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Messages posted by: Tim Endres  XML
Profile for Tim Endres -> Messages posted by Tim Endres [6]
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If you are a BioLogo fanatic like I am, you will quickly accumulate lots of interesting turtles. Then you will begin to wish you could organize those turtles. Part of the solution lies in proper use of the Turtle Web website, which provides Portfolios and Galleries to help you organize and share your turtles.

The BioLogo application is not the most advanced Windows application you will ever use. It was designed mostly as a proof of concept, so it does not provide many features that you might expect (e.g., scrollbars, documents, etc.).

However, there is one simple mechanism in BioLogo that you can use to help you organize your turtles: Populations.

Think of a Population in BioLogo the same as a Portfolio on Turtle Web. It is a collection of turtles, like a folder containing papers. Of course, most of the time you are using a population for evolution, not organization. But populations can serve both purposes.

For example, there are times when I find myself with a little time on my hands. So I open BioLogo to fish for some new turtles. What I do is open two population windows. The first population will be the one that I evolve. The second will be the one I use to save the turtles I find. So, I spend my time evolving population one. When I see a turtle that I like, I select it, copy it (Ctl-C), then paste it (Ctl-V) into population two. I will save population two when I am done, and reload it the next time I open BioLogo. I will continue this until the population is full of turtles that I wish to save.

I have a folder on my hard drive that is full of populations of turtles that I have collected over the years.

Finally, once you have filled a population with awesome turtles, you can then upload the population to the Turtle Web to populate a Portfolio. Add this newly uploaded Portfolio to one of your Galleries, and anyone in the world can browse your turtles.
Look for the login menu on the left side of the page, or click on the "Login/Register" link http://www.evolvedturtle.com/turtleweb/loginpage.do in the navigation bar at the top of the page. Locate the Password field and just to the right of the field label "Password" should be a link "Forget?" or "Forgot Your Password?". Click on this link http://www.evolvedturtle.com/turtleweb/reqpassreset.doand enter the email address that you use to login. Turtle Web will send an email message to you with a link and instructions on how to reset your password.
This topic will discuss the relationships of turtles, portfolios and galleries on the Turtle Web website.

A turtle is the most obvious, and easiest to understand, of the items defined on the website. A turtle is exactly the same item that you evolve in the BioLogo application. It is a program that was evolved to draw a picture. When you upload a turtle to the website, you transmit only the turtle's program. Once the turtle's program is uploaded, you will see its thumbnail, and you can click on the thumbnail to see the full size picture that the turtle draws. You can give the turtle a name and a description, as well as define the number of steps it should draw and the pensize it should use for drawing.

A portfolio is a collection of turtles. You can think of it as a population similar to the populations you evolve in BioLogo. In fact, you can upload a turtle population directly into a portfolio. However, a portfolio is not a population, in the sense that the turtles it contains did not have to come from the same BioLogo population, and thus, were not necessarily evolved together and might not have any genetic relationships. The turtles may have been a population in BioLogo that was uploaded to the portfolio, but they may also be turtles uploaded individually from many different populations. Another way to look at a portfolio is simply as a folder containing turtle drawings.

A gallery is a collection of portfolios and other galleries. Galleries are used both to help user's organize their portfolios, and to present portfolios to users browsing the website. Because a gallery can contain other galleries, the galleries are organized in a tree structure. The root gallery, named 'Main Gallery' on the website, is the parent of all other galleries. Each user has their own gallery under which they can organize their personal galleries and portfolios. The best way to conceptualize galleries is to think of them the same way you do the folders on your hard drive. Folder contain folders and files. If you think of it in this fashion, the folders are galleries and the files are portfolios, and the files (or portfolios) contain turtles.

Portfolios, as a general rule, are not browsable by a Turtle Web visitor. Portfolios are meant as an organizing tool for the owner of the portfolio. Portfolios help to group turtles. However, to make the website more interesting as a general attraction, it is desirable to present turtles to the visitor who wishes to browse. Yet, as a rule, a user's portfolio of turtles may not be the content or the selection that the user wishes to present to the public. For this reason, galleries are used for public presentation to organize and present specific portfolios. This allows a user to have a large number of portfolios, and yet, present only some of them to the public at large. It also allows for the organization and presentation of portfolios of general interest. For example, a gallery could be defined for the Portfolio Of The Week, which might be voted upon or selected based upon some criteria such as view count.

When you registered with Turtle Web, your account was created with a portfolio named "My Favorites", which was placed into a gallery created under the "User Galleries" gallery and named with your full name. Then, some sample turtles were placed into your My Favorites portfolio. This was done to help you get started. It is also nice to have a consistent user model in the sense of everyone having a portfolio of favorite turtles available under their gallery. Of course, you are free to delete the portfolio.

Finally, galleries have the concept of privacy. By default, a gallery is marked as public, meaning that the portfolios within that gallery may be viewed by any user on the site including guest visitors. If a gallery is marked private, the gallery and its portfolios will be visible only to their owner. This allows users to organize their portfolios within galleries without making them public.
Paste Turtle

The quickest and simplest way to upload a turtle from your BioLogo application to a portfolio in your Turtle Web account is to perform a Paste Turtle command.

  • First, before you can upload a turtle to the Turtle Web website, you must evolve one in your BioLogo application. If you are not clear on how to do this, please refer to the BioLogo QuickStart guide here: http://www.evolvedturtle.com/turtleweb/doc.do?page=quick

  • Login to your Turtle Web account.

  • Click on the Portfolios link in the navigation bar at the top of the page.

  • Click on the "Paste Turtle" link in the "Portfolios" menu on the left side of the page.

  • Select "My Favorites" from the Turtle Portfolios combobox when the Paste Turtle page appears.

  • Enter a turtle name in the Turtle Name field.

  • Modify the pensize and maxsteps fields if you wish.

  • Enter a note for the turtle.

  • In the Population window of your BioLogo application select the turtle that you wish to upload.

  • Select Copy from the Edit menu to copy the turtle's program to your computer's clipboard.

  • Back in your browser:

  • Click the mouse in the Turtle Program text field to move the text focus to that input area.

  • Select Paste from the Edit menu to paste your computer's clipboard contents into the Turtle Program text input field.

  • Click the Upload Turtle button to send the turtle to the server.

    At this point, your browser will upload the turtle's program and other information to the server. After a moment, your browser will be redirected to display the turtle's definition.
  • Release 3.5.4 of the Windows application BioLogo is now available for download at http://www.evolvedturtle.com/turtleweb/downloads.do
    The first time that you create a new population in BioLogo, you are presented with the New Population dialog box. The dialog contains a few text fields, and a number of sliders. Other than the number of turtles in the population, most of the settings in this dialog are a mystery. This post will attempt to document this dialog.

    The dialog inputs are broken down into three categroies:

  • Population
  • Probabilities
  • Fitness Multipliers


    The population inputs deal with the initial generation of the turtle population.

  • # Turtles The number of turtles the population will contain.

  • Max Children The maximum number of children in a program node. When a turtle program is parsed, it looks like a tree. Children are nodes that all share a common parent. Increasing this number allows turtle programs to get more complex.

  • Max Depth The maximum number of levels of children nodes a program can contain. This value also controls the complexity of turtle programs.


    The probability settings affect the population generation and evolutionary processes. When the initial population is being generated, each turtle's program is randomly constructed by rolling dice to determine the program's nodes. Each time you evolve a new generation, there are certain steps that depend on the roll of dice. For example, the selection of two turtles for mating is done randomly. The parameters below affect the "dice" and how they roll.

  • Crossover When two turtles are chosen to mate, there is a question of the resulting offspring. The offspring can be a result of "crossover" of the two parents, or they can be straight clones of their parents. This probability determines how often crossover occurs, versus cloning. The higher this value, the higher the probability of crossover.

  • Mutation When a turtle is chosen to reproduce, there is always the chance of a mutation. An incorrect copying of the turtle's program or DNA. The higher the value the higher the probability of mutation. Be warned, if this value is too high, your populations will become "unstable".

  • FuncNode When a population is initially generated, each turtle gets a randomly generated program. Each program consists of two types of "nodes": function or terminal. Terminal nodes are "leaves on the tree", because they have no children nodes. For example, FORWARD_1 is a terminal, since it moves forward one step and nothing more. REPEAT_5 is a function node, since it has children nodes, and will repeat its children's steps five times. The value of this slider will determine how often a function node is generated versus a terminal node. The higher the value, the higher the probability of a function node. The more function nodes your turtle's program contains, the more complex the program can be.

  • Color When a population is initially generated, each turtle gets a randomly generated program. This slider determines how many color change instructions will be included in that program. The higher this value, the higher the probability that a terminal node will be a color instruction, as opposed to any other terminal instruction. In other words, the higher this value, the more colorful your turtles will tend to be.


    Each time a turtle population is asked to evolve a new generation (reproduce), the process involves randomly selecting two turtles to mate and performing the crossover which produces two children. The random selection of two turtles to reproduce is influenced by the "fitness" factor. Each turtle is assigned a "fitness" based on certain measurable characteristics of the drawing that the turtle makes. The fitness factor is computed by adding together a number of characteristics of the turtle. Each characteristic has a "weight", which makes the characteristic more or less important. The higher the weight, the more important. Each of the multiplier sliders in the dialog sets the weight for the named characteristic.

  • Forward The number of forward steps that the turtle makes. The higher this multiplier, the more the turtle draws.

  • Turns The number of turn instructions the turtle performs. The higher this multiplier, the more the turtle will turn.

  • Loops The number of times that the accumulated turning the turtle makes adds up to 360 degrees in either direction. The higher this multiplier, the more "circling" your turtle will perform.

  • Colors The number of color changes the turtle makes. The higher this multiplier, the more colorful your turtles will tend to be.

  • Repeats The nuimber of REPEAT instructions your turtle has performed. The higher this multiplier, the more complex, and yet repetitive, your turtles will be.

  • Repititions The number of steps within REPEAT instructions. The higher this multiplier, the more times your turtle will repeat parts of its drawing, typically leading to more symmetry.
    Profile for Tim Endres -> Messages posted by Tim Endres [6]
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