Tag Archive for cell

3D Cell Explorer

solute pump

Today, I launch a new site, 3D Cell Explorer, a teaching tool for cell biology using visual representation. It provides 40 animations of cellular structures and processes, accompanied by audio narration. Anyone may comment on a page or copy the embed code to display animations on one’s own web site.

Many students learn best from what they can see — visual learners often struggle in science classes in which the vast majority of instruction is text-based. This site complements the textual materials an individual may already have. Text is kept to a minimum, so as to not distract from one’s attention to the visual model. Three of the animations provide a simple level of interactivity.

The site is pretty much Web 1.0 — lots of good content ready for consumption. The learning theory is primarily cognitivist. I want to help students of cell biology better comprehend basic cellular processes. Still, I did throw in a little Web 2.0 goodness. Comments are enabled on all pages, making it possible for visitors to start a dialogue about the animations. Providing the embed code allows teachers (or students) to integrate the animations into their own teaching materials, for example on a Moodle site or other CMS.

In 1994, I began to create simple 3D animations to help explain biological and chemical processes to my students. Over the following three years, I created dozens, especially on the topic of cell biology. A colleague and I decided to package the cell biology animations on a CD-ROM, but by 1997, CD-ROMs were no longer so popular. Although I did ultimately release the package, it never caught on, as teachers moved toward web-based instructional content.

In our enthusiasm to embrace Web 2.0 tools, we have left behind some of the strengths of the CD-ROM era: visual richness, simulations, interaction with content, and vast, visual libraries. I of course love the ease of distribution and social qualities of Web 2.0, but we must not discard the successful educational innovations of the past in our rush toward the future.

After a ten-year hiatus, I am pleased to re-introduce 3D Cell Explorer. Please do let me know what works and what doesn’t, and do spread the word to potentially interested teachers.

Here are some brief technical notes.

I created the original animations using Strata StudioPro and Adobe (Macromedia) Director. The project was saved by the continued support for Director by Macromedia and then Adobe. Director was the standard for authoring interactive media, but like CD-ROMs, it quietly disappeared as Flash produced smaller, faster-loading web files. I don’t know whether the new Strata3D can read my old StudioPro files. It would be good to preserve the time and effort I put into those models and animations.

To make the project more web-friendly, I exported all of the old Director files to QuickTime and then used VisualHub to make them into Flash Video (FLV) files. I kept the three interactive animations in Director format using the built-in Shockwave converter. I installed Drupal 6 for the content management platform and then built out a page for each animation. The Amadou theme gave the site a clean, modern look — I changed the background to black in order to match the animation backgrounds. I used JW FLV Media Player to deliver the Flash video files.

Ten years ago, I was amazed that an ordinary classroom teacher could access great-quality 3D animation tools. Still, it took three years of evening and weekends to produce these 40 animations. Today, I find it incredible that I could convert the entire thing to a web-based format in about two days’ time. Experiences like this provide a visceral reminder of the exponential increases in computing power over time.

Update March 31, 2008

I came across this very modern cell visualization from Harvard — quite interesting that it’s set to music.