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Biotech Education Graphics Software Science

Biochemistry Animations Using SVG 26

Posted by timothy from the save-your-questions-til-the-end dept.
Milo Fungus writes "I've been working on a project for my biochemistry research lab that may be of interest to a few Slashdotters. We study the enzymes in an important biochemical pathway that produces (among other things) terpenes, carotenes, and sterols. I have been making a web-based tutorial to summarize our research, with animations of the proposed reaction mechanisms of the enzymes. I'm finding that SVG is a very good tool for the job because it is easy to learn (because of my experience with HTML) and the file sizes are amazingly small, even for complex animations. The files are typically ~5 KB for a g-zipped animation about 1:00 minute long, compared to 2 MB or more for a lossy-compressed video file of the same length, which is locked into a certain resolution. I have been wanting to do this project ever since I saw Hongyun Wang and George Oster's animations of ATP synthase. I would appreciate any feedback about the tutorial's usablilty, etc."
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Biochemistry Animations Using SVG More

Biochemistry Animations Using SVG

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  • SVG Viewer (Score:2, Redundant)

    by I_Love_Pocky! ( 751171 )
    If you are looking for an SVG viewer (as I was), Adobe has one for download [adobe.com].

    • Re:SVG Viewer (Score:4, Informative)

      by I_Love_Pocky! ( 751171 ) on Tuesday May 25, 2004 @06:08PM (#9253932)
      Sorry, this is a more direct link [adobe.com].
    • Or you can just use a browser that can support SVG natively [mozilla.org].
      • Epiphany, which uses the mozilla engine, doesn't show SVGs it seems.

        Epiphany 1.0.8
        Mozilla 1.6

        Additionally, the page you linked to states that the Mozilla SVG implementation doesn't yet support animations (if I understand it correctly). So not only is it only in, I presume, a bleeding edge version, but even then it won't view this page!

        It's cool to pimp your fav. software, but it won't reflect well on Mozilla when you say it does stuff that it don't.

        • Re:SVG Viewer (Score:3, Informative)

          by Sparr0 ( 451780 )
          Epiphany should render SVG if you configure the engine with '--enable-svg' before you compile it. Ditto for Mozilla 1.6. That page doesnt say it doesnt support them, it says the support is lacking. Running through the 'official' SVG test suite Mozilla renders almost all of them perfectly.
          • I tend to be one of those guys that likes mostly packaged stuff. But fair enough, it's probably just my distro's fault (Debian). I'm not at all surprised that it wasn't compiled that way. :(

            I really should not judge open source software by using Debian since it tends not to be .. uh... optimal for desktop. *ducks and runs from debian fans*

            Thanks for the clarification.

    • Re:SVG Viewer (Score:2, Interesting)

      by Eric Pierce ( 636318 )
      I'm hopelessly depressed to see how little interest there appears to be on Slashdot with regards to SVG animations in web browsers.

      Is SVG not our only hope to usurp Macromedia's proprietary hold on all things vector on the internet?

      Sorry to wimper... Eric
      • If it makes you feel better, I would have to install flash if I wanted to look at any SWF files too.

      • Re:SVG Viewer (Score:3, Insightful)

        by azav ( 469988 )
        Flash's file format is open.

        The authoring tool is created by MM and is payware.

        Sooo, the format's open. If you're frustrated, time to get to work writing your own authoring tool.
        • No, the format is available. But it is absolutely under the control of Macromedia. So I would definetely not call it "open". Also, if I'm not mistaken they only make the previous version of the file spec available. SVG and SMIL are open on the other hand.
          • The term the use is "open" as in not proprietary. I remember the VP of products telling me this.

            Maybe it's not the same "open" as in open source.

            • They make the file format, so they can make money off of it. It is not in their best interest, to have a format that can be implemented better on a free platform. This is why they decide new features, to deprecate the superiority of the truly "open" alternatives.
  • I viewed your SVG animations using Mac OSX 10.3, in Safari 1.2.1 (v125.1), using the Adobe SVG viewer 3.0, and there was one noticable problem I thought perhaps you were unaware of. For some reason on my platform, the alpha in alpha-ketol was not rendering properly. In place of the alpha was an empty box (most probably a font problem). Interestingly, the HTML "MEP Synthase (&#945-ketol rearrangement)" showed the alpha just fine for me.

    Just thought you would like to know.

    Other than that, the anima

    • Yeah, I've noticed that problem. I bought a 12" iBook a few months ago and started doing my animations on it. That was one of the first things I noticed.

      There are big inconsistencies between the different versions of Adobe's SVG viewer. Version 3 for win32 doesn't support the end-marker attribute that I use for making arrowheads, but version 3 for Mac does. Version 6 (win32 only) is the only one that didn't crash Mozilla Firebird.

      Before I got my Mac I was using win32 for development, and version 6 sup

  • Mac?? (Score:2)

    by azav ( 469988 )
    Any mac viewers out there?

  • Feedback. (Score:3, Interesting)

    by azav ( 469988 ) on Tuesday May 25, 2004 @08:45PM (#9255101) Homepage Journal
    Ok, I've already mentioned that you need a mac viewer. For those people who use these macs.

    Your inspiration's example is terrible - with respect to bandwidth.

    It is good because it has Mpeg AND Quicktime. That's a choice that is nice. Almost everything plays mpeg1 and quicktime is a FREE and easy to get download that is xplat.

    The bandwidth on the QT is terrible - 852 Kbps. It is using the wrong codec.
    The bandwidth on the Mpeg 1 is also rather high - 355 Kbks.
    Quality on both is good.

    Bandwidth can be improved by exporting the quicktime to Sorenson or 3ivx and running a few comparison tests to compare quality and bandwidth.
    What is LOVELY about 3ivx is that is can create pure MPEG 4 output so Quicktime can create a movie that can be played outside of quicktime. Like in WMP.

    Using 3ivx I was able to get the videos output as pure MPEG 4 at almost identical quality at 150 K per second with just a few tests. That's taking a 5 meg movie and turning it to 860 K. I'm sure we could do better if we tried.

    Now, If you've got a mac plugin, I'd love to see those 5 K movies!!

  • Ok (Score:2)

    by azav ( 469988 )
    Thanks to someone else on this thread, I found an SVG viewer (adobe) and installed it. Safari required a restart, I restarted it.

    You really need to set up instructions for people who may not have svg viewers.

    Also, your animations were lovely but the greek characters were replaced with square blocks. Alpha, lambda, anything else, I can't tell what they are on the mac since they are square blocks.

    Looks like you've got a great start there. Just time to wrap up the details to bullet proof it.
  • SVG seems to me to be a very good user interface tool. Instead of programmatically defining objects, "UI" Artists could define it all with their authoring program, then set the files in an embedded SVG player for 'playback' and 'interaction'.

    Has anyone seen this done yet? I know that Flash animators are quite capable of creating very nice interactive unique interfaces which often put "Windowing systems" and "Standard GUI's" to shame ... what about the possibility that SVG can be used to replace/supplant/
  • It was great to see really good use being made of SVG, but I let myself get sidetracked by some of the technical comments elsewhere in this thread and managed to blow away my browser, so I'm writing this before attempting a second look.

    Having used the smallest possible amount of non-animated SVG on one of my own sites, I some time ago settled on the still current release Mozilla (1.6) with the Adobe plug in, because the SVG build for Mac really isn't there yet. There was a brief period in which I was check

    • I use Safari for developing, and I'm not sure what to do about the missing unicode character. I just looked through the SVG recommendation [w3.org], but I can't find anything about character entity references like in HTML. I suppose I could create an alpha using alternate glyphs [w3.org]. I'll have to think it over. That was one of my disappointments when I started using my Mac for SVG.

      I haven't ever used an SVG build of Mozilla, but Adobe's SVG viewer slows Firefox to a crawl on OS X. (I have a G3 with 128 MB RAM.)

  • I wish Mozilla (and friends) would ship with --enable-svg compiled by default.

    I know the SVG implementation in Mozilla isn't 100% (the builds I've tried do crash more often), but neither has the DOM-JavaScript implementation been 100% in all the major browsers all these years, and we've worked around it (albeit a pain but) with great success.

    I say turn SVG on by default and let the SVG websites a cometh. Soon enough you'll have the Mozilla crowd surfing a slew of fantastic SVG sites and their IE frie

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