click (right now, you need to make two clicks in order to expand)

Remove images option

Sometimes the images on the cards are a bit distracting or overwhelming (specially when there are a lot of cards on screen). We would have a cleaner interface and improved readability by having an option to hide images and just have the cards with dark grey background.

Highlight for newly added cards

It would be nice that when a new card is added to the tree via the search box, it is highlighted in some way (and the view pans to where it was added). This is useful when trying to add a card that is already in the tree.

Vertical mode default position is off

Seems like the default position for the vertical mode is off.

Chimpanzee pictures

Not sure what happens with the image search function on some species such as Chimpanzee, since it shows a landscape:

This is part of a larger issue regarding the images selected. Is there a way to manually «re-wire» images for particular species?

«Share» button

Comment from David:

If the goal is to let people create cool trees and share them, we should make that easier to do so. They likely wont know they can copy and paste, since most things like this use ajax or something to make it impossible to do so. Maybe just make a big button somewhere that says “share this tree” that copies the url from above (and maybe even shrinks it so it’s more shareable). Might also be neat to let people write notes on their trees.

Not sure if integrating Twitter and FB social is easy (or effective), but at least a «Share this Tree» button will let people know that it’s possible.

Display of Species Names

Sometimes, names could be displayed in a better fashion. Take the example of this tree where the six children names start with Limenitis. Seems like in some cases is way more important to show the last part of the name than the first part. For example seeing Arthemis, Astyanax, etc here would be more useful. We can:

Also, what’s the issue with the Red Spotted Admiral name here? Why it only shows «Red. «?

Both friends i showed the tree to, independently asked for a «zoom out» feature.

Since building a zoom out feature that actually scales everything adds a lot of problems, I was wondering if maybe we could do one of the following:

Some suggestions for visual changes

I played around with the settings, and I think this looks good:

The changes I made are the following:

Also, I think that some of the lines are pretty long, so, can we shorten some of them? So they look like this:

«Start fresh» button

Buttons stop working if the page is loaded or reloaded with URL tags set to 0

So, for example, if you go to this link (notice the &im=0&h=0&w=0 part in it), none of the buttons will work. In general, whenever «im=0», «h=0», or «w=0» are in the URL, the buttons don’t seem to identify them and thus they’re not able to swap between states. If you manually change the URL, it works.

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The Tree of Life

Educational posters of this Tree of Life are available from our shop. We also make custom posters of the Tree of Life using a design and size of your choice. Contact us at https://www.evogeneao.com/en/contact-us

Go to our page for teachers to see how the Tree of Life is used in the classroom to teach evolution.

Distortions and Limitations

In order to make the Evogeneao Tree of Life easy to understand, a number of distortions have been purposefully built in.

First, this Tree of Life is drawn from the human point of view. That is why humankind, instead of some other organism, occupies at the end of the tree, and why our vertebrate cousins (animals with a backbone) occupy a large part of the tree. This falsely suggests that humans are the ultimate goal of evolution. In fact, if that asteroid or comet that hit the earth 66 million years ago had instead missed the earth, there might not be a dominant, tool-using, space-faring species on earth. Or if one evolved, it might be a dinosaur, not a mammal.

Second, the world of bacteria holds far more genetic diversity, and accounts for far more biomass than animals and plants do, yet bacteria occupy only a relatively small portion of the Evogeneao Tree of Life. Trees of Life drawn from the bacterial point of view look very different; the whole world of animals and plants occupy only a tiny part of the tree.

If the asteroid or comet that triggered the mass extinction 66 million years ago had by chance missed our planet, the space-faring species on Earth today might be a dinosaur rather than a mammal.

Third, the Evogeneao Tree of Life suggests life steadily increased in diversity through time, such that the greatest diversity appears to exist at the present time. This is not at all the case and only appears that way because, for space reasons, only a few of the branches of life are shown. The evidence suggests that 99% of species that have ever existed on earth are now extinct.

Fourth, for space reasons many minor branches of life have not been included or labeled on the Evogeneao Tree of Life diagram. Also, the diagram suggests a specific time of common ancestry where branches join, but DNA and fossil data only suggest a broad time window in which the common ancestor lived.

Fifth, the Evogeneao Tree of Life breaks out Birds as a separate major branch, although the scientific consensus now is that birds are a branch of theropod dinosaurs that survived the mass extinction 66 million years ago. The branch could be labeled «Avian Dinosaurs,» but to make the diagram easier to follow, the more familiar designation «Birds» has been retained.

Sixth, current thinking proposes that 1) Bacteria and Archaea probably evolved from a common ancestor, either a non-living proto-cell, or something alive but more primitive than either, but now extinct, and 2) that Eukaryotes evolved from Archaea. Everything alive on earth today can trace ancestry back to that common ancestor between Bacteria and Archaea, which is known as LUCA (Last Universal Common Ancestor). Hug, et al., 2016 (Nature Microbiology 1:16048)

In order to keep the diagram simple for beginning students, the Evogeneao Tree of Life shows a simple, traditional progression from Bacteria to Archaea to Eukaryotes.

Seventh, for a recent common ancestor, we can reasonably be sure it didn’t look too different from a modern descendant, and fossil data is often available to guide the illustrations that we’ve created for the Evogeneao Tree of Life Explorer.

But science has only an approximate idea of what ancient common ancestors may have looked like. For these ancient ones, we’ve made highly speculative illustrations and assumed in most cases that they looked like a modern example of the next oldest branch. This assumes that little evolutionary change has taken place in the form of that organism, which is a big assumption. But this admittedly flawed protocol has been followed, rather than just replace those common ancestor illustrations with a big question mark.

Teachers are encouraged to examine issues raised in the Distortions and Limitations text for those students able to dive a bit deeper into evolution.

How to Use the Tree of Life

The geologic time scale begins at the center bottom, at Earth’s birth, more than four billion years ago. As you move away in any direction from this point toward the outer margin of the tree, geologic time gets younger and younger, until at the outer edge of the tree you arrive at the present day. Times on the geologic time scale are shown at the base of the diagram in millions of years before the present. These are traced through the tree of life along curved, dashed lines of equal time value. Any point on the Evogeneao Tree of Life can be placed in geologic time by using these curved timelines.

Biological evolution proposes that all living things, including humans, have a common ancestor with any other living thing. On the Evogeneao Tree of Life, students can discover when in the distant past these common ancestors lived. For example, trace the human branch back through time along the yellow guidelines using the partial Evogeneao Tree of Life below. Follow it back in time to the point where you meet the bright blue fish branch. This point on the Tree of Life represents the common ancestor between humans and fish (in this case, salmon). By using the time scale, you can see that this creature lived roughly 430 million years ago. The time of a common ancestor between any two of life’s branches, large or small, can be found in the same way.

Another example: Follow the Reptile branch back in time to the point where it meets the Amphibian branch. The curved timelines indicate that the common ancestor between amphibians and reptiles lived about 355 million years ago. Each of the major branches on the Tree of Life is color-coded to make them easier to distinguish from neighboring branches.

Our Understanding Will Evolve

As our understanding of life’s history improves (by fossil discoveries and genetics), some of the branching relationships and times of common ancestors depicted on this tree of life will inevitably become outdated.

Tree of Life by Ernst Haeckel

Many trees of life have been drawn since Darwin published On the Origin of Species in 1859. One of the first was by renowned German naturalist and embryologist Ernst Haeckel (1834-1919). He published this tree in his book The Evolution of Man (1879). Haeckel accepted the common ancestry of life but differed from Darwin in favoring inheritance of acquired characteristics over natural selection as the means by which species form.

The Evogeneao Tree of Life in Other Languages

Visitors to Evogeneao come from all over our planet and have voiced their support for evolution education and the fact that all Life on Earth is One Big Extended Family.

Our Tree of Life image is available in Spanish, French, German, Russian, Dutch, Catalan, and Chinese, for all of our Spanish, French, German, Dutch, Catalan, Russian and Chinese friends!

Italian

Dr. Emanuele Serrelli from the University of Milano Bicocca used Evogeneao in a science fair in Milan, Italy in the fall of 2013. We also donated a box of Evogenao tee shirts for the event, and they were a big hit! These are some of the exhibits Dr. Serrelli created to explain evolution the Evogeneao way.

Interactive Tree of Life

Explore your relationship to all the world’s creatures!

Welcome to evogeneao.com!

Our mission is to promote the teaching of evolution by emphasizing its greatest lesson: LIFE ON EARTH IS ONE BIG EXTENDED FAMILY! Every human being is related genealogically not just to all other humans, but to all other living things. And not only organisms living today, but to everything that has ever lived. This view of life can be thought of as ‘Evolutionary Genealogy’. Evogeneao (pronounced «ee-voh-gee-nee-oh») is a play on this term.

The Tree of Life

To illustrate evolution we use the Evogeneao Tree of Life diagram and cousin and removal relationships with other living things.

The Evogeneao Tree of Life is a colorful family tree that helps students understand evolution at a glance. Cousin and removal estimates make the evolution connection fun and personal. The Evogeneao Tree of Life is the centerpiece of two educational posters, available in our shop, along with tee shirts, hoodies, and other garments which feature cousin and removal estimates and original artwork. Evogeneao products and techniques have helped teachers worldwide teach the fundamentals of evolution in the classroom.

The Evogeneao Tree of Life diagram shows all the major and some of the minor branches of life tied to a geologic time scale, all in the colorful shape of a living tree. It also shows some major branches of life that have gone extinct, and hints at changes in diversity through time, especially at mass extinctions. Evogeneao numerical estimates of cousin and removal relationships are made by counting generations along lines of descent back to common ancestors.

Life of Earth is One Big Extended Family

Biological evolution is one of the three most profound discoveries in science. The other two are the vastness of the universe and the depth of geologic time. As such, these three discoveries should be the foundation of all science learning.

If the typical fourth grader can name planets in their order from the sun, she should also know that life is all related by descent from common ancestors. Life on Earth is One Big Extended Family.

Interactive Tree of Life

Explore your relationship to all the world’s creatures!

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README.md

Tree of Life Explorer

Built by the MinuteLabs.io team

For a detailed explanation on how things work, check out the vuejs guide.

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Explore Earth’s species and the relationships between them easily.

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Evolutionary Genealogy

Conventional genealogy describes the descent of members of a family or a group of closely related families. This is usually depicted graphically by a family tree, which typically goes back only a few generations, but only because of lack of information. The family tree of course really keeps going, to great-great-great grandparents, great-great-great-great grandparents, and so on. In fact, if you keep going back in time, any family tree will eventually join up with the family tree of every other person on the planet. You are related somehow and in some way to every other human on the planet, living or dead, whether it be Martin Luther King, Madam Curie, Charles Darwin, Genghis Khan or Queen Victoria.

Even without a family tree, genetic studies are able to broadly suggest how any two humans are related. Pick any person on the street. Travel far enough back in time and you will meet the common ancestor the two of you share, which makes that person your cousin. If the common ancestor is just two generations in the past (in other words, a shared grandparent), that person is your first cousin. If the common ancestor is three generations in the past (in other words, a shared great grandparent) that person is your second cousin. That person’s child would be your second cousin, once removed, and their grandchild your second cousin twice removed. If the common ancestor happens to be 30 generations in the past (in other words, a shared 28-greats-grandparent) that person is your 29th cousin.

‘Every individual living thing is your cousin. And approximately your x th cousin, n times removed.’

The Tree of Life

The Evogeneao Tree of Life is like a standard family tree; the only difference is that it goes back millions of generations, back to the start of life on Earth. Just as in a standard family tree, the genealogical relationship between any two living things, past or present, can be described. Every living thing, whether it’s a bird, a tree, or a dinosaur, can be described as your x th cousin, n times removed.

Calculating your genealogy with other life forms

To make an estimate of the cousin and removal relationship between you and any other living thing, count up the generations back to the common ancestor on both lines of descent. This sounds easy, but is complicated in practice. First, make an estimate of the number of generations along the human line of descent back to the common ancestor. Use commonly accepted estimates for generation times of humans, as well as those creatures likely to be templates for our successively older ancestors; chimpanzees, other apes, various species of monkey, treeshrews, and so on.

Second, apply the appropriate generation times to time intervals defined by ages of meeting points with common ancestors. For example, between 27 and 42 million years ago, that is, between the approximate ages of our common ancestors with old world and new world monkeys, respectively, the ancestor on the human line would be assumed to be a creature somewhat similar to a new world monkey and thus have an average of ten years per generation. In the absence of direct information on generation times for a species, it can be estimated by noting average life expectancy in the wild, years to first birth, and average age at last birth. With this sort of information, one can pick a time midway between years to first and last birth to get generation time.

Third, calculate the number of generations along the non-human line of descent back in time to the common ancestor with humans. Helpful data would include evolutionary history, generation times of the modern organism, and the generation times of modern organisms likely to serve as templates for intermediate forms along the evolutionary path to the common ancestor with humans. In the absence of such data, generation times can be estimated from likely body size; smaller forms generally having shorter generation times. If no data are found on forms intermediate between the modern species and the common ancestor, one can evenly distribute the change in generation times between points with data. Generation times should be the same along the human and non-human lines of descent at the point of common ancestry.

The same process can be used to estimate cousin and removal relationships between any two organisms; a bat and a cat, a salmon and a butterfly, a coral and a rat. The interactive Evogeneao Tree of Life Explorer illustrates this in a fun way all students of evolution can enjoy. https://www.evogeneao.com/en/explore/tree-of-life-explorer

An excellent source for animal generation times is http://animaldiversity.ummz.umich.edu/

An excellent source for times of common ancestors is http://www.timetree.org/

Other helpful sources are listed on the bottom of our In the Classroom page

Our Evogeneao cousin and removal estimates encompass a wide range of organisms from humans to bacteria. Samples of the graphic technique used to post data and make Evogeneao cousin and removal calculations are shown below.

Note: The cousin relationship in formal genealogy is determined by which line of descent has the fewest numbers of generations to a common ancestor. In the chart of relatively recent cousins shown above, it is always the human line of descent. But for some other species, the non-human line of descent has the fewer number of generations, which therefore determines the cousin relationship. For example, frogs (because of their large-sized, and therefore long-lived, amphibian ancestors of the late Paleozoic), are approximately 98 millionth cousin to humans. If instead the cousin relationship was determined on the human line of descent, (frogs were determined to to have a larger number of generations to the common ancestor), frogs would be approximately 151 millionth cousins to humans. This aspect of genealogy can be confusing, but if one bears in mind how the cousin relationship is determined, it will make sense.

The reader will certainly see that there is unavoidably a potentially huge error in any single estimate used to determine a cousin and removal relationship. The age of the common ancestors, their likely forms, and their generation times may be poorly known. However, it is at least reasonably likely that errors cancel each other out and that the overall result yields a reasonable estimate. The goal is not to determine an exact relationship, only to get reasonably close to illustrate the point. Science can determine that our common ancestor with chimpanzees is between our 150,000-greats-grandparent and our 400,000-greats-grandparent. But the real point is that that individual chimpanzee at the zoo looking you in the eye has a genealogical relationship with you, such that the chimp could be something like your two hundred and eighty-three thousand three hundred and fifty sixth cousin, eleven thousand seven hundred and twenty times removed.

Note that, except for close relations, there is NOT a unique genealogical path between two organisms. It is much more likely to be a tangled web of interrelationships. For example, a husband and wife might be, exactly, fifteenth cousins twice removed, as well as thirteenth cousins thrice removed, depending on which tortuous path of ancestors one followed back to the last common one. But as long as this is understood, the exercise of counting generations back to a common ancestor is really an eye-opener for all who make the journey.

Interactive Tree of Life

Explore your relationship to all the world’s creatures!

Big Fish Games, Inc

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Unlock the complete adventure with a single purchase! No in-app purchases!

For your whole life, you’ve thought that you were an orphan, and that your parents were long gone. But one fateful night, a stranger emerges from your mirror claiming not only to be your uncle, but that your parents are actually still alive, only in a different world! Their home is under attack from an evil force, and you may be only one who stands any chance of stopping it!

• TAKE A TRIP TO THE OTHER SIDE OF THE MIRROR
Some dark creature pulled your uncle back through the portal. To find out if what he said was true, you’ll have to follow deep into unknown territory!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

• CONTINUE YOUR ADVENTURE IN THE EXCITING BONUS CHAPTER
Unravel another part of the story and enjoy additional Collector’s Edition exclusives including collectible Leaves, morphing objects, and more!

Big Fish Games, Inc

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Play the trial for FREE! Pay once & complete the adventure!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Big Fish Games, Inc

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Описание

Play the trial for FREE! Pay once & complete the adventure!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Big Fish Games, Inc

Снимки экрана

Описание

Unlock the complete adventure with a single purchase! No in-app purchases!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

A view of all known life

The tree of life

Everything that is alive, or has ever been alive has a place somewhere on the complete tree of life. Each leaf represents a different species and the branches show how they are evolved from common ancestors over billions of years.

Our vision

Our vision for OneZoom is to do for the tree of life what online mapping tools have done for the globe; to make the complete tree of life a public good at everyone’s fingertips, free of charge and free of advertising.

What we’ve been doing

We have been working on this resource since 2011, but all that time we have not done much curating of our own. Instead we have been building tools to automatically connect together information that is already available from scientifically accurate resources. We then developed new technology to present these data in a visually stunning way that is easy to navigate. We’re now on version 3.6-151-gfbdbde4a.

Brief instructions

Explore OneZoom like you would a geographic map, zoom in to reveal more detail by pinching on your touch screen or scrolling on your mouse. To move around click and move your mouse or use your touch screen.

What you can see on the tree

OneZoom is the only tool where you can explore the complete tree of all known life, over two million species, on one page. You can find everything here from the Aaa Water Treader Bug to the ZZ Plant. In fact, there are so many species on the OneZoom tree, that if it were printed, the paper would span our entire solar system… at least sixty times over. This is also the only resource with images and common names of species in the complete tree of life. Here, you can discover your favourite species, see which species are under threat, and be amazed by biodiversity.

Finding out more

As you explore the tree you can click on the creatures you see to quickly reveal information from other resources such as Wikipedia and the Encyclopedia of Life. So you need look no further whenever you want to find out more about the diversity of life on earth.

Different views of the same tree

There are many different ways to look at the same tree of life apart from our default spiral view. Try some of the others, but remember that they all show the same information.

What the colours mean

Leaves corresponding to species that are vulnerable, endangered, or critically endangered according to the IUCN Red List are shown in red. These are all the species that are known to be under threat of extinction. The leaves shown in green represent species that are known to be okay for now (not under threat of extinction). Most of the leaves are grey meaning that their risk of extinction is not known.

Changing the colour scheme

You can change the colour scheme from the menu of settings on the bottom left of the tree. A colour key can also be opened from the information panel to the left of the tree of life explorer. Another colour scheme on offer shows how popular each species is according to our index of species popularity.

The settings menu on the bottom left of the tree also has a tick box for colour blind friendly versions of all colour schemes.

What we don’t know yet

You&#39re now ready to get started exploring the tree. However, we’ve prepared a more advanced user guide in case you want to learn more about how to use the tree of life explorer. The same guide is available from within the tree view by pressing the information button on the bottom left then selecting &#39how to use&#39

What is Evolution?

The word evolution is used in science to describe change through time. We can speak of the evolution of the Earth, evolution of a molten magma, or evolution of a solar system. Biological evolution refers to how life has changed through time.

Online resources:

What is Biological Evolution?

Simply stated, biological evolution proposes that through the process of natural selection and other natural processes acting over many generations, living things diversify, branching from one species into many. Natural selection acts on genetic variation in a population, such that those best adapted to current conditions have a better chance of surviving to reproduce and thus pass on a favorable trait to succeeding generations. Changes in the genetic composition can also occur without the push of natural selection, especially in small, isolated populations, in which a more or less neutral mutation can spread by chance. Either way, genetic variation can accumulate in a population to the point that it can no longer interbreed with its parent population, and a new species is born. Recent work on ‘epigenetics’ is looking at evidence that environmental conditions can affect the expression of genetic content of an organism, and that such changes can be passed on, to not only the next generation, but subsequent ones as well.

What all this means is that all living things are related to one another through common ancestry with earlier, different life forms. In other words, if you follow your family tree far enough back in time, you will find a common ancestor not only with every other living thing, but also with every thing that ever lived.

We are related not only to every living thing, but to every thing that has ever lived!

Life has changed through time. Life is One Big Extended Family, all related by descent from common ancestors. These statements are as fundamental to scientific understanding of our world as the fact that the earth is a sphere (an oblate spheroid to be precise), is billions of years old, and orbits the sun. Only slightly less sure is the exact mechanism by which life has changed through time. We certainly know that natural selection, lateral gene transfer, genetic drift and other natural processes, including perhaps epigenetics, act to produce this result, but details of the processes involved, and the relative contribution of each one, are an active topic of debate within science. Opponents of evolution use these debates to portray biological evolution as ‘a theory in crisis’ or just one of several equally plausible models. Nothing could be further from the truth. To accept the opponent’s view would be equal to thinking that because scientists debate details of gravitational theory, or quantum theory, or chemical bond theory, that these are ‘theories in crisis’! The evidence is clear: Biological evolution is one of the best documented and strongly supported theories in science.

Biological evolution is one of the best documented and most strongly supported theories in science.

Biological Evolution Background

In 1858, Charles Darwin and Alfred Russel Wallace independently proposed a theory of biological evolution to explain the diversity of life on Earth. Since then the fossil record, DNA studies and other evidence have added, and continue to add, overwhelming support for this view of life’s history.

In science, the strength of any theory rests in large part on its ability to make testable predictions and to see those tests confirm the predictions. Darwin’s work made several bold predictions that have been spectacularly confirmed since On the Origin of Species was published in November 1859.

First, in Darwin’s time the fossil record was just starting to be investigated. One significant observation of the time was that sedimentary rocks beneath (older than) the Cambrian layer appeared to be without fossils. In sedimentary rocks above (younger than) the Cambrian boundary, many different life forms left numerous fossils, which changed gradually, or sometimes abruptly, in younger and younger rocks. If Darwin’s theory was correct, fossils of simpler life forms than those in the Cambrian should be present in pre-Cambrian rocks. The fact that at the time they were not known was a problem Darwin acknowledged, but he predicted such fossils would be found eventually. In the last half century at several sites around the world paleontologists have found exactly the sort of simple Pre-Cambrian fossils Darwin predicted.

Third, in Darwin’s time science had no idea how characteristics of living things were passed from one generation to another. But the theory of evolution predicted that a biological mechanism existed which 1) accounted for mutations, 2) explained how they affected bodily form, and 3) recorded the history of genetic changes through time. Just such a mechanism was discovered in the 1950’s in the DNA molecule. Since then everything we have learned about DNA and genetics supports the theory of biological evolution. It is perhaps its most spectacular and strongest confirmation. See: ghr.nlm.nih.gov/handbook/basics/dna

Fourth, Darwin reasoned that because chimpanzees, the apparent closest relatives of humans, lived in Africa, fossils of creatures transitional between humans and apes would be found in Africa, and that the older the fossils the more ape-like they would appear. Starting in the 1920’s and continuing through very recent discoveries, this prediction has been spectacularly confirmed. The American Museum of Natural History has a fantastic exhibition on human evolution.

To be scientific, any theory must be falsifiable. There are many ways that biological evolution could be proved false. One example would be if human fossils were to be incontrovertibly found in any rocks older than a few million years. But even after 150 years, no solid evidence has ever been found that would prove evolution false. In fact, all observations have supported evolutionary theory. The idea of intelligent design on the other hand, although touted as an alternative to evolution, is in fact not a scientific theory because it cannot be falsified. Worse, if intelligent design were taught on an equal footing with evolution, alchemy could be taught alongside chemistry, and astrology alongside astronomy. An intelligent design proponent admitted this absurdity under oath during the famous Kitzmiller trial.

There is no better way to celebrate the wonder of evolution and the family of life on Earth, than to use Darwin’s own words…

To find out more about evolution and science, please visit these interesting websites:

Interactive Tree of Life

Explore your relationship to all the world’s creatures!

Tree of life explorer

Lifemap is an interactive tool to explore the tree of life. The concept used in Lifemap is similar to the one used in cartography with tools like Google MapsВ© or Open Street Maps: exploring is done by zooming and panning.

The current tree contains 802639 species: 3733 Archaea, 277426 Bacteria and 521480 Eukaryotes. It is based on the taxonomy publised by the NCBI and updated regularly.

All the nodes in the tree are clickable. It displays information (description and picture) concerning the taxa (retrieved from the ikipedia page, if any). If you have description or pictures you would like to see in Lifemap, simply create or update the corresponding ikipedia page.

Itineraries between taxa can be computed by clicking on the icon on the left of the search field. When filling the two new search fields, the route is drawn between the taxa and the Most Recent Common Ancestor (MRCA) of the two groups/species is returned. The user gets also access to a list of all the nodes that are encountered in the way from one group to the other. This list is clickable.

‘Expert’ versions of Lifemap, dedicated to the researchers in genomics, genetics and evolutionary biology also exist. Lifemap-ncbi displays the entire NCBI taxonomy (more than 1.1 million taxa) and allows (i) an easy access to NCBI web pages, (ii) the visualization and count of genomes completely sequenced and (iii) the possibility to download every subtree for every node in Newick format. Lifemap-otol allows exploring the whole tree produced by the ‘Open Tree of Life’ project (around 2.2 Million species). Again, it allows easy access to other taxonomic resources at each node, and the possibility to download every subtree in Newick format.

Lifemap was written by Damien M. de Vienne (web page), a CNRS researcher working in the Laboratory of Biometry and Evolutionary Biology (LBBE) in Lyon (France) with support from the informatics departement (especially Stephane Delmotte and Bruno Spataro).

For any question, remark, suggestion, or bug report, please contact Damien de Vienne: damien.de-vienne@univ-lyon1.fr
Lifemap by Damien de Vienne / CNRS is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Welcome to iTOL v6

Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic and other trees.

Manage and visualize your trees directly in the browser, and annotate them with various datasets.

Tree annotation made easy.

Annotate your trees directly from Microsoft Excel, LibreOffice or Google Sheets, or use the integrated web dataset editor. Advanced users can create the dataset template files and drag/drop them directly onto the tree, with complete control of all visualization options.

Adjust branch and label colors, styles and fonts interactively or by using annotation template files.

Unlimited number of datasets.

All datasets can be be displayed simultaneously, with fine-grained interactive control of their position, size and other visualization parameters.

Create publication quality figures.

iTOL provides What-You-See-Is-What-You-Get high quality export into several vector and bitmap graphics formats. Interactively adjust all tree and dataset visualization options as you like, and the exported figure will exactly mirror your screen.

OneZoom: Tree of Life explorer

OneZoom is a freely available Tree of Life, connecting all species together in a spiraling beanstalk that shows evolutionary history.

Each leaf on the OneZoom tree represents a species and the branches show how they are connected through evolution. Discover your favourites, see which species are under threat, and wonder at 105,307 images on a single page. It is a great way of visualising all life on Earth.

Our guide hopes to give you some examples of ways that you can explore OneZoom to gain new information about planet Earth’s vast Tree of Life.

Suggested activity 1: Without using the search-bar, find Homo sapiens.

Keep zooming inwards, following the Animal line and asking if we are more closely related to one side of the tree or the other.

Suggested activity 2: Find out when there was a common ancestor of lions and bears

Lions and bears are different creatures, obviously, and they look very different. However, they both have four feet (quadrupeds), eat meat (carnivorous) and give birth to live young (mammals).

Use the common ancestor tool to find out when their common ancestor lived. You can click on circles and leaves which provides more information from different sources like Wikipedia.

In this case, the common ancestor might have looked something like this.

Trees of Life – A Visual History

The idea of a tree as a metaphor for understanding and graphically displaying relationships among organisms is most often attributed to Charles Darwin (1809–1882), who fully developed the notion in his 1859 Origins of species by means of natural selection. However the concept is considerably older, and can be traced back to the Greek philosophers Aristotle and Plato, and the Great Chain of Being, which was developed throughout the Middle Ages and well into the 18th century.

As part of the launch of a new explorer for the complete tree of life produced by the UK charity OneZoom, a display in the Library of the Linnean Society explores the visual history and wide variety of forms of trees of life. The display starts from Carl Linnaeus (1707–1778) and his use of dichotomous diagrams, which were the ubiquitous amongst 18th century naturalists. It then explores other forms of displaying relationships between organisms: Charles Bonnet’s (1720–1793) staircase Great Chain of Being, or Scala naturae (ladder of nature), which portrays the temporal order in which God created life on Earth, with man at the top; George Louis Leclec de Buffon’s (1707–1788) genealogical diagram of the races of dogs; and early evolutionary trees such as Nicolas Charles Seringe’s (1776–1858) dichotomous branching tree representing the species of the willows of Switzerland (genus Salix) or Antoine-Nicolas Duchesne’s (1747–1827) upside-down tree of nine races or varieties of strawberries.

The first concept of a tree of life as a diagram that shows the evolutionary divergence or branching of groups of organisms through time was first drawn by Jean-Baptiste Lamarck (1744–1829) in 1809, fifty years before Darwin’s famous branching diagram. The end of the 19th century and early 20th century signalled the end of all other ways of displaying relationships between organisms in favour of the tree of life. Some biologists were great tree makers, such as Ernst Haeckel (1834–1919), who drew hundreds of visually striking genealogical trees to which specific biological taxa were assigned.

Over the last century, the discovery of genetics and molecular biology have made the tree of life one of the most important organizing principles in biology. Attempts have been made to design a universal tree of life, most notably by David Mark Hillis (1958–), in the form of a radial branching diagram. But even an approximation of the full scale of the tree has remained elusive.

Reference

PIETSCH, Theodore W. Trees of Life : A Visual History of Evolution. Baltimore, Md.: Johns Hopkins University Press, 2012.

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Play the trial for FREE! Pay once & complete the adventure!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
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• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Big Fish Games, Inc

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Play the trial for FREE! Pay once & complete the adventure!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

OneZoom/OZtree

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README.markdown

If you simply want to run a local copy of OneZoom, but not modify the code yourself, we recommend using our Docker image. The rest of this README provides details for compiling and running a OneZoom instance (something that is done under the hood when creating the docker image).

There are two ways in which you can install OneZoom on a personal computer: full installation and partial installation.

Partial installation does not create a standalone OneZoom site, but simply creates a local web file containing the javascript tree viewer. Instead of your tree viewer getting information from your own computer, it must do so by constantly requesting data from the OneZoom website (via the OneZoom APIs). This restricts your OneZoom viewer in various ways: you cannot make your own bespoke tree, you cannot change languages in the viewer, and you are dependent upon a permanent, fast internet connection. Also note that this installation method is also relatively untested, and there are unfixed problems with e.g. displaying lists of popular species. However, partial installation may be suitable for developers who simply want to re-program features of the tree viewer, such as colours, branch geometry, etc.

Full installation creates an entire duplicate of the OneZoom website, which is built using the web2py framework. This creates a fully self-contained local system (apart from the picture files, which can be downloaded separately). This is the most reliable installation method, but requires you to install and run extra software packages, in particular web2py and a MySQL server. Since this can be quite complicated, the majority of this readme contains instructions for full installation.

Requirements and packages

For all installation methods, you will need to install node.js (and npm, the node package manager), and the webpack package. To compile the OneZoom javascript codebase automatically, you will then need to install grunt. To generate documentation or make a partial install, you will also need perl installed on your system.

For full installation, you will additionally need to install web2py, and ensure that you have the programming language python installed on your system, which is what web2py uses. You will also need access to a database backend (e.g. mySQL running on your own computer, or on a remote server which you can administer).

To create trees, you will need python and perl, along with a number of libraries, as listed below.

Required packages (you will need these even if you’re not creating trees)

The OneZoom codebase uses the following software (licenses for each listed in braces). The first three are programming languages which may well already be installed on your computer.

Quick installation steps

For a partial installation (less tested):

For a full installation (recommended):

Downloading the OZtree app

Download a copy of the OZtree application from GitHub at https://github.com/OneZoom/OZtree, either as a zip file (not recommended), or probably better (easier to update), by cloning the repository (e.g. using git clone https://github.com/OneZoom/OZtree or if you have GitHub Desktop installed, click «Open in Desktop» from the OZtree repo). Make sure the git folder is called «OZtree» (this is the default when you clone the repo, but not if you download it as a zip file).

For full installation, you will also need to download the source code version of web2py, either via git (https://github.com/web2py/web2py/) or simply from the download link at http://www.web2py.com/. You can then place the OZtree directory into the applications directory of the web2py folder.

Building the OneZoom tree viewer

Compiling and creating the OneZoom explorer javascript code requires grunt to be installed. This compiles javascript code from multiple sources into a single file. You will need to install the node package manager, npm, then do

To install this is likely to require administrator privileges. Other required packages can then be installed from within the OZtree folder by simply typing the following (which may take a while to complete!)

Once these are installed you can run grunt as follows (feel free to examine the configuration options which are stored in Gruntfile.js in the main OZtree directory):

In development mode:

grunt dev : This command bundles multiple js files into one.

In production mode:

grunt prod : This command does three things. Firstly, it pre-compiles python code. Then it bundles multiple js files into one. Lastly, it minifies bundled js files.

The server-side database

Setting up the database backend

The web2py instance requires a database to be running. We previously used sqllite, and code for interfacing with sqllite is still present in the codebase, but probably will not work, as we have switched to using mySQL.

So a major step when installing OneZoom is:

Install a locally running copy of mySQL. Make sure the server is installed and not only the client There are many ways to do this: see http://dev.mysql.com/downloads/mysql/.

On Windows we recommended downloading the MSI installer as it will make it easier to configure the new server during the installation

Once mysql is installed, you will need to set a root password, and create a database for web2py to use. See http://dev.mysql.com/doc/refman/5.7/en/default-privileges.html.

The mysqld program is responsible for running the new database just created. When this program is running, you can connect to the database.

(optional) We find it useful to have a GUI interface to connect to the database and run SQL scripts, this can be used instead of using MySQL command line (similar to Windows command line) that is installed by default with MySQL. On Mac OS X we use the (excellent) http://www.sequelpro.com. On windows you could try http://www.mysql.com/products/workbench/ or https://www.quest.com/products/toad-for-mysql/

The database is now up and running. We recommend that you do not load data into it immediately, but first create the tables by installing web2py with migrate=1 set in the appconfig.ini file. After running an instance of web2py and visiting the new site, the correct table structure should be automatically created (see below). After that you can populate the data into the tables using downloaded files.

Configuring the OneZoom application to use the database involves creating a file called ‘appconfig.ini’ in the private folder within the OZtree app, modified to use the username and password that you supplied above. A minimal appconfig.ini file to get the site working is

In order to use web2py you need to have a python v3 installed, the latest version can be found at https://www.python.org/downloads/

NB: on Windows, make sure that you add python (and ideally python3 ) to the windows path during install, or the commands below will not work

Assuming you have python version 3 installed, should now try starting web2py as follows.

Starting and shutting down web2py

On the OneZoom main site, web2py is run using a combination of nginx and uwsgi. This is complete overkill if you just want to run a local copy of OneZoom for testing purposes. You can simply run a temporary and basic web2py server using Python 3. The simplest is to open a command-line prompt in the root web2py folder, and run the following (assuming the command python3 is linked to something like Python 3.7)

If this is a new installation you should now visit http://127.0.0.1:8000/OZtree/default/ or https://127.0.0.1:8000/OZtree/default/ to force web2py to create database tables. To load data into the tables, see «Loading Data», below.

Also, if you want to make OneZoom the default application, make a copy of the routes.py file in the folder labelled _MOVE_CONTENTS_TO_WEB2PY_DIR and place it in the top level web2py directory (see _MOVE_CONTENTS_TO_WEB2PY_DIR/README.markdown ).

Web2py folder structure

databases stores all the database structure.

models stores the python back end server code.

OneZoom special folders

OZprivate stores external files that are not formally part of web2py, such as the tree viewer code itself, and scripts which we use for updating the tree and our own database tables. The most important are:

Filling the database

Creating auth users & groups

Web2py uses an auth_ based system, which has tables for users, roles, and a mapping table assigning rols to users. This can be edited through the web interface: assuming you are running a temporary version of web2py on localhost, you can access the admin pages through http://127.0.0.1:8000/admin/design/OneZoom, which will require you to enter the temporary administrator password (‘pass’, above) that you used in the web2py startup command. The database tables can be seen at the url http://127.0.0.1:8000/OZtree/appadmin. You need to click to edit the db.auth_user table, from where you can click to add a «New Record», and submit a first name, last name, email, username, and password. You then need to go back to the appadmin page and create a «manager» role by adding a New Record to db.auth_group table (you can type anything in the description box). Finally, you need to create a New Record in the db.auth_membership table, and assign the «manager» group ID to your user ID in the resulting page.

The main bulk of the data returned from the API is stored in the rest of the tables in the database, as detailed below. To get the API and the rest of the website working, you will have to obtain a database dump of the OneZoom tables by emailing the normal OneZoom address. If you are loading new data on top of old, it is a good idea to truncate all the non-auth tables before loading data.

Optimising tables (IMPORTANT)

The commands to create indices also include commands to convert some of the columns to 4-byte unicode if necessary (to incorporate e.g. full Japanese/Chinese common names), and to drop the indexes if they already exist. Some of these commands may cause SQL errors (e.g. «Can’t DROP XXX») if you have not previously created any indices. These errors can be safely ignored. If you are using mysql workbench you may want to untick the option under Query to «Stop Script Execution on Errors», so that the index creation continues after each error.

Table information, for reference

Server unit tests

The server unit tests have no additional dependencies. To run, do:

Big Fish Games, Inc

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Descripción

Unlock the complete adventure with a single purchase! No in-app purchases!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Big Fish Games, Inc

Снимки экрана

Описание

Unlock the complete adventure with a single purchase! No in-app purchases!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Big Fish Games, Inc

Снимки экрана

Описание

Play the trial for FREE! Pay once & complete the adventure!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Оценки и отзывы

Game of life

It’s really great, because there are very big space for experiments with life and I can set so many different pattern. But there are one bug: top and bottom edges sometimes communicate, but generally they stop the evolution. Finally I have a request: please extend the speed settings. Often I get weary when wait the end of reactions or when glider or another spaceship will get the goal. Thanks for reading my comment.

Конфиденциальность приложения

Разработчик Theo Calmes указал, что в соответствии с политикой конфиденциальности приложения данные могут обрабатываться так, как описано ниже. Подробные сведения доступны в политике конфиденциальности разработчика.

Сбор данных не ведется

Разработчик не ведет сбор данных в этом приложении.

Конфиденциальные данные могут использоваться по-разному в зависимости от вашего возраста, задействованных функций или других факторов. Подробнее

Big Fish Games, Inc

Снимки экрана

Описание

Unlock the complete adventure with a single purchase! No in-app purchases!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

To-do list, habit tracker

AppFinca Inc.

Designed for iPhone

iPhone Screenshots

Description

# 2,000,000+ happy users around the world
# 80,000+ real trees planted on earth
# Official partner of Trees.org, a tree-planting NPO

Flora is a new way to stay off your phone, clear to-do lists, and build positive, life-changing habits. Whenever you want to make progress towards your goals, plant a seed in Flora. As you work hard, the seed will grow into a healthy tree. Let the tree be your coach and grow yourself with it. You will be amazed by how great you can be.

Have trouble putting down the phone? Flora blocks distracting apps in a pleasant way to help you focus on what’s more important in real life. If you cannot resist the temptation of using your phone and leave the app while growing a tree, the tree will be killed! But if succeeding, you’ll unlock new trees.

DOUBLE EFFICIENCY WITH FRIENDS

Things get even more interesting when you challenge your friends to plant trees together—you will see who kills a tree (ouch). However, if you successfully stay away from your phones together, each of you will win an additional tree from a random friend. You can also chat and share your progress to motivate each other and keep everyone on track.*

* Flora is the original app for multi-user tree planting and delivers the best features that help you and your friends be productive.

TO-DO LIST & WIDGET

Flora is a to-do list, and more. Simply create a to-do item and set a reminder, then you will never forget a thing. Even better, you can tag your trees with a to-do item to easily track the progress towards each of your life goals. No matter if your goal is daily, weekly, or monthly, Flora will help you follow it through and achieve it.

Enjoy a rewarding daily habit routine. If you grow trees regularly, you will earn yourself a beautiful, vibrant garden. Take a look at it and feel proud of yourself! Each tree records your perseverance and a step towards a healthy life. You can also view the daily, weekly, or monthly statistics of your activities in Flora to find opportunities to improve your time-management and planning skills.

REAL TREES, REAL IMPACT

Why not plant REAL trees while improving yourself? Flora proudly offers the opt-in Price and Care services that let you plant real trees on the earth if you kill or successfully grow a tree in the app. We partner with tree-planting organizations in Africa and East Asia, such as the Trees.org, to plant fast-growing soil rebuilding trees, fruit trees that diversify incomes and nutrition, and trees that can provide forage and fuel-wood. All these trees help make the earth greener and provide long-term financial aid to families who need it most.

Sounds good? Download Flora and join our 2,000,000+ productive users now!

Big Fish Games, Inc

Capturas de pantalla

Descripción

Play the trial for FREE! Pay once & complete the adventure!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Big Fish Games, Inc

Capturas de pantalla

Descripción

Unlock the complete adventure with a single purchase! No in-app purchases!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Big Fish Games, Inc

Снимки экрана

Описание

Unlock the complete adventure with a single purchase! No in-app purchases!

• CAN YOUR AMULET UNLOCK YOUR DREAMS?
This family heirloom will come in handy in a world of fantastic hidden object scenes.

• YOUR WISE LITTLE FRIEND WILL HELP YOU ALONG THE WAY
Use your owl’s special abilities to solve bizarre puzzles and magical mini-games.

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Tree of life explorer

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Tree of Life Web Project

Explore the Tree of Life

Browse the Site

Darwin 200: the celebration continues. read more

The Agaricales, or euagarics clade, is a monophyletic group of approximately 8500 mushroom species. read more

The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny).

Each page contains information about a particular group, e.g., salamanders, segmented worms, phlox flowers, tyrannosaurs, euglenids, Heliconius butterflies, club fungi, or the vampire squid. ToL pages are linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.

«The affinities of all the beings of the same class have sometimes been represented by a great tree. As buds give rise by growth to fresh buds, and these if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.»

Charles Darwin, 1859

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer-Master Your Life 12+

XUNTONGWUXIAN(Guangzhou)Network Technology Co., Ltd.

Разработано для iPhone

Снимки экрана (iPhone)

Описание

Heart Rate Monitor:
Only one action that puts your finger on the camera to know your heart rate immediately. We apply special technology to measure the heart rate by using the camera light through an artificial intelligence algorithm.

Love Challenge:
Wondering if you lover are love you enough? Come and challenge our love game. Life Explorer has selected a large number of love tests, waiting for you to challenge them!

Discover life:
Life Explorer collects interesting encyclopedia articles around the world, they can help you open the door to the unknown world, satisfy your curiosity and learn more useful knowledge.

Love Recorder:
Life Explorer help you do the math in love. Record every day in sweet love. Attend your relationship under our help.Write down your memorable events in your daily life. Design your own love journey to share with your lover or friends!

The app is free to download, but we also offer a subscription service, and subscribers can enjoy more features and content.

Subscription Terms:By joining you accept our Terms of Service and Privacy Policy.Subscriptions automatically renew unless auto-renew is turned off at least 24-hours before the end of the current period).Payment will be charged to iTunes Account at confirmation of purchase.It is an auto-renewing subscription.You can subscribe one week or one month, one year auto-renewing subscription, the price may be vary from countries depend on price matrix.We offers you all the fancy current and weekly-updated articles and tests.Account will be charged for renewal within 24-hours prior to the end of the current period, and identify the cost of the renewal.Subscriptions may be managed by the user and auto-renewal may be turned off by going to the user’s Account Settings after purchase.No cancellation of the current subscription is allowed during active subscription period.

If you have good suggestions or ideas, you can contact us at the following email address: lifeexplorer2020@outlook.com

Terms of Service : http://resource.bestlifementor.com/agreement/lifeexplorer/service.html
Privacy Policy : http://resource.bestlifementor.com/agreement/lifeexplorer/privacy.html

Explore yourself and master your future at this moment!
Download and play it now!

The Life Tree 4+

Blutulip Publishing Ltd

Разработано для iPad

Снимки экрана

Описание

Join these fun and loveable animal characters as they journey through The Life Tree, and listen to their funny captivating and magical stories in a fun and engaging format.

Based on the hugely popular picture, The Life Tree, this new app engages children through its beautifully illustrated characters and captivating interactive dialogue, creating an immersive reading experience that will surprise and delight young and old alike.

Что нового

A few new hidden treasures- here and there!

Конфиденциальность приложения

Разработчик Blutulip Publishing Ltd указал, что в соответствии с политикой конфиденциальности приложения данные могут обрабатываться так, как описано ниже. Подробные сведения доступны в политике конфиденциальности разработчика.

Не связанные с пользователем данные

Может вестись сбор следующих данных, которые не связаны с личностью пользователя:

Данные об использовании

Evolutionary Genealogy in the Classroom

Teachers! I guarantee that if you start your lesson on evolution by stating «Did you know that your dog is your twenty-one millionth cousin?» you WILL receive the full attention of the class. It never fails to get the kids engaged, asking questions and offering thoughts. Evolutionary genealogy makes a personal connection between students and evolution like no other method. Feedback from teachers has been very positive.

Teachers world-wide use the Evogeneao tree of life diagram to introduce evolution to students. Students intuitively grasp the idea of a family tree. The geologic time line yields estimates of the age of common ancestors. To order, visit our shop!

We have shipped posters all over the United States and to many other countries, including:

Classroom Game Plan

Effective use of the ‘family centered’ approach to teaching evolution centers around these core activities.

Geologic time

Evolution cannot be understood unless geologic time is clearly understood.

The vastness of geologic time is bread and butter to the oil and mining industries, and students should know this core finding of science as well. Evolution achieves major changes only by being able to operate over vast spans of time.

Explanation of key evolution concepts

Trace the evolution family tree

Students pick their favorite animal, (or what they had for dinner), find the organism on the diagram, and trace along its line of descent to where it intersects the human line of descent. They then use the curved time lines to determine the approximate time when the common ancestor lived. Students can also trace lines of descent between any two organisms on the diagram to find the time of their common ancestor; for example, between a dog and a frog, or a butterfly and a fungus. Students line up to do this activity because they are so intrigued to make this connection.

For older or more advanced students: Construct a chart or spreadsheet of the results, to form a list of times of common ancestors. These can be between humans and another organism, or between two non-human organisms.

Our Tree of Life Explorer is an interactive animated teaching tool that traces lines of descent and shows age of common ancestor, and cousin and removal relationships. It has proven to be very popular in classrooms.

Calculate cousin and removal relationships

For older or more advanced students, an excellent exploratory activity is to have students work out the number of generations down each line of descent to a common ancestor. This involves determining what sort of intermediate forms existed between the present form and the common ancestor, what the generation times of these forms might have been, and totaling the results. A comparison of the number of generations down each of the two lines of descent yields a rough cousin and removal relationship, just as in a standard genealogy. (See the Evolutionary Genealogy page of the website for more details).

‘Biological evolution is one of the three most profound discoveries in science. The other two are the vastness of the universe and geologic time. As such, biological evolution, along with the other two, deserves to be the foundation of all science learning, and should be taught from an early age.’

Resources for the Classroom

Evogeneao Slideshow

The author of this website created a digital slide show about evolution for presentation to classrooms, museums, and civic groups. It has been continuously updated and presented at numerous schools and other venues very successfully. It uses Gary Larson cartoons and refutations of evolution opponents’ talking points to explain biological evolution. A few of the slides used in this talk are posted here. Teachers are welcome to a free PDF file of this slide show for use in their classroom, or as inspiration for their own illustrations. Click the Download Slideshow button below.

The first part of the talk discusses the two main conclusions of biological evolution: 1) that life on earth is all related by descent with modification from common ancestors, and 2) modification takes place mostly by natural selection. The second and longest part of the talk includes a number of evolution-opponent talking points (at the top of a slide in orange) and the evidence that refutes them.

Teachers are welcome to contact the author if there are questions about any of the slides. The author of this website would also be willing to present this talk to classrooms or communities if reasonably convenient for me to travel to the site. (No payment is required from the teacher or community.) Contact Us.

Online Resources

Numerous excellent websites on evolution provide a wealth of information for teachers. These are some of the best:

Vast mounts of easily accessed information on generation times, life span, years to sexual maturity, etc. is from University of Michigan. http://animaldiversity.ummz.umich.edu/

An excellent overview of many aspects of science, including biology and evolution, in a classroom-friendly format. https://phet.colorado.edu/en/simulations/category/new

A huge trove of excellent resources for teachers to explore geologic time is: http://www.geosociety.org/GSA/Education_Careers/GSA/edu-career/Home.aspx

Addressing Creationism

Yes, conservative religious belief and evolution can collide in the classroom. An excellent resource for dealing with this issue comes from an evangelical Christian, and the current head of the National Institutes of Health, Francis Collins. He reconciles his faith with the accepted scientific view on evolution at biologos.org Well worth reading in detail the information on this site. Another excellent source for defense of evolution is https://ncse.com

An excellent book that examines evidence for an ancient age of the earth (and pointedly refutes young-earth creationist ideas) is The Grand Canyon: Monument to an Ancient Earth. Can Noah’s Flood Explain the Grand Canyon?, 2016, Hill, Davidson, Helble and Ranney, eds. Kregel Publications, Grand Rapids, Michigan, 240pg.

To see for yourself how some creationists mislead and distort the evidence for evolution, you can visit these creationist websites:

Interactive Tree of Life

Explore your relationship to all the world’s creatures!

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Оценки и отзывы

The Only One That Works

I downloaded literally every other Conway’s Game of Life app in the app store, and this is the only one that let’s you zoom, draw, and play on a large board. The clear function doesn’t work for some reason, so it lost one star for that.

it’s (almost) perfect

for the people complaining about no reset, you can shake your phone and an option for it pops up. The only things i would change is that it needs a random board option and an infinite board.

Excellent Game of Life app

Definitely one of the best GOL apps for the iPad. Huge library with nice explanation of each pattern, all in the standard features except it’s missing a generation counter/population indicator. I’d take off half a star for that, but they don’t allow half stars here so I’ll round it up to five stars.

Конфиденциальность приложения

Сбор данных не ведется

Разработчик не ведет сбор данных в этом приложении.

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Розроблено для iPad

Знімки екрана

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Що нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Оцінки та відгуки

Game of life

It’s really great, because there are very big space for experiments with life and I can set so many different pattern. But there are one bug: top and bottom edges sometimes communicate, but generally they stop the evolution. Finally I have a request: please extend the speed settings. Often I get weary when wait the end of reactions or when glider or another spaceship will get the goal. Thanks for reading my comment.

Приватність програми

Розробник ( Theo Calmes ) зазначив, що до процедур забезпечення приватності програми може входити обробка даних, як це описано нижче. Докладніші відомості наведено на сторінці політики приватності розробника.

Дані не збираються

Розробник не збирає жодних даних із цієї програми.

Процедури роботи з конфіденційною інформацією можуть відрізнятися з урахуванням, наприклад, вашого віку або функцій, якими ви користуєтеся. Докладніше

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Конфиденциальность приложения

Data Not Collected

The developer does not collect any data from this app.

DailyTech Solutions Ltd.

Разработано для iPad

Снимки экрана

Описание

Curious about your future looks? Do you want to know more about yourself? You will find all answers here.

Aging Camera
Whether you are a boy or a girl, this can help you predict what you will look like in the next 20, 40 or even 60 years. How many years later you want to see yourself, you choose!

Baby Predict
Find out how your and your partner’s future baby will look like. Try it with your boyfriend’s/girlfriend’s photo and amaze your partner and friends!

Palm Reader
Your hand is a map reflecting your life, your personality, past, present, future, and potential. This app reads your palm lines and provides detailed and personal palm reading results.

Art Portrait
The app instantly generates awesome portraits of a hand-drawn quality making it a go-to app for all non-artists out there.

Cosplay
Turn your photos to world famous paintings and sculptures.

ASMR Sounds
Just the most popular ASMR sounds to help you fall asleep. Great for insomniacs, anxiety and relaxation.

Random Tests
Don’t know which question you want to ask yet? Let the random tests help you know yourself better than ever.

*Disclaimer:
Our app is only for entertainment purposes. The results of our app is not guaranteed as 100% correct, and it is only for reference.

Upgrade to our premium service and enjoy more benefits:
See the old face effects.
Enjoy the young effects.
Know what your baby look like.
Read your palm secrets.
and more.

Subscribe to take advantage of the features described above.
•Subscription length: weekly, monthly and yearly.
•Your payment will be charged to your iTunes Account as soon as you confirm your purchase.
•You can manage your subscriptions and turn off auto-renewal from your Account Settings after the purchase.
•Your subscription will renew automatically, unless you turn off auto-renew at least 24 hours before the end of the current period.
•The cost of renewal will be charged to your account in the 24 hours prior to the end of the current period.
•When canceling a subscription, your subscription will stay active until the end of the period. Auto-renewal will be disabled, but the current subscription will not be refunded.
•Any unused portion of a free trial period, if offered, will be forfeited when purchasing a subscription.

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Конфиденциальность приложения

Data Not Collected

The developer does not collect any data from this app.

The Tree of Life: A Simple Exercise for Reclaiming Your Identity and Direction in Life Through Story

As I read this book so many things about the nature of stories and their role in human life came into sharp focus. Things that I have been working out for years on my own but could only vaguely express in comparison to the clarity I found in this book.

Just having the idea of using story to work through trauma or a crisis of identity validated was a big deal for me. I knew it was possible (because I had done it in my own life) but I was completely unaware that there was a whole subset of psychologists and therapists dedicated to using stories (in a non-religious context) to heal and empower people all over the world.

To discover this has filled me with a new wellspring of passion for learning all that I can about the power, utility, and essential nature of stories. And of course, sharing those lessons with anyone who cares to read this blog.

That’s why I’m excited to share an exercise from Denborough’s book called The Tree of Life. It’s something literally anyone can do in under an hour and yet the results can positively shape the rest of your life.

The Tree of Life Concept

The tree of life concept is pretty simple and straightforward. It is a visual metaphor in which a tree represents your life and the various elements that make it up–past, present, and future.

By labeling these parts, you not only begin to discover (or perhaps rediscover) aspects of yourself shaped by the past, but you can then begin to actively cultivate your tree to reflect the kind of person you want to be moving forward.

Just as we learned in my last post that the stories of our lives are the events we choose to highlight and contextualize, in this post we will learn how to discover and highlight alternate paths through our past–which in turn create new horizons in our future.

Follow the instructions below to give it a try for yourself.

The Tree of Life Exercise

The image below is an example of what the tree of life exercise will look like once complete. I was able to complete this rough draft in about an hour. The instructions below will describe how you can create your own.

The first step of course is to draw a tree. I’ve included a video below that should help if you feel lost. However, I should note that–at least for your first draft–it might be helpful to keep it rough. You can always go back later and redraw or touch-up your existing drawing for aesthetics. This round is all about getting the information down.

Next, follow the labeling instructions below. If you can only think of one or two things per section at a time, don’t worry about it. The nature of this exercise is that as you complete each step, it unlocks more memories and ideas for other parts. You can skip around and fill things in at any time. The most helpful thing in the beginning is to just write stuff down and see where it takes you. You might be surprised!

The Compost Heap (Optional–But Highly Recommended!)

Write down anything in your compost heap that would normally go in the other sections described below but which are now things you no longer want to be defined by.

These are often sources of trauma, abuse, cultural standards of normality/beauty/etc. or anything else that shapes negative thoughts about yourself in your mind. You can write down places, people, problems, experiences. Whatever you need to.

I blurred mine out above, but you can see it has several items. Generally they all have to do with past trauma and damaging relationships I’m trying to let go of. I’ve found that the idea of a compost heap is an extremely helpful way to think about these things. Especially since many of them are not neatly categorized as “all bad”.

There are in fact quite a few life defining lessons I learned through the things that ended up in my compost heap. And like a compost heap is supposed to do, I will eventually break those things down and re-sow the rich parts back into my life.

You can do the same with yours.

The Roots

Write down where you come from on the roots. This can be your home town, state, country, etc. You could also write down the culture you grew up in, a club or organization that shaped your youth, or a parent/guardian.

The Ground

Write down the things you choose to do on a weekly basis on the ground. These should not be things you are forced to do, but rather things you have chosen to do for yourself.

The Trunk

Write your skills and values on the trunk. I chose to write my values starting at the base of the trunk going up. I then transitioned into listing my skills. For me this felt like a natural progression from roots to values to skills.

The Branches

Write down your hopes, dreams, and wishes on the branches. These can be personal, communal, or general to all of mankind. Think both long and short term. Spread them around the various branches.

The Leaves

Write down the names of those who are significant to you in a positive way. Your friends, family, pets, heroes, etc.

The Fruits

Write down the legacies that have been passed on to you. You can begin by looking at the names you just wrote on leaves and thinking about the impact they’ve had on you and what they’ve given to you over the years. This can be material, such as an inheritance, but most often this will be attributes such as courage, generosity, kindness, etc.

(Tip: if your tree is pretty crowded by this point, perhaps try drawing some baskets of fruit at the base of your tree and label them accordingly there.)

The Flowers & Seeds

Write down the legacies you wish to leave to others on the flowers and seeds.

(Tip: again, you may wish to de-clutter your drawing by visualizing saplings, baskets of flowers, etc. on which to write these items down.)

Going Further

After completing this exercise you are no doubt swimming with ideas and possibilities. My best advice is that if an idea has occurred to you that will help you process the things you have uncovered in a positive way, do it!

Here are three things that I have chosen to do as a follow up to my initial experience.

Journaling

I’ve decided to journal about the various elements on my tree. I want to explore the connections between my roots, values, skills, people, etc. in a safe way before sharing it with others in any organized manner. But I do intend to share it with others. And I already know two of the ways in which I plan to.

Writing Letters

Some of the connections are pretty easy for me to determine. I know that I wrote certain values or lessons on my tree and immediately followed them up with the name of a person or group of people. These are the people who have instilled something special in me and I intend to tell them how much that means to me by writing some letters.

Meditation Through Art

I found that the drawing part of this exercise was particularly satisfying and therapeutic in and of itself. I’ve decided to follow this initial exercise up with some more study sketches of trees followed by a series of paintings and collages that express more than mere labels can. I hope to be able to share these with my friends, family, and community in the future too.

Final Thoughts

Even though I’ve spent this whole post talking about how great of an exercise this can be, I know how scary it can feel to take the first steps in claiming the storytelling rights over your life. It usually means confronting aspects of our past that we might feel are better left unchallenged. And that’s a valid concern.

If you are worried that an exercise like this might stir up a lot of raw emotion or trigger traumatic flashbacks, I would encourage you to complete this exercise with a therapist. Or, at the very least, with a friend or family member who will be there to talk to you and support you through the process.

Regardless of how you choose to complete this exercise, or what personal spins you put on it (which is half the fun!), I’d love to hear how it goes. Feel free to reach out to me about it via any of my social channels, my contact page, or the comments section below.

Life Explorer 4+

Theo Calmes

Được thiết kế cho iPad

Ảnh chụp màn hình

Miêu tả

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Có gì Mới

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Xếp hạng và Nhận xét

The Only One That Works

I downloaded literally every other Conway’s Game of Life app in the app store, and this is the only one that let’s you zoom, draw, and play on a large board. The clear function doesn’t work for some reason, so it lost one star for that.

it’s (almost) perfect

for the people complaining about no reset, you can shake your phone and an option for it pops up. The only things i would change is that it needs a random board option and an infinite board.

Excellent Game of Life app

Definitely one of the best GOL apps for the iPad. Huge library with nice explanation of each pattern, all in the standard features except it’s missing a generation counter/population indicator. I’d take off half a star for that, but they don’t allow half stars here so I’ll round it up to five stars.

Quyền Riêng Tư Của Ứng Dụng

Data Not Collected

The developer does not collect any data from this app.

Phương thức đảm bảo quyền riêng tư có thể khác nhau, chẳng hạn như dựa trên các tính năng bạn sử dụng hoặc độ tuổi của bạn. Tìm hiểu thêm.

oseiskar/tree-of-life

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README.md

This is an interactive visualization of the recently published Open Tree of Life using d3.js. The entire tree with approximately 2.3 million identified species as leaf nodes is browsable through the application. The width of the branches in the visualization represents the number of species they contain.

The search feature can be used locate taxa in the tree by their scientific (Latin) names such as Canis lupus familiaris, Amanita muscaria or Streptococcaceae.

The program also constructs a prefix tree of the taxon names. This tree, which powers the search feature, is also split into subrees that are loaded on demand.

All the resulting data can be hosted as static files, to create a «no-backend» web application.

first download a suitable tree archive here

run make jsons (this requires make and g++ installed on the system)

Life Explorer 4+

Theo Calmes

Navrženo pro iPad

Snímky obrazovky

Popis

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Novinky

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Hodnocení a recenze

Game of life

It’s really great, because there are very big space for experiments with life and I can set so many different pattern. But there are one bug: top and bottom edges sometimes communicate, but generally they stop the evolution. Finally I have a request: please extend the speed settings. Often I get weary when wait the end of reactions or when glider or another spaceship will get the goal. Thanks for reading my comment.

Ochrana soukromí v aplikaci

Vývojář „ Theo Calmes “ uvedl, že součástí opatření na ochranu soukromí v této aplikaci může být zpracování dat níže popsanými způsoby. Další informace najdete v zásadách ochrany osobních údajů poskytnutých vývojářem.

Сбор данных не ведется

Разработчик не ведет сбор данных в этом приложении.

Postupy v oblasti ochrany osobních údajů se mohou lišit, například v závislosti na funkcích, které používáte, nebo na vašem věku. Další informace

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Конфиденциальность приложения

Data Not Collected

The developer does not collect any data from this app.

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Конфиденциальность приложения

Keine Daten erfasst

Der Entwickler erfasst keine Daten von dieser App.

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Tree of Life: Oddria!

Минимальные:
ОС: Windows 7 64 bit
Процессор: Intel Core i3-7100
Оперативная память: 4 GB ОЗУ
Видеокарта: NVIDIA GeForce GTX 750
DirectX: Версии 11
Место на диске: 5 GB

Рекомендуемые:
ОС: Windows 10 64 bit
Процессор: Intel Core i5-9400
Оперативная память: 8 GB ОЗУ
Видеокарта: NVIDIA GeForce GTX 960
DirectX: Версии 11
Место на диске: 10 GB

Tree of Life: Oddria! – это экшен в открытом мире с необычной графикой и симуляцией выживания, где десять случайных игроков оказываются на необитаемом острове и стараются выжить в суровых условиях. Им необходимо построить дом или шалаш, развести костер, собрать ягоды, наловить рыбы или найти источник питьевой воды. Помешать могут другие выжившие, злобные монстры и загадочные тайны острова.

Выживание в мире игры подразумевает кооперативное прохождение, хотя в настройках можно включить возможность наносить урон других выжившим. Вместе гораздо легче строить дом, защищаться от зомби, собирать ресурсы и изготавливать необходимые предметы. Также можно занимать фермерством, охотой, исследованиями мира, купанием в море и даже покорением действующих вулканов!

Информация о сетевых режимах:

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Конфиденциальность приложения

Сбор данных не ведется

Разработчик не ведет сбор данных в этом приложении.

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Конфиденциальность приложения

未收集数据

开发者不会从此 App 中收集任何数据。

phylogeny-explorer/explorer

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README.md

The Phylogeny Explorer is a navigable, online encyclopaedia of the entire evolutionary tree of life.

Join the Facebook Group to get involved with the community that is making this project a reality.

Read Getting Started With Development to learn more about how to help develop the explorer.

The software (code) is distributed under the MIT License. But the DATA is not. The data is distributed under the «Creative Commons, Attribution-NoDerivatives» license.

Reasoning: In order to prevent fragmentation and ensure the data is properly vetted, the data must go through a verification process in order to be included in the Phylogeny Explorer Project database.

About

The Phylogeny Explorer is a navigable, online encyclopaedia of the entire evolutionary tree of life.

Life Explorer-Master Your Life 12+

XUNTONGWUXIAN(Guangzhou)Network Technology Co., Ltd.

Suunniteltu iPhonelle

iPhone-näyttökuvat

Kuvaus

Love Challenge:
Wondering if you lover are love you enough? Come and challenge our love game. Life Explorer has selected a large number of love tests, waiting for you to challenge them!

Discover life:
Life Explorer collects interesting encyclopedia articles around the world, they can help you open the door to the unknown world, satisfy your curiosity and learn more useful knowledge.

The app is free to download, but we also offer a subscription service, and subscribers can enjoy more features and content.

If you have good suggestions or ideas, you can contact us at the following email address: lifeexplorer2020@outlook.com

Terms of Service : http://resource.bestlifementor.com/agreement/lifeexplorer/service.html
Privacy Policy : http://resource.bestlifementor.com/agreement/lifeexplorer/privacy.html

Explore yourself and master your future at this moment!
Download and play it now!

Tree of Life: Oddria!

В Tree of Life: Oddria! пользователь будет управлять забавным персонажем со странными пропорциями, наблюдая за его увлекательными приключениями на острове. Он и еще несколько человек потерпели крушение корабля и теперь должны приспосабливаться к новому дому. Поскольку главная задача обитателей этого места заключается в выживании, сильно расслабиться не получится, но, несмотря на это, пользователи получат хорошие впечатления от прохождения. Игровой процесс Tree of Life: Oddria! состоит из нескольких элементов. Днем герои заняты поиском еды и ресурсов, а ночью они должны быть начеку, чтобы дать отпор кровожадным ходячим мертвецам, жаждущим убийства. Герой может и сам отправиться на охоту для сбора душ монстров, благодаря которым у него получится попасть на вершину острова.

Также придется строить и укреплять дом, заботясь не только о безопасности, но и комфорте. Природа здесь сурова, поэтому нужно убедиться, что особенности климата не сократят продолжительность жизни протагониста. Чтобы получить пропитание, пользователю придется выращивать продукты на личной ферме, разводить скот и рыбачить. Для прохождения доступны одиночный режим, где противником выступает искусственный интеллект, и мультиплеер, где получится создать собственную карту. Мир здесь открытый, поэтому исследовать его можно неограниченно. Кто знает, что ждет персонажа впереди?

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer-Master Your Life 12+

Daily Horoscope & Baby Maker

XUNTONGWUXIAN(Guangzhou)Network Technology Co., Ltd.

Designed for iPhone

iPhone Screenshots

Description

Love Challenge:
Wondering if you lover are love you enough? Come and challenge our love game. Life Explorer has selected a large number of love tests, waiting for you to challenge them!

Discover life:
Life Explorer collects interesting encyclopedia articles around the world, they can help you open the door to the unknown world, satisfy your curiosity and learn more useful knowledge.

The app is free to download, but we also offer a subscription service, and subscribers can enjoy more features and content.

If you have good suggestions or ideas, you can contact us at the following email address: lifeexplorer2020@outlook.com

Terms of Service : http://resource.bestlifementor.com/agreement/lifeexplorer/service.html
Privacy Policy : http://resource.bestlifementor.com/agreement/lifeexplorer/privacy.html

Explore yourself and master your future at this moment!
Download and play it now!

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Designed for iPad

Screenshots

Description

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

What’s New

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

App Privacy

Data Not Collected

The developer does not collect any data from this app.

Privacy practices may vary based on, for example, the features you use or your age. Learn More

Life Explorer 4+

Theo Calmes

Разработано для iPad

Снимки экрана

Описание

Life Explorer allows you to dive deep into the world of Conway’s Game of Life.

Gigantic world, supports 300,000 cells!

Customize the look and feel of your cells and grid.

Comes with hundreds of pre-built patterns.

Save your own creations.

Zoom-in and pan around the game world.

Что нового

Fixed a couple of bugs and add ability to run on modern devices and iOS versions.

Конфиденциальность приложения

Data Not Collected

The developer does not collect any data from this app.

Lifemap: Exploring the Entire Tree of Life

Affiliation Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Villeurbanne, Lyon, France

Lifemap: Exploring the Entire Tree of Life

Figures

Abstract

The Tree of Life (ToL) is meant to be a unique representation of the evolutionary relationships between all species on earth. Huge efforts are made to assemble such a large tree, helped by the decrease of sequencing costs and improved methods to reconstruct and combine phylogenies, but no tool exists today to explore the ToL in its entirety in a satisfying manner. By combining methods used in modern cartography, such as OpenStreetMap, with a new way of representing tree-like structures, I created Lifemap, a tool allowing the exploration of a complete representation of the ToL (between 800,000 and 2.2 million species depending on the data source) in a zoomable interface. A server version of Lifemap also allows users to visualize their own trees. This should help researchers in ecology and evolutionary biology in their everyday work, but may also permit the diffusion to a broader audience of our current knowledge of the evolutionary relationships linking all organisms.

Citation: de Vienne DM (2016) Lifemap: Exploring the Entire Tree of Life. PLoS Biol 14(12): e2001624. https://doi.org/10.1371/journal.pbio.2001624

Published: December 22, 2016

Copyright: © 2016 Damien M. de Vienne. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: Ancestrome project (grant number ANR-10-BINF- 01-01). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: MRCA, most recent common ancestor; OSM, OpenStreetMaps; OTOL, Open Tree of Life; ToL, Tree of Life

Provenance: Not commissioned; externally peer reviewed.

Introduction

An exhaustive knowledge of the evolutionary relationships linking all organisms (the whole biodiversity) would produce a tree-like structure, referred to as the Tree of Life (ToL). The decrease of DNA sequencing costs [1] associated with improved phylogenetic and phylogenomic methods for reconstructing phylogenetic trees [2–4] helped resolve, in the recent years, many parts of this ToL. The aggregation of these portions produces a phylogenetic classification scheme describing the evolutionary relationships among the species under consideration [5]. The NCBI taxonomy is one of these classifications, describing relationships among

1.4 million species (as of Oct 2016), that is widely used by biologists. Another version of the ToL, the Open Tree of Life (OTOL), was published recently [6]. It adds to the taxonomy some evolutionary information retrieved from published phylogenetic trees, in order to provide a more accurate and more comprehensive description of the ToL. It currently contains around 2.2 million species.

Despite huge ongoing efforts to assemble the ToL [6,7], no tool exists today to explore it entirely and interactively in a satisfying manner. More generally, the visualization of very large trees still remains a challenge [8]. A parallel has been drawn earlier between what has been achieved in cartography with the development of Google maps or OpenStreetMaps [9] (OSM), and what could be done for exploring the ToL [8,10]. The logic behind the use of the cartographic paradigm for visualizing a taxonomy is straightforward: like geographic entities (countries, regions, cities, etc.), taxonomic levels have names (kingdoms, families, classes, orders, genera, etc.) and are nested within each other. Consequently, it is possible to propose a visualization where zooming in increases the level of detail displayed while hiding upper-level information. This idea was first exploited in a tool called OneZoom [10] that allows visualizing, on demand, large trees by zooming and panning. This tool introduced the concept of deep zooming for visualizing large phylogenies (along with [11]), which motivated other research along the same line, including the present one. The main limitation of OneZoom that makes it inappropriate for visualizing the complete ToL is that the fractal representation it uses prevents the presence of multifurcations in the trees (one node connected to more than two descendants), which is very common (83% of the nodes in the NCBI taxonomy and 72% in the OTOL are not binary).

Three Versions of the Tree of Life

I developed Lifemap, a tool largely inspired by the technology developed for cartography that is free of the limitation described above. Its approach differs from that of OneZoom [10], both in the representation of the tree and in the way images are displayed and interacted with on the screen. This allows a fast and smooth exploration of the biggest tree ever proposed on a single page for exploration.

Lifemap uses a representation inspired by Treemaps, a method developed in the field of computer sciences in the early 90s for turning file system tree structures (directories in a computer) into a planar space-filling map [12] for clearer visualization. In Treemaps, directories are represented by rectangles that are recursively split in as many subrectangles as there are subdirectories, leading to a fully-filled map. The size of the rectangles is proportional to the number of files in each directory. This approach cannot be directly used to visualize the ToL because it is incompatible with the representations of links between the nodes, which is important in an evolutionary context where branches represent time and must be visible. I, however, kept the idea of filling the map recursively, using a base shape whose size is proportional (but with a square root transformation) to the number of elements in it. In Lifemap, this base shape is a half-circle, and the way these half-circles are arranged within and between each other (Fig 1) ensures that there is space to draw all the branches and guarantees that the branches never intersect (unlike other solutions, [13]).

OneZoom: A Fractal Explorer for the Tree of Life

Affiliation Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom

Affiliation Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, United States of America

OneZoom: A Fractal Explorer for the Tree of Life

Figures

Citation: Rosindell J, Harmon LJ (2012) OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biol 10(10): e1001406. https://doi.org/10.1371/journal.pbio.1001406

Published: October 16, 2012

Copyright: © Rosindell, Harmon. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: James Rosindell was funded by the Natural Environment Research Council (grant NE/I021179). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: IFIG, interactive fractal-inspired graph

We Can’t See the Trees for the Data

Our knowledge of the tree of life—a phylogenetic tree summarizing the evolutionary relationships among all life on Earth—is expanding rapidly. “Mega-trees” with millions of tips (species) are expected to appear imminently (for example, see http://www.opentree.wikispaces.com). Unfortunately, there has so far been no practical and intuitive way to explore even the much smaller trees with thousands of tips that are now being routinely produced. Without a way to view megatrees, these wondrous objects, representing the culmination of decades of scientific effort, cannot be fully appreciated. The field really needs a solution to this problem to enable scientists to communicate important evolutionary concepts and data effectively, both to each other and to the general public.

Displaying large trees is a hard problem that has so far resisted solution. We are still waiting for the equivalent of a Google Maps. (Page in [2], June 2012)

In this manuscript, we introduce a new approach that solves the problem. Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps.

Escaping the Paper Paradigm

Much of the difficulty with phylogenetic tree visualization (and with data visualization more generally) is that we all too often constrain ourselves to the “paper paradigm”—the practice of displaying data in ways that are optimized for printing on paper. Many applications fail to take full advantage of the freedom that a computer display gives us over printed sheets; we read and write documents and browse web pages that are constrained to be optimal for printing, but fail to realize that such documents are unlikely to be optimal for visualization on a digital device. Of course, the paper paradigm of visualization seems most natural to us, but is this only because we are too familiar with the paper format? Society is undergoing a rapid transition in terms of its use of computing devices. Computers have enabled us to generate and store large amounts of data that would not have been possible using paper. We now need to take the next step with a transition to data visualization that is optimized for interactive displays rather than printed paper.

Recent methods of phylogenetic tree visualization attempt to buy extra space in the paper paradigm—for example, by using walls consisting of multiple displays (see Figure 7a in [3]). This approach is costly and does not give tree visualization capabilities to the masses, which is what is really needed. Furthermore, expensive display technology does not really solve the problem—according to our estimates, even the most advanced technology, such as NASA’s “Hyperwall2” of 128 LCD displays [4], would not be large enough to clearly display 5,000 tip trees using conventional techniques. Other currently available methods make exploration of phylogenetic trees interactive, enabling the user to expand or magnify parts of the tree [5] that may be too small to see in detail at the scale of the screen. Hyperbolic tree browsers [6],[7] are a good example of this and they can display large trees, but users do not find them intuitive [3] and we don’t see the inclusion of rich metadata as being realistically achievable. An optimal tree viewer should be able to 1) handle large megatrees; 2) be explored in an intuitive way; 3) incorporate significant amounts of metadata; and 4) be visually appealing and immersive, especially if public users are expected. We have yet to find an existing viewer that we feel convincingly meets these requirements.

Zooming in on a Potential Solution

We introduce a new phylogenetic tree viewer that allows interactive display of large trees. The key concept of our solution is that all the data is on one page so that all the user has to do is zoom to reveal it—hence the name OneZoom (http://www.onezoom.org). Our interface is analogous to Google Earth, where one can smoothly zoom into any local landmark from a start page showing the whole globe, recognizing familiar landmarks at different scales along the way (e.g., continents, countries, regions, and towns). Equivalently, OneZoom can zoom smoothly to one tip of the tree of life—say, human beings—passing the familiar clades of animals, vertebrates, mammals, and primates at different scales along the way (see Figure 1, which used data from [8]). Trees with millions of tips may require a page of paper larger than the observable universe to be printed: they break the paper paradigm, but on screen, users can still easily zoom in through the tree to any point of interest (see Figure 2, which used data from [9]).

In order to place the phylogenetic data on a scalable two-dimensional map, OneZoom uses concepts inspired by fractal geometry. Fractals are objects that look similar at different scales and have a dimension that is not a whole number; they often appear in the natural world [10],[11]. For example, an effective lung requires a large surface area to be packed into a small a volume—its surface is therefore so convoluted and labyrinthine that at some scales it can be regarded mathematically as having a dimension greater than two (a surface) but less than three (a solid object). Fractal geometry can be used to produce stunning and apparently complex images—including many that resemble trees and other plants—based on remarkably simple sets of underlying growth rules that are applied repeatedly (“L-systems” [12]). Our algorithms (Text S1) build on this to produce a zoomable object, inspired by fractals, but embellished with useful data (such as images, graphs, and text) at every scale—an interactive fractal-inspired graph (IFIG). We give the branches of the tree a width so that they appear as filled shapes rather than narrow lines and thus can contain rich metadata within them that is easily accessible through zooming. Ultimately, these methods should make it possible to usably view the complete tree of life together with all its metadata on any modern computing device (Box 1 and Software S1, S2).

Box 1. Features of OneZoom

Fractal structures

By varying the angles between the branches and the successive ratios of branch lengths and widths, many different fractal structures are possible for an IFIG of a phylogenetic tree (Figure 3). By allowing these to be defined uniquely at each split according to the tree’s properties, the balance can be seen at a glance for every part of the tree.

Time scales and dated trees

Many phylogenetic trees also include branch lengths, which provide information about the time scale of evolution. Our software plots the phylogeny in a shape that can reflect the topology and balance, whilst the timescales are expressed in ways that are independent of shape including color, text, and animation. In future work it should be possible to express timings with additional new fractal forms.

Polytomies

Phylogenetic trees frequently include polytomies, which are nodes with more than two descendent branches. These generally represent phylogenetic uncertainty in the relationships among clades. Our software can highlight the nodes that make up polytomies in one of a number of ways, or, alternatively, it can not draw branches of length 0 so that polytomies appear as physical breaks. In the future, it should be possible to display polytomies as a number of branches joining at a single point.

Search functionality

In a tree of the proportions OneZoom can visualize, it is necessary to have an efficient search function so that users can find leaves or clades easily. OneZoom’s search function ranks clades according to the total number of search hits and the proportion of tips in a clade that represent a hit. Search results can be highlighted on the tree or shown instantly. OneZoom also allows users to fly through the tree to search hits with an animation feature.

Metadata

There is no theoretical limit to the amount of metadata that can be put on a leaf or branch of the tree because these data can be displayed at any size and zoomed in on. Allowing branches to have a thickness assists the concept of scale when zooming and allows data such as graphs, maps, paragraphs of text, and images to be embedded inside branches and leaves. There are many further possibilities for using the colors and shapes of branches and leaves to reflect different metadata (Figure 4).

Zooming to reveal further details as implemented in OneZoom feels intuitive because it is akin to the way we explore the real world by moving closer to objects of interest to see them in greater detail. Data is always displayed in both intuitive and raw formats. For example, in the “natural” view of the tree of life (see Figure 3), the balance at each node (indicative of the ratio of species richness in each descendent branch) can be taken in at a glance from the thickness and angles of the branches, but the raw numbers can also be found by zooming in on the nodes. In OneZoom, we can be wasteful of space because there is an infinite quantity of space available. For example, structures that do not form a strict hierarchy, such as food webs, could be expressed by repetition of the same elements in multiple places. OneZoom is effective without fast processors, large high-resolution screens, stereoscopic vision, or multi touch inputs; however, these technologies, where available, could be straightforwardly exploited to provide an enhanced user experience.

Visions for the Future

A significant issue with all tree visualization is that the ordering of descendent branches from any node and the positions in space of any node can be changed whilst still describing exactly the same tree [3]. This means that there are many ways to view a tree, each of which might emphasize different properties. We included three forms in the first release of OneZoom (see Figure 3), but all these have the common property that evolutionarily distinct species and clades appear larger. The natural view emphasizes tree balance over rates of diversification. We envisage the development of further forms for OneZoom in the future. For example, nodes could be aligned based on their dates using a non-linear timescale, with branches becoming progressively thinner towards the present day. This would complement the other forms by placing emphasis on diversification rates, timescales, and the species richness of clades; the tree would also then appear more like a familiar cladogram.

The concept of deep zooming for data presentation is not novel (see for example http://www.prezi.com), but we believe the idea has been under-utilized. We suggest that this may be because suitable methods for automatically laying out information on an infinite space are lacking; we hope that the OneZoom concept of using fractals will help resolve the problem. The fractal forms used within OneZoom need not look like trees, and further alternatives may be better and allow OneZoom to have applications outside of biology. For example, we speculate that an IFIG of the global financial markets could give an intuitive overview of the relative performance of each sector and subsector whilst allowing the more minute details to be revealed by zooming. Scientists exploring a scatter plot or color map could zoom in on any point or pixel to reveal further graphs, text, and information associated with just that data point. The files on a computer, the Internet, news, mind maps, genealogies, online stores, complex software structures, and industrial plants are all further examples of large and complex data sets that we imagine could be explored with OneZoom, even on a smartphone.

We most look forward to seeing OneZoom bring to life the remarkable and powerful phylogenetic datasets that many evolutionary biologists have strived to collect over recent years. We hope, together with a range of collaborators, to use OneZoom in the near future as a way to tackle the challenge of public education about evolution. For example, we envisage putting “microdots” on the branches of the tree, that when zoomed into, show fossil images and other evidence backing up the hypothesized evolutionary path of that branch. A richly annotated IFIG may help make the evidence, logic, and beauty of evolution easy to explore and understand in a way that is compelling and fun. The phylogenetic tree is also the most logical structure within which to explore the breadth of biodiversity on Earth, and so OneZoom could potentially be used to browse existing ecological databases of species such as the Encyclopedia of Life (http://eol.org/). These databases do face difficulties besides visualization, for example lack of available data and inconsistent naming of species. Nevertheless, we are confident that these problems will eventually be resolved simply by making gradual improvements to the many databases over a long period of time.

Our dream for the more distant future is an easily accessible web page presenting all that we know about life on Earth in one place. The logical way to do this is to build around the tree of life visualized using OneZoom; we may yet see the Google Maps equivalent for all life on earth.

Supporting Information

Software S1.

A self-contained version of the OneZoom software as a single html file. This file contains an embedded mammal tree using data from [8] and incorporates IUCN red list metadata and common names [13]. For further information we refer readers to the website www.onezoom.org, launched on the day of publication. Phylogeneticists are encouraged to download the latest editable version of OneZoom from the website and use it to create personalized IFIGs of their own data that can then be redistributed as supplementary material, in talks, and on the web. We welcome feedback on the software emailed to mail@onezoom.org.

Software S2.

A self-contained version of the OneZoom software as a single html file (as Software S1). This file contains an embedded 408,135-tip phylogeny of small-subunit RNAs using data from SILVA [9] and is zipped to allow easy download.

Text S1.

Technical details of the algorithms used in OneZoom.

Acknowledgments

We thank Rod Page and one other anonymous reviewer for their comments on earlier versions of the manuscript. We also thank the following people for their feedback, suggestions, and support (in alphabetical order): Austin Burt, Stephen Cornell, Jonathan Eastman, Robert Ewers, James Foster, Mark Hammond, James Keirstead, Mike Kiparsky, Bill Kunin, Curtis Lisle, Georgina Mace, Jack Nijjar, Ian Owens, William Pearse, Matt Pennell, Albert Phillimore, Jacqueline Phillimore, Andy Purvis, Erica Bree Rosenblum, Jill Rosindell, Owen Rosindell, Nilay Shah, Nina Thornhill, and Oliver Worsfold.

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