Posts Tagged ‘OnScreen DNA’

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We’re Celebrating DNA Day (April 25) with a One-Day Sale: All DNA Apps Only 99¢!

Wednesday, April 24th, 2013

Sixty years since the double helix structure of DNA was discovered! Ten years since the human genome was mapped!

From the Centers for Disease Control and Prevention (CDC) website: “National DNA Day is a special day when teachers, students, and the public can learn more about genetics and genomics. The National Human Genome Research Institute (NHGRI) at the National Institutes of Health has sponsored DNA Day for the past nine years, to commemorate the completion of the Human Genome Project in April 2003 and of Watson and Crick’s discovery of the double helix structure of DNA.”

To celebrate DNA Day, we are reducing our price on DNA-related apps to 99¢ for the day (with comparable price reductions on app stores for every country). The apps to be priced at 99¢ on April 25 are:

OnScreen DNA Model for iPad (regularly $3.99)

OnScreen DNA Replication for iPad (regularly $2.99) 

OnScreen Gene Transcription for iPad (regularly $2.99) 

OnScreen DNA Model for iPhone (regularly $2.99) 

OnScreen DNA Model for Mac (regularly $2.99)

The OnScreen DNA Model apps (on iPad, iPhone, and Mac) focus on the details of DNA’s double helix structure, using a 3D, color-coded, virtual model that the user can rotate and zoom. Explanatory text deals with the molecules and chemical bonds of the double helix. Animations show two important lab and biotechnology phenomena of DNA: denaturation, in which the strands separate, and renaturation, in which they reunite.

OnScreen DNA Replication makes use of the same DNA model to show how, through the action of specific enzymes, a DNA molecule is perfectly duplicated before cell division. The various steps in the process, including the action of telomerase to prevent strand shortening, are shown in 3D animations and described in some detail.

OnScreen Gene Transcription makes use of the same DNA model to show how a genetic recipe stored in the sequence of molecules of DNA is copied by construction of a messenger RNA molecule. The various steps in the process, shown in 3D animations that make it clear that messenger RNA is constructed as part of a hybrid RNA/DNA double helix, not a 2D ladder, are described in some detail, emphasizing the role of certain enzymes.

The apps show details of structure and processes that are sometimes depicted in erroneous ways in places that should know better. Animations make the processes memorable. Discussion of the chemistry involved is at an introductory level, so the apps are useful for learning about DNA to a wide range of students or anyone interested in the science of Life. There really is nothing comparable on the internet.

For iPad users, DNA Day is a chance to get all three OnScreen Science’s DNA apps for less than the regular price of OnScreen DNA Model alone. The apps work great and look great on an iPad Mini.

Educational purchasers enrolled in Apple’s Volume Purchase Program still get 50% off the sale price when buying twenty or more copies at a time.

Spread the word. This is a one-day-only sale.

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We’re Celebrating DNA Day (April 20) with a One-Day Sale: All DNA Apps Only 99¢!

Friday, April 20th, 2012

From the National Humane Genome Research Institute website: “DNA Day is a unique day when students, teachers and the public can learn more about genetics and genomics! The day commemorates the completion of the Human Genome Project in April 2003, and the discovery of DNA’s double helix. This year, NHGRI will celebrate National DNA Day on April 20, 2012.”

We are reducing our price on DNA-related apps to 99¢ for the day. The apps to be priced at 99¢ on April 20 are:

OnScreen DNA Model for iPad (regularly $3.99)

OnScreen Gene Transcription for iPad (regularly $3.99)


OnScreen DNA Model for iPhone (regularly $2.99) 

OnScreen DNA Model on the Mac App Store (regularly $3.99)

The OnScreen DNA Model apps focus on the details of DNA’s double helix structure, using a 3D, color-coded, virtual model that the user can rotate and zoom. Explanatory text deals with the molecules and chemical bonds of the double helix. Animations show two important lab phenomena of DNA: denaturation, in which the strands separate, and renaturation, in which they reunite.

OnScreen Gene Transcription makes use of the same DNA model to show how a genetic recipe stored in the sequence of molecules of DNA is copied by construction of a messenger RNA molecule. The various steps in the process, shown in animations, are described in some detail, emphasizing the role of certain enzymes.

The apps show details of structure and process that are sometimes depicted in erroneous ways in places that should know better. Discussion of the chemistry involved is at an introductory level, so the apps are useful for learning about DNA to a wide range of students or anyone interested in the science of Life.

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Taking OnScreen DNA Model to the Mac App Store

Thursday, February 10th, 2011

I’m happy to say that OnScreen DNA Model for Mac, barring an unexpected delay by Apple’s gatekeepers (it’s been waiting for review for a week), will soon be available on the Mac App Store. Check out nondummies.com for news. I’ll intersperse a few screen shots from the app below as a preview of things to come. While I’ve read of some independent Mac developers worrying about what the advent of the Mac App Store might mean for their sales and profits, I am almost certain it will be beneficial for the OnScreen Science, Inc. apps.

macapp

The Mac App Store (limited to Macs running at least OS 10.6.6) provides a virtual shopping center for Mac users wanting to purchase software to run on their Macs or just to browse through the selections—conveniently categorized—for future reference, much as the iTunes App Store has been doing for iPhone and iPad users for quite some time.

Of course Apple keeps 30% of each sale for itself, but in addition to the great drawing power of an Apple-run app store, it’s providing a lot more for that. Start with buyer confidence. If an app is for sale on an Apple-run app store, Apple has at least verified that it is not obviously buggy nor, in the reviewer’s judgment, totally worthless. Furthermore, buying the app is very simple, as the buyer’s credit card info is already in Apple’s (presumably secure) possession, and installation of the app on the user’s computer is automatic and immediate. And the procedure will already be familiar to many users from earlier experience with iTunes and its App Store.

Each app approved for sale on the app store is given a chance to present its best face through the developer’s own description and up to five screen shots (chosen by the developer), showing the app’s features. I should add that the feature page for the app can also serve to give users clues as to which apps are likely “crap apps.” Personally, I’m always a little suspicious of apps with only one or two screen shots.

Apps not only appear (with name and icon) in the array of apps displayed by category but can be found via keyword search. This search feature is crucial for niche apps such as those sold by OnScreen Science, Inc. because after a few days an app that’s not a big seller tends to become practically invisible to all but the most dedicated browsers, as the app moves farther down the list ordered by release date. The big sellers remain visible by virtue of their sales in a separate list devoted to the most popular apps.

Now, for games, the importance of being on the list of popular apps is obvious, and this is what has driven the “race to the bottom” for app prices, as the presence of high quality games selling for 99¢ can make an app, even a “serious” one in a very different category, seem outrageously expensive at $4.99 in some minds. I think there’s also something about the ratio of the price of the app to that of the device it runs on (and screen size) that makes app prices so low for apps on the iTunes App Store. But in the final analysis it’s really the ability of some developers to make a lot of money selling apps at a low price, thanks to the enormous number of potential customers, all funneled to a single buying point, that keeps prices low. That and the “free” apps, which I may write something about at a later time.

Let me say a little about the “desktop” OnScreen DNA apps from which the OnScreen DNA Model apps spring. OnScreen DNA, sold in three flavors—Lite, Standard, and Pro—has been available for Mac and Windows computers for several years. All these apps, especially aimed at biology teachers for use with students or for classroom demonstrations, are presented in a tutorial format that guides users through activities, complete with animations, designed to teach the structure and function of DNA.

Anyone that already has OnScreen DNA Lite will not be getting anything essentially new by buying OnScreen DNA Model on the Mac App Store. Rotating the model with the mouse is easier in the new app, as it is done with mouse drags requiring no key to be depressed. Some might prefer the new presentation of DNA facts to the old tutorial method. But as far as the basic model and the two simulations go, nothing much has changed.

single

The Lite version deals mainly with the structure of DNA, though it includes simulations of denaturation and renaturation. OnScreen DNA (without the “Lite” qualifier) adds simulations of gene transcription and DNA replication with a good deal of detail about the enzymes involved and an accurate depiction of the basic steps (hydrogen bond breaking, strand unwinding, nucleotide chain forming, etc.), including proper direction of chain-building, primer RNA and Okazaki fragment construction, and even the role of telomerase in solving the “end problem” of DNA replication.The Pro version adds simulations in which the user, not limited to observing processes unfold, tests his or her knowledge by actively selecting the proper enzymes at the proper time and choosing the next nucleoside to add to a growing polymer chain. I should add that these apps, being designed mainly for teachers, include interactive tests, the results of which can be stored on the computer (under password protection if desired). More details about these apps, which are still unique and still for sale, can be found at onscreen-dna.com.

The aforementioned web site has been (and is still at the time I write) the only place to buy these apps. Thus sales have largely been limited to the hardy Googler that seeks DNA teaching software, or is at least searching for detailed information about DNA. No one with just a vague interest in science and biology is likely to stumble upon the web site. The price for advertising in even a relatively small circulation magazine for science teachers is really too high to justify from the sales it would likely produce, based on past experience. Though a ninety-day, no-questions-asked, satisfaction guaranteed policy for complete refund is in effect for our apps, I’m sure many people are hesitant to buy from an unknown online source. Thus the Apple seal of approval could be extremely valuable.

dnamenu

After the iPad was announced, I came to see it as a opportunity to bring some of the OnScreen DNA software to a larger audience (using the existing code for displaying the three-dimensional DNA images on the iPad). I knew from experience with “DNA Day” sales for which I announced large discounts for a short period via a few Mac news sites that there were people who were not teachers that might be interested in a way to learn more about DNA for a price that wasn’t too high.

By far the easiest path seemed to be to start with a port of OnScreen DNA Lite to the iPad. Partly from screen space considerations I decided to scrap the tutorial format. I refer the interested reader to an earlier blog post The Thinking Behind the OnScreen DNA Lite™ iPad App for more about the iPad app. In some ways I felt the iPad app to be better than the Mac/Win versions just because of the direct response to the fingers, unmediated by a mouse. But, due to limitations of the somewhat stripped down version of Open GL (graphics programming API) available on the iPad, some features were lost, such as the ability to ctrl-click on any component of the DNA model to see it labeled. Of course ctrl-click has no meaning for the iPad anyway. In place of the labeling feature I added a popover image with a key showing how all the different parts were represented in the model.

The iPad app was launched with the old name OnScreen DNA Lite, which didn’t make all that much sense in the iPad context. This was rectified by the new and current name OnScreen DNA Model, which is more descriptive and avoids the implication that there is a more advanced version of the app available for the iPad. At the same time as the name change, the app gained a significant enhancement with an on-screen (popover on iPad) guide to facts about DNA’s geometry, molecular components, and chemical bonds and how they are displayed in the model. The blog post OnScreen DNA Model for iPad and iPhone: New Name, More DNA Background illustrates the changes. Oh yes, as the title of that post indicates, a version for the iPhone and iPod Touch is also available.

grooves

When the Mac App Store was announced, I had no doubt that I would want to bring the OnScreen Science, Inc. science education apps (OnScreen DNA and OnScreen Particle Physics) to it. It took a bit of thought to decide what to do first, but based on the relative success on OnScreen DNA Model on the iPad (sales have continued to rise, contrary to the usual fate of apps on the iTunes App Store), I decided to get a version of OnScreen DNA Model ready for the Mac App Store.

This was a decision to make the Mac version very similar to the iPad version, rather than a small modification of the existing OnScreen DNA Lite. Thus the tutorial and the division into activities are not found in the Mac App Store version of OnScreen DNA Model. I think this is a net improvement due to the greater freedom it gives the user, even at the risk of some important points possibly being missed and without the potential benefit of a guided discovery that aims to get the user thinking.

To a certain extent, how successful the new app is on the Mac App Store will determine how quickly I move to bring the simulations of OnScreen DNA to the store. There are a number of decisions, really, about what to attempt in the way of simulated DNA processes for the iPad version and whether to work on the iPad or the Mac version first. It may make more sense to get OnScreen Particle Physics (onscreen-sci.com), our classic particle detection chamber simulation, onto either or both App Stores first.

Time will tell whether I’m being too optimistic, but I’m really encouraged by the opportunity the Mac App Store is giving me and other independent developers to get our apps before a lot of new eyes and minds.

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OnScreen DNA Model for iPad and iPhone: New Name, More DNA Background

Tuesday, September 28th, 2010

I’m pleased to say that OnScreen Science has a new iPad app on the iTunes App Store—OnScreen DNA Model 2.0—with another app—OnScreen DNA Model for iPhone 2.0—awaiting review and hopefully available in a matter of days. Actually, they are major updates of apps previously called OnScreen DNA Lite and are free to anyone who purchased either of those apps.

The main change to the two apps is the addition of accessible background material on DNA and explanations of how different features of DNA structure are represented in the virtual DNA model in a memorable, instructive way. For example, there are now discussions of DNA strand polarity—what it means and how it is represented in the model—and the major and minor grooves of the DNA double helix—what they are, their physical origin, and how to make them appear in the model. This new material makes the apps more self-contained than before, although they are still not meant to be a sole source for learning about DNA structure. The point is made that the model represents certain molecular components of DNA, not atoms.

The new material is found in a popover view in the iPad version of OnScreen DNA Model. The popover view appears at the tap of a new button called “Useful Stuff”. The image below shows the interactive table of contents listing the various topics dealt with. The user only has to tap on a disclosure button (blue arrow) to see a discussion of the corresponding feature and how it is modeled in the app.

contents

Below is shown the Nucleotides item, or rather the beginning of it since there is more text to be read after scrolling down in the app.

nucleotide discussion

Because of the smaller screen size the iPhone app cannot display the full table of contents on a screen, but all items can be seen and accessed by scrolling. The content of the various items are the same in iPad and iPhone versions of OnScreen DNA Model. Below is the top of the table of contents in the iPhone app.

iphone contents

Seen below is the Nucleotides item from the topic list. Less text is visible at a time in the iPhone version, but everything in the iPad version is accessible by scrolling. The text shown below is what would be seen in the iPad version after scrolling down from the point shown in the iPad example above.

iphone item

Why the name change? OnScreen DNA Lite implies there is a “full” or standard version, but there isn’t. “Lite” also gives the idea of limitations, perhaps severe limitations. The name just sort of snuck over from the desktop software, where there are Lite, Standard, and Pro versions of OnScreen DNA. Each higher version adds something to the version at the level below it, and there is a policy of letting customers apply the price they’ve already paid to the price of the higher level version whenever they want to upgrade. That is not possible for an app, given the way the iTunes App Store is set up.

The plan is to bring some of the simulations of DNA processes to the iPad (less likely to the iPhone with its smaller screen) in the future, but the names of those apps will more directly reflect what they simulate.

In any case, OnScreen DNA Model perfectly fits the app, which consists of a virtual 3D model designed to make essential features of DNA readily apparent. It is a superior model that stands on its own and shouldn’t have a name that could diminish it in the mind of anyone first encountering it.

While the name and the extended background guide are new, the basics of the model remain the same as presented in earlier blog posts: OnScreen DNA Lite™ for iPhone Now Available, An OnScreen DNA Lite™ for iPad Gallery, and The Thinking Behind the OnScreen DNA Lite™ iPad App. See the iTunes App Store descriptions of OnScreen DNA Model and OnScreen DNA Model for iPhone and iPod Touch too of course.

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iPhone App Update Roundup

Wednesday, August 11th, 2010

I’ve gotten three of the OnScreen Science, Inc. iPhone apps reworked for iOS 4 and the new iPhone 4. Two of them—OnScreen Pitch Count 1.5 and OnScreen GPA Pro 1.2—have been approved and are now on sale. OnScreen DNA Lite for iPhone 1.1 is still in the queue for review. If things proceed as for the other two (week of waiting, a few hours in review), then the update of the third app should be on sale August 12 or 13. The update of the fourth app, OnScreen QB Stats, involved more than just making it work and look good under the new system and on the high-definition “Retina” screen of the new iPhone. I wanted to give it the same improved user interface and navigation among games and players that OnScreen Pitch Count had recently received, so it is taking a little longer. Given that football season is still a ways off, OnScreen QB Stats was a lower priority. Assuming the rest of testing and debugging is not prolonged, that update should be on sale by around August 20.

One of the nifty new features of iOS 4 on later generation iPhones and iPod Touches is multitasking. Whether or not it’s “true multitasking,” Apple’s implementation of the feature allows for keeping an app in memory when a new app is chosen to run on the same device, and then later to quickly switch back to the original app without having to load it again. Since the OnScreen Science apps had been programmed to remember where they had been whenever the user jumped to another app, so that they could resume right where they left off upon relaunch, the only difference with multitasking will be in the speed of resumption, but a second or two is a second or two.

The other essential part of updating for the latest iPhone is to make sure the screen displays of the app look good on the Retina screen. That means a developer has to produce and include higher resolution versions of any images and icons that the app displays. New screen shots for the iTunes App Store display of the app also have to be submitted. These were straightforward but somewhat tedious tasks. There weren’t many such images, so I had it easy compared to some people.

The one app I was worried about providing a nice iPhone 4 version for was OnScreen DNA Lite for iPhone. The virtual DNA model is drawn in 3D using the iOS implementation of OpenGL ES. The drawing assumes a certain pixel density, which is way off for the Retina display of the iPhone 4 which has a higher pixel density. Images drawn with the unmodified OpenGL code are displayed on the Retina screen just by blowing them up, so that they actually look worse—much more jagged—than they did on the old iPhone. It took me a while to figure it out, but the solution was very simple. I only needed to put in a test for what device the app was running on, and in case it was iPhone 4 make a change to one line of the old code (doubling the dimensions of glViewport for the iPhone 4) and add a call to scale the image by a factor of 2. I couldn’t believe my luck when I tried just that and saw it was all my code needed. Not only does the iPhone 4 version look better than the old version did on the iPhone 4, it looks better than the old version did on the old iPhone, since it takes advantage of the higher definition screen (extra pixels) during the image rendering. This can be seen in the comparison below.

old dna image

Above is a screen shot from the original iPhone running OnScreen DNA Lite for iPhone.

iphone4 dna image

Above is a screen shot from an iPhone 4 running OnScreen DNA Lite for iPhone.

There was another update to OnScreen Pitch Count before the latest version 1.5. A user had encountered the problem of not being able to view the pitching stats for the last couple of pitchers when he’d kept track of pitches for numerous pitchers on both teams. This turned out to be a bug I’d introduced in version 1.4 when I failed to take into account a change in view dimensions made necessary by the addtion of a toolbar at the top of the screen. The user called me to point out the bug, and I was grateful for that. I had a fix submitted in a day or two. I had already been working on the iOS 4 upgrade, but felt I needed to get the bug fix online as soon as possible without waiting for completion of the other changes, which is why 1.5 followed 1.4.1 so closely.

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OnScreen DNA Lite™ for iPhone Now Available

Tuesday, May 11th, 2010

I’m happy to say that OnScreen DNA Lite™ for iPhone can now be downloaded from the iTunes App Store. This is basically a smaller-screen version of the iPad app that was released when the iPad first became available, though adapting the app to the iPhone and iPod Touch required some modifications, which I’ll mention. Everything I said in the blog post “The Thinking Behind the OnScreen DNA Lite™ iPad App” applies to the new iPhone version. The same desire to “provide students (and all persons interested in DNA) with a way to reach a deeper, more intuitive understanding of DNA structure” motivates the development of both apps, and the same care to show DNA’s correct handedness, base-pairs per helical turn, etc. with a ball-and-stick virtual model was taken for each. What’s more, it’s a lot of fun to play with the DNA model through the touch screen control of its orientation and size in both versions of the app.

My last blog post, “An OnScreen DNA Lite™ for iPad Gallery“, showed the screen shots that are a part of the iTunes listing for that app and commented on them. As one way of comparing the two versions, let’s consider the corresponding screen shots for the iPhone app. Below is shown a screen shot from the iPhone version in which the linear (“GCAT”) representation of the base sequences of the DNA model is visible below the model. Because of the smaller screen area of the iPhone, this linear representation of the bases is only shown on demand. The button at the top designated GCAT shows and hides that view. Another accommodation to the smaller screen is the shortening of the DNA model. Instead of the thirty-five base pairs of the iPad model, the iPhone version has twenty-one, which is still sufficient to show adequately the full double helix structure and its features.

gcat

The screen shot below shows the DNA model enlarged (by means of the iPhone pinch-to-zoom technique) and with the linear view of the base sequences hidden. The structure is shown with major and minor grooves as the result of a button tap.

grooves

The next screen shot shows the key to the ball-and-stick model, indicating what each colored ball (molecule) and stick (chemical bond) is meant to represent. This is essentially the same view as the Details popover view in the iPad app.

key

As in the iPad app, one can view a single strand of the DNA model, as shown below. This may be especially useful for grasping the meaning of the handedness of a helix, and the app also allows one to switch back and forth between natural right-handed DNA and imaginary left-handed DNA. The screen shot was taken with the model rotated by means of a finger swipe.

single

The screen shot below shows the simulated process of renaturation (rejoining together of the two strands, separated during denaturation) as it nears completion.

renat

Rather than repeat myself, I’ll just refer the interested reader to my previous two posts for more details about the virtual DNA model of OnScreen DNA Lite for iPad and now iPhone and iPod Touch.

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An OnScreen DNA Lite™ for iPad Gallery

Tuesday, May 4th, 2010

Apple’s iTune App Store provides one standard way (and place) for “apps” developed for the iPhone and iPad to be displayed. The app store listing is really a pretty good way to learn something about an app once you’ve managed to reach the page devoted to it. Apple lets developers describe the app in under 4,000 characters and choose up to five screen shots of the app for display in its listing. The screen shots are presented without captions, so they basically need to tell their own story.

I chose the screen shots used for the OnScreen DNA Lite listing on the iPad app store with the aim of trying to show various features, but I think a little description could be useful, so I’m presenting here those same screen shots with some explanatory text. The dimensions of these screen shots have been squeezed down to fit into the blog column, so the area of the images is less than a quarter of the iPad display’s.

Here below is the thirty-five base-pair double helix of OnScreen DNA Lite’s virtual model. Note the row of control buttons at the top. The display mode is what we have called “Balloon,” which just means that the balls used to represent molecules in the DNA structure are substantially larger than they are in the “Skeletal” mode in which the double helix structure may be more apparent. The Balloon mode is closer to the “space filling” representations sometimes shown, but not so much as to hide the structure. Since Balloon mode is in use, the button that controls this feature reads “Skeletal” to indicate that a tap of it will shift to the Skeletal representation.

double helix

The sticks connecting the balls (molecules) in the model represent chemical bonds, which are less apparent in the Balloon mode. The model is shown above with “Tilted Bonds” (a button choice), which means that the sticks representing the glysosidic bonds between the deoxyribose phosphate molecules (white balls) and the nitrogenous bases (colored balls) are at an angle to the line between opposite sugar phosphates in the DNA strands. This bond tilting is what causes the unequal spacing of the grooves (major and minor) that wind around the double helix structure. I expect to add a feature for making it obvious what these grooves are in a future update. The text in the panel above the image makes the point that the model with unequal grooves is more like the real DNA structure than the simpler model used for the simulations.

Note that the bottom of the screen shots show the base sequences of the DNA strands of the model using the familiar letters GCAT (for guanine, cytosine, adenine, and thymine). The color coding is the same for the linear (letter) representation and the model.

The screen shot below shows the popover view that has the key to the model of OnScreen DNA Lite. It gives the names of all the molecules and chemical bonds shown in the model. Note that the phosphodiester bond has two parts indicated. The bond is shown with two colors to make it clear that there is a polarity to the DNA strands, and that they are of opposite polarity (“point” in opposite directions).

popover

The screen shot below shows the DNA model with one of the two strands hidden, which is accomplished by a button tap. This makes the helical structure of each strand apparent. Note that this shot is with the Skeletal mode selected. Natural DNA is right-handed, meaning that a strand circles around the axis of the helix in a clockwise fashion as it advances down the axis. This handedness may be easier to see with a single strand. To further make the concept of handedness clear, OnScreen DNA Lite also has the option to show what left-handed DNA would look like. In the screen shot the model has been rotated to the side and held there. This is easily (and satisfyingly) accomplished by a swipe of a finger on the iPad screen.

single strand

In addition to displaying the DNA model in various static (though rotatable) forms, OnScreen DNA Lite features a couple of simulations of phenomena that can occur with DNA in the laboratory. The first is denaturation, in which heating the DNA breaks the hydrogen bonds that keep the two strands joined together, thus allowing the strands to separate as single threads no longer bound to a helical shape. The screen shot below shows the two strands after denaturation has occurred, but the simulation that preceded it would have shown the strands being stretched and jiggled as the temperature increased, with individual bonds breaking until the double helix couldn’t be maintained. Note that, while showing that the hydrogen bonds are the most easily broken, an essential property for the functioning of DNA, which requires controlled strand separation at life-supporting temperatures (not the boiling temperature that brings on denaturation), denaturation is not a natural process occurring in living cells.

denatured

After the DNA strands have been separated in denaturation, it is possible (after the temperature has subsided) for them to recombine in the opposite process called renaturation. A few bases in one strand may come into sufficient contact with their complementary counterparts in the other strand to form a string of hydrogen bonds which can serve to hold the strands together long enough for other bonds to reform. This can be simulated in OnScreen DNA Lite after denaturation has occurred. The screen shot below captures an instant in the renaturation process after much of the double helix has been reformed, but before the process has been completed.

renaturation

Screen shots can be useful in getting a picture of what an app is like, but static pictures can’t really do justice to an app with dynamic simulations and with a model that can be rotated by touch. For the true experience you’ll need an iPad and the OnScreen DNA Lite app. But soon there will be a version for the iPhone and iPod Touch. For more on OnScreen DNA Lite for iPad see The Thinking Behind the OnScreen DNA Lite™ iPad App.

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The Thinking Behind the OnScreen DNA Lite™ iPad App

Friday, April 2nd, 2010

My first iPad app, now ready for sale on the iTunes App Store even before the iPad has gotten into many hands, is called OnScreen DNA Lite. Check it out! I plan to relate something of the hectic development of this app in a later post. Here my aim is to describe the iPad app a little and to motivate its development. The app is based on OnScreen DNA, a science education program I created a few years ago, first for the Macintosh OS X, and somewhat later for the Windows side. My primary goal in developing OnScreen DNA was to provide students (and all persons interested in DNA) with a way to reach a deeper, more intuitive understanding of DNA structure than I felt they were likely to obtain from reading text and looking at two-dimensional static images of a DNA model. I wanted to create a virtual, three-dimensional model that had most of the virtues of a real, physical one plus the enhanced power to simulate DNA processes with animations.

OnScreen DNA Lite’s computer model, programmed with three-dimensional perspective, is of the simple ball-and-stick type, in which the balls represent molecules, and the sticks represent the chemical bonds between these constituent molecules. A guiding principle in development was to make the relative dimensions of the model agree with those of the actual DNA molecule to the degree that makes sense for a ball and stick model. This meant getting the ratio between helical radius and the distance along the helix required for the molecular chain to make a complete revolution right, as well as showing the proper offset between molecules paired oppositely with one another in the two DNA strands. The distance between molecules in a strand, and hence the number of molecules in a complete revolution of the helical strand also had to be right.

Another crucial structural detail of the virtual helices that needed to conform with that of natural DNA was the handedness. The concept of handedness, which refers to the sense in which each helical strand winds around its axis, is one that seems largely to have escaped notice by those who make artistic renditions of DNA. My observation is that roughly half (the fraction predicted by a random guess) of all depictions of DNA show left-handed DNA, when in fact natural DNA (or all but a tiny fraction of it) in living cells is right-handed. OnScreen DNA Lite makes it easy to see the difference between right and left handed DNA by allowing the user to switch back and forth between the two.

In addition to showing the relative positions of constituent molecules in the DNA strands, the OnScreen DNA model uses color coding to identify the various molecular parts and chemical bonds. This is meant to give visual reality to the idea that a molecule of one type (color) will make a cross-strand bond with only one other type (a different color). The molecules that form a connection between their respective strands are represented by one another’s complementary colors. The color also makes the visual point that the molecules (nucleotides) making up the DNA chains differ from one another only in the parts (nitrogenous bases) that make up the cross-strand pairs, while the connections that form the individual strands are between molecular components that are identical. This can all be said, of course, and should be said, but the colors in the model make the point in an immediately memorable way.

The molecules (sugar phosphates) that link together to form the chain of a strand do so in a particular way. Think of elephants forming a line by each elephant (except for the lead elephant) grasping with its trunk the tail of the one in front of it. The molecules have an asymmetry (think of trunk and tail) as well, and they form bonds between dissimilar parts (the “tail” being the part of the molecule where the phosphorus atom is). Thus we can think of a strand of DNA as “pointing” in a given direction just as the line of elephants heads in a certain direction. We say the DNA strand has a certain polarity (as a bar magnet has polarity: N at one end, S at the other). It turns out that in the real world, the two DNA strands in a double helix are aligned with opposite polarity. They point in opposite directions. The color coding of the OnScreen DNA model reflects this feature as well, visually indicating it in the colors of the relevant chemical bonds.

In order to perform its biological function in living cells, the DNA molecule must at times have portions of its two strands separate from each other. The separation and unwinding of the strands, and the nucleic acid chain constructions involved in these processes are orchestrated by complex proteins called enzymes that catalyze just the right reactions at the right time and place in the required sequence. In the full OnScreen DNA edition, animated simulations are used to show how this occurs. OnScreen DNA Lite does not include these biological processes, but it does show how the laboratory process called denaturation takes place. The temperature required to achieve this is too high for a living cell to survive, but in the lab, the jiggling of the the double helix at the high temperarture is strong enough to break the bonds holding the two strings together. OnScreen DNA Lite for iPad animates this process, finally arriving at the point where the two strands are completely separated from each other and no longer have any helical shape, just as happens to real DNA in the lab under heating. The reverse process, in which bonds reform between complementary pairs to recombine the two strands into a double helix can also occur, and OnScreen DNA simulates this phenomenon of renaturation also.

Even though the biological functioning of DNA is not demonstrated by OnScreen DNA Lite, its animations can serve to make the point that the hydrogen bonds connecting the two intertwined strands to each other are much weaker than the other chemical bonds of the DNA molecule, a fact that is crucial for the strand separation that has to take place in the biological processes. Furthermore, I believe that seeing the strands in the act of recombining makes the fact of their entwinement all the more memorable, which is important because it seems it can be lost to consciousness when only two-dimensional images or the typical ladder-like double strand renderings are seen.

The desktop version of OnScreen DNA allows the user, by means of the mouse, to rotate the model about its helical axis and about an axis perpendicular to that. Making these rotations serves to enhance comprehension of exactly how the double helix structure is put together and to fix its three-dimensional geometrical shape in the mind. Causing the on-screen rotation by dragging the mouse pointer across the screen is fun, but the pointer on the screen is at a distance from the hand directing it. I, along with almost all other developers of iPad apps, was without the benefit of an actual iPad on which to test the app I was making and thus had to use the iPad simulator that runs on the Macintosh to see what the app should look like on the real device. Thus I was deprived of the tactile part of the iPad experience, as mouse clicks and drags had to simulate their finger-on-screen counterparts. I did, however, have a chance to test on a real iPod Touch the prototype of OnScreen DNA Lite for iPhone, and I loved how I could make the double helix rotate by moving my finger on the screen. It was much closer to dealing directly with a physical object, and much more satisfying. I can’t wait to get my iPad and to start making further improvements to OnScreen DNA Lite for iPad.

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Only Three More Shopping Days Until DNA Day! Save Big!

Wednesday, April 22nd, 2009

Let’s face it: knowing the structure and workings of DNA is part of basic scientific literacy these days, which is why, after all, millions of us celebrate DNA Day. If you’re still doing last-minute DNA Day shopping, do we have a great deal for you! OnScreen DNA, the world’s best three-dimensional computer model of the double helix structure of DNA, complete with on-screen, tutorial-based simulations of how DNA works, is on sale at 50% off.

And what better way could there be to celebrate fifty-six years since the 1953 publication of the Watson and Crick paper elucidating DNA’s double-helix structure than buying OnScreen DNA for only $19.53? It’s perfect for those students, teachers, and science lovers of all ages on your shopping list. And don’t forget to treat yourself.

Don’t worry if you don’t see this until DNA Day itself—the online offer and the ability to get the software immediately by download will still be available right through April 25. Yes, we are celebrating with the “traditional” April 25 instead of moving to April 24, as many national national organizations, evidently wanting to avoid a weekend day, have done this year.

Seriously, there is nothing that I know of that teaches DNA structure and functioning in such a complete and thoroughly three-dimensional way as OnScreen DNA, which I designed and programmed myself. The software runs on Macintosh OS X or Windows XP/Vista. The on-screen tutorials explain everything you’re seeing, and practically no prior knowledge is assumed.

The animations of DNA and RNA chain-construction in OnScreen DNA are a lot of fun. I still enjoy them after having gone through them countless times during programming, debugging, testing, and just playing. You really need to see the three-dimensional structure of DNA, not just the two-dimensional ladders which animations encountered on the internet seem to invariably fall back on. Having programmed the OnScreen DNA animations, I can see why they do that—it’s a pain to do the three-dimensional programming. But it is worth it. Take a look at the results and judge for yourself. Just go to <onscreen-dna.com/buy_dna_online.php> to take advantage of this special offer.

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A Commercial (with Money-Saving Coupon), Some Thank Yous, and an Animal Identification

Friday, September 26th, 2008

First, the big news: OnScreen DNA’s price has been reduced by $30! The standard edition of OnScreen DNA is now $39, and the Pro edition, which empowers user-controlled simulations of gene transcription and DNA replication, costs $69. You can read the press release; but, if you haven’t already—just to get an idea of how much easier it is to visualize and understand DNA’s double helical structure and the chemical bonds that underly it when you have a three-dimensional model to play with—why not download OnScreen DNA Lite (it’s free)?

OnScreen DNA is a virtual model, of course, which is good from a number of standpoints. It costs a lot less than a hardware one, and it can be animated to show the essential three-dimensional details of how DNA works. If you know someone who teaches DNA at any level, please tell them about OnScreen DNA. If you’ve wanted to come to a deeper understanding of DNA and how genes work yourself, please note that it is now a lot easier and less expensive to do so.

As an extra inducement to readers of this blog to try OnScreen DNA, here’s a coupon code to save an additional $20: hs908. Just enter that code in the appropriate box on the order page to get OnScreen DNA for only $19. This won’t work forever, so don’t count on it being there a month from now. OK, commercial over.

I need to catch up on thank yous and acknowledgements. As always, another blog’s linking to this one implies no endorsement of views in either direction.

David, the Christian physicist and novelist who writes the He Lives blog, linked to Conversations in the Club of Truly Smart People. Thanks again, David. Another Dave, he of the Not the Religious Type blog, mentioned the same post favorably and linked to On the Breaking of Bad Habits Acquired in One’s Youth: Smoking and Atheism. Thank you, Dave. Ropata of the Earth is My Favorite Planet blog also linked to the Bad Habits post. Thanks, Ropata.

Denyse, a very busy Catholic journalist and author on topics of religion and science, keeps three blogs going. We have exchanged some emails, and she has added the onscreen-scientist to the blog roll of Colliding Universes, which I’d say examines physics and biology from a thoughtful Intelligent Design standpoint. She also (with comments) linked to the two previously mentioned posts related to atheism and to the one on animal suffering, Cries in the Night. Thank you, Denyse.

My post about the anti-LHC campaign, Large Hadron Collider: What’s the Risk?, coming as it did a couple of days before the first proton beam circulated in the LHC, drew more traffic than even the computer troubleshooting ones have in the past. John of the Refugees from the City blog linked to my aforementioned LHC post in two separate posts: Mixed Nuts, in which he makes a thorough exposé of the dishonestly exaggerated credentials of Walter Wagner, the main instigator of the doomsday hysteria, and also looks at Rainer Plaga’s background and work, and Whooooo Hoooooo!, which summarizes the credentials of all notable LHC opponents. Thanks, John.

I have also exchanged emails with JoWynn, who wrote to tell me how much she and her husband appreciated my Reading Proust for the Last Time post. JoWynn, in addition to being a voracious reader (including books on particle physics!), maintains a blog largely devoted to her embroidery art (Parkview 616), despite a disabling condition that confines her to one room most of the time. Thanks, JoWynn. Judy of the Reading Proust in Foxborough blog said good things about the Proust post and also linked to it. Thanks again, Judy.

Finally, I’ve decided that the predatory animal whose strange wild sounds I couldn’t identify in my Cries in the Night post was almost certainly a raccoon, based on some sounds I’ve found online. It’s funny that out of all the raccoons I’ve seen in my life, I’ve never heard one make a sound that I can remember. So, just to return to that disturbing death struggle I overheard in the middle of the night, I now imagine that it was a raccoon that had caught a squirrel. The raccoon, lacking big, powerful jaws like a dog, could have been holding the squirrel in its mouth waiting for it to die of blood loss, internal injuries, etc. The squirrel, being still alive, could have made its cries and also have mustered up the strength for a desperate struggle to escape every few minutes, which would explain the fierce raccoon sounds mixed with thrashing around that I heard periodically.

On the one hand, I’d just as soon get those sounds and speculation about what was going on out of my head, but it’s also good to have the drama linked to known animals. It changes my view of raccoons, which I had known to be scrappy fighters by reputation (able to drown dogs that were foolish enough to pursue them into the water, for example), but had never seen or heard in action.

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