Using scientific modelling/visualisation tools in e-learning

an article by Dan Stowell

In the life sciences and the physical sciences, there exist all kinds of useful computer-based modelling tools. As well as being used for research, they can now be used to present data (e.g. in an online journal article, or an online addendum to a printed journal article), and in teaching too.

In this article, I'm going to discuss the hows and the whys of using modelling tools in e-learning - as part of teaching material, but also in assessments. The examples focus on biological molecular modelling, since that's my academic background, but the scope is hopefully more generic.

You should be able to see, to the left, a slowly-rotating protein molecule. (If you can't, then you probably don't have the right plugin installed in your web browser - but UCL's managed desktop service does have the plugin, so I'll assume that you have it and carry on!) It's an enzyme called Protein Disulfide Oxidoreductase.

It's not just an animated picture - if you click-and-drag the molecule, you'll find you can rotate it yourself. And if you right-click on the molecule, you'll find a mind-boggling array of options for different ways to view the molecule.

You may even be surprised to learn that the second molecule displayed on this page is exactly the same molecule - in fact it's generated from exactly the same data file. I've set the webpage up so that the two instances display in different ways. By right-clicking on the molecule and setting various options, you can turn one into the other.

The software used to display interactive 3D molecules like this is a browser plugin called Chime, manufactured by a company called MDL. The file format is a standard format used by various systems, and Chime happens to be a good piece of software for visualising data in this format.

Further down the page you may also be able to see a graph displaying the infrared spectrum of a chemical (acetophenone). This too is interactive - you can click on a point to see a read-out of the x-y co-ordinates, and you can click-and-drag to zoom in on a region of the graph.

The spectrographic data, again, is just a file of data in a fairly standard format, being displayed to you by a plugin.

What tools/data can be used?

Most scientific disciplines make use of standard data formats, and there's a fair chance that you'll be able to find something relevant to your discipline.

For example, for astronomical data, FITS (Flexible Image Transport System) seems to be a fairly standard data format for the astronomy community. I haven't found a plugin which directly displays FITS data in a webpage, but the Sky Image Processor is a free online tool (it's a Java applet which pops up as a self-contained window) which can be used in almost the same way.

Should we use these types of tool in e-learning?

There's no doubt in my mind that interactive simulations like these can enliven web-based material. If the medium is an actual tool used within the discipline, as in my examples, then these interactions double in value. If you're putting together some online material, consider using these where you can. They need to augment a student's learning, of course, rather than distract from it, so it might not be a good idea to insert an interactive protein structure where it's tangential to the topic - except as light relief!

One important caveat for interactive models such as these is that they often don't print out well, or at all (depending on the browser and on the plugin) - and you will consider this a curse or a blessing, depending on your point of view. If you want your online material to translate well to printed material, then a clear image may serve your purposes better than an interactive model. If you are expecting your students to be able to sit at their computer and work through a set of online exercises, however, then interactive elements of any sort will help maintain their engagement.

Another important consideration is accessibility. Just as with static images, movie files, etc, there's the possibility that some students such as the blind or partially-sighted will not be able to make use of the material. The often-quoted guideline is that multimedia should have a "text description" available alongside; but for such simulations this may not be practical (the description might need to be very long!). A better solution may be to place a message near the beginning of the online material, telling students that if they are unable to make use of the electronic models, they should contact the tutor directly - you can then provide a satisfactory alternative when required, such as a physical model made with a ball-and-stick model kit, textual material or using material from the [Royal National Institute of Blind People (edited with updated links)].

How can we use these types of tool in e-learning?

As you'll realise if you've read my sidebar about how plugins work, you need two elements in order to build these molecular models into a webpage: the plugin, and the data. When you have these two elements, you need to be able to combine them in a webpage, in a way that says, "[plugin], display [data] for me."

Let's work through this process.

1. The plugin

You'll need to have the plugin installed in your browser. Often, you'll be teaching using a piece of software which is common currency in your academic work, so you'll already have it. (It certainly sounds sensible to me to use the software which is common currency in your field.)

More importantly, you need to be sure your students either have the plugin or can easily access it for free. Companies or organisations who provide these plugins often distribute them for free; but do make sure to check. Chime is one of the few plugins that is installed on UCL's managed computer service (WTS).

2. The data

You shouldn't have to put too much effort in to develop this material, so ideally the data will already exist and you won't have to create it from scratch.

Once you have the data-file(s), you need to make them available exactly as you would with an image. For example, upload it into your website or into your WebCT course files. (N.B. I'm assuming that no copyright issues arise here. The protein data I'm using has a copyright notice which explicitly allows for academic use.)

3. Embedding the data into a webpage

In Dreamweaver, you can embed the data very easily, by choosing Insert > Media > Plugin from the menu options, and then selecting the data file. You can then resize and reposition the inserted object just as you would an image. However, you may need to use the "parameters" button to specify your desired settings for the display, and you should also fill in the box in the Dreamweaver properties inspector marked "Plg URL" - this should be a URL which people can visit to download the plugin if they don't already have it.

If you're not using Dreamweaver, you can do the job yourself by adding the HTML <EMBED> tag, which is the tag used to embed fancy objects into a webpage. The HTML for one of the visualisations I've used near the top of this article looks like this:

src="1a81.pdb" width="200" height="200"
type="chemical/x-pdb" display3d="spacefill" color3d="temperature"
bgcolor="#ffffff" />

If you're comfortable with looking at HTML you'll be able to see the parameters which I've added, such as display3d="spacefill", which specify various commands about how the molecule should be displayed.

Using these tools in a VLE - in tests and other areas

You now know how to embed these tools into a webpage, so you will probably be able to use them in content modules and other webpage-based activities.

You can even use them in a WebCT Quiz! In order to put them in a Quiz question, you'll need to paste the HTML (similar to the HTML I used above) into the question-text box. For proof of concept, you might like to look at my protein visualisation self-test - I created it as a WebCT Quiz, but I have copied the actual quiz webpage and saved it here so that you can view it without logging in to WebCT. (You won't be able to submit your answers, but I've created a separate page with the correct answers, which you can check against.)

One caveat: WebCT can give you problems with "relative links". In my examples, the webpages and the data files were all in the same directory, so I could reference the file 1a81.pdb just as "1a81.pdb". But in my WebCT course, I needed to use the full URL for the file, "" - otherwise the plugin wouldn't be able to find the file, and would just display blackness!


"Plugins" are one of the easiest ways to incorporate scientific simulations and visualisations into a webpage, and they can be used effectively in e-learning - in tuition material, and even in testing. They have the benefit over ad-hoc simulations (e.g. a Flash animation) in that they are often actual tools used by practitioners in your discipline.

They are simple to incorporate, but you must make sure that your students are going to be able to access them - i.e. ensure that the plugin is freely available.