Comp. Sci. / Eng. News

Help requested of readers to advance design detection in DNA

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DNA Skittle was a DNA visualization program pioneered by John Sanford to help identify design features of DNA that are recognizable to the human visual system. The program is available for free, but the Skittle developers need help with ensuring it is usable through internet channels.

Can you spare 10 minutes and review the product and post comments here at UD or:
CEU DNA Skittle Feedback. If you want an account at CEU just post here at UD that you want an account, and I’ll have a temporary password emailed to you (your UD profile email) using your UD handle as your CEU username.

Here is the first round of feedback the Skittle team needs:

Are all the buttons functional or does it lock up and not respond?

The browser which DNA Skittle may have been developed on may not be the browser you are using, and if the buttons don’t work on your browser, the Skittle developer team needs to know.

State what kind of computer, operating system and browser you are using.

Any other helpful comments are welcome, especially relating to the implementation of DNA Skittle from an Information Technology standpoint.

Here is the website:
www.DNASkittle.com

20 Replies to “Help requested of readers to advance design detection in DNA

  1. 1
    TSErik says:

    I’d like access to the CEU site.

  2. 2
    scordova says:

    Hi TSErik,

    There is a username already there by the name of “T.S.Erik”. If that is you, you should be able to change the username if you like. Let me know if you have problems.

    Thanks for responding.

    Sal

  3. 3
    TSErik says:

    That should be me. I thought I remembered registering already. I forgot that for that site I used ‘.’ in the username. Thanks Sal!

  4. 4
    JoeCoder says:

    I knew they’d been working on it for a while but didn’t realize it had been released. When it works it looks really cool and seems useful. However in both the latest versions of firefox and chrome I often get a security error on draw_canvas.js line 174:

    Uncaught SecurityError: Failed to execute ‘getImageData’ on ‘CanvasRenderingContext2D’: The canvas has been tainted by cross-origin data.

    Here’s the complete stack trace:

    draw_canvas.js:174 – drawRasterGraph()
    draw_canvas.js:161 – drawGraph()
    draw_canvas.js:131 – anonymous function
    jquery-2.0.1.min.js:4 – x.extend.each()
    draw_canvas.js:128 – drawGraphs()
    draw_cavas.js:36 – anonymous function

    It looks like the rendering canvas is pulling in data from another site, and the browser won’t let it re-read that data due to security issues. Hoping this gets fixed soon so I can play with it some more.

  5. 5
    jstanley01 says:

    I’ve spent eight or ten minutes clicking around (Xp, Firefox v. 28.0), having about as much idea of what I’m doing as a Kindergartener. I can’t get the thing to hang up, but don’t worry. Having an unexpected day off from work, I’ll keep trying to see if I can break it… 😀

    UPDATE: On the intro page, both buttons work fine. But I’m getting no responses clicking the four links beginning with “What is….?”

    Another thing, using the browser’s back arrow does nothing. Okay wait a minute. Now it is working…

    Scrolling using the arrow keys on the default display (Human (hg19) > chrY) seems to freeze up fairly quickly; e.g., will scroll to the bottom but not back up.

    Hope this helped…

  6. 6
    scordova says:

    I can’t get the Desktop version of skittle to download. Anyone else have the problem?

    Ok, here is the situation. I’m writing up a list of DR (deficiency reports) and am collecting them on behalf of Dr. Sanford. We’re trying to work out a time to conference to discuss user needs, so your input is valuable.

    DNA Skittle was showcased at the Cornell conference and it has already passed peer-review. See:
    http://www.biomedcentral.com/1471-2105/10/452

    The project has been kept somewhat under wraps especially while it was going through the peer-review process.

    It is not specifically an ID project, but well, like all biological analysis, one can’t help but draw the inference when it’s staring you right in the face. 🙂

    The project is now going into a phase where it might be useful that researchers know it exists. When I spoke to Dr. Tomkins at ICC 2013, he said he uses DNA Skittle!

    Chormosome banding is blatantly obvious just looking at the Chromosomes, but there are many other kinds of design structures that DNA skittle is optimized to identify and locate.

    There is an on-going (perhaps never ending) debate over the frequency of transition vs. transversion mutations. There are other kinds of debates about what random DNA mutations should look like. When you use Skittle, it sort of destroys notions that DNA is randomly organized.

    The colored dots and their arrangement visually emphasize grammatical structures readily.

    Thank you all for your inputs and help!

  7. 7
    snelldl says:

    Looks like the link to the desktop version is wrong or the site has the wrong start page:

    http://genomeskittle.org/

  8. 8
    snelldl says:

    I’m using MSIE11, and none of the top level menu items go anywhere (What is Skittle, Visualizations, etc.).

  9. 9
    snelldl says:

    I have the same issues as JoeCoder with the security error at File: draw_canvas.js, Line: 174, Column: 5

  10. 10
    JoeCoder says:

    Perhaps the developer has the cross-site security checks disabled in their local environment? It’s an easy thing to forget you have on and I know I’ve made bigger blunders myself.

    BTW Sal, how does one get into this line of work? Are they hiring? Is there even pay?

  11. 11
    scordova says:

    I think the developer generously volunteered a lot of his time for the first version of DNA Skittle. As far as I know, the other big simulation, Mendel’s Accountant was a labor of love and involved 7 people.

    There is occasional pay, perhaps not at the level of a typical IT professional.

    There are other “blackwork” projects that can’t be talked about, probably 50 geneticists, biologists and computer scientists involved. A few names are known like John Sanford, Jeff Tomkins, Paul Gibson, Robert Marks, Winston Ewert and others. Many have identities hidden to protect the guilty.

    The poly constrained DNA simulation — wow, that was under wraps. Even I didn’t know about that project. Wow!

    I don’t think one can make a living doing this right now. I feel some bitterness lots of money was donated to building the creation museum whereas basic research money is almost non-existent. I’m even more bitter that 40 million was wasted by the government for some national center for evolution. Their research projects are a bit of a farce, imho:

    http://www.uncommondescent.com.....ng-darwin/

    Dr. Sanford was independently funded from making the gene gun, so his activities now are a labor of love.

    John Baumgardner managed to get his catastrophic plate techtonic creationist idea funded by the government because it had application outside creationist theory.

    John Hartnett got 5.7 million in science grants because of his ability to build sapphire controlled atomic clocks and a host of other goodies. His YEC stuff makes hardly any money, if any, for him.

    Robert Carter was successful genetic engineer before joining CMI, etc.

    The last big funded initiative that I recall was the RATE project, and a lot of scientists worked for free. Most of the money was spent for lab tests (like getting diamonds and crushing them and testing them for C14!).

  12. 12
    JoeCoder says:

    Sal I’m convinced you’re some type of historian of creation science. Thank you for the detailed response.

    The poly constrained DNA simulation

    Was this part of Skittle? If not where can I find it?

  13. 13
    JoeCoder says:

    It looks like the links at the top of the page don’t work because it’s an https page but is loading jQuery from the google cdn over http. The browser gets scared because it’s insecure content and doesn’t load it. I think changing the jQuery url to https would fix the problem.

  14. 14
    scordova says:

    Was this part of Skittle? If not where can I find it?

    It wasn’t part of skittle as far as I know. I think the sim details are in the Cornell papers, or at least it will point you to the right people.

    If the sim isn’t public domain, maybe it needs to be made public domain!

    Winston is well-connected to Robert Marks who might have worked on the sim.

    Sal

  15. 15
    JGuy says:

    I’ve used skittle before. It’s interesting, but I don’t know enough about genetics to critique it well. I was simply using it to look for/at patterns in the DNA. I’d like to be able to change colors (customize colors) around more. And get skittle to allow for defining nucleotide sequences (triplets) and assign colors to them. For example, I’d like to have each triplet be a different color or an assignable color. With a default pallet for the genetic code.

    The only other improvement would be to create new transformations of the data that are greater than two dimensional displays, or that the current two dimensional display can be modified to customizable non-rectangular displays.

  16. 16
    JGuy says:

    I feel some bitterness lots of money was donated to building the creation museum whereas basic research money is almost non-existent.

    Don’t feel that way. It’s a personal choice people make where to send some of their monies. I think if CMI or those interested in YEC friendly projects need funds, they need to do more to ask for it instead (maybe straight-up ask on kick starter or something like that?). Also, AIG has a large pool of supporters they have developed a relationship with over the years – their work that has apparently paid off to allow them to grow and fund raise for their projects. I suspect CMI – though much smaller at this point I think – is on it’s way to building up for potentially the same kind of support.

  17. 17
    JGuy says:

    ps. I’d bet the potential well for donations is much much larger than you think. And would argue AIG’s creation museum is small in comparison to what could be collected. In fact, I’d be willing to bet that there would be plenty of non-YEC that would donate to these CMI or related projects for the sake of doing the interesting science. If one really wanted to do something for YEC and science, then he/she’d need to put disproportionately more effort into seeking funding than thinking of science projects to do with the little funds. Because, there are already good ideas on projects to do, imo.

  18. 18
    JGuy says:

    pps. I should re-enforce that the ultimate reason for pursuing these should not be for the sake of YEC or science, imo, but for God’s glory.

  19. 19
    DATCG says:

    If not to late Sal, please sign me up at CEU.

    Love to help QA, debug, new versions and releases.
    Test any browser not on a MAC.

    Read the paper by Seaman and Sanford. They showed hypothetical 3D cylindrical view. That’s great to see.

  20. 20
    scordova says:

    Hi DATGC,

    I just sent you an e-mail with your username and temporary password. Post here at UD if you have any problems logging in. You can change your password after you log in.

    Thanks for you willingness to help!

    Sal

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