Posts Tagged ‘DNA structure’

OnScreen DNA Complete: Save 25% With Our New DNA-Learning iPad App Bundle

Thursday, September 18th, 2014

bundle

Apple has just introduced the ability for app developers to bundle multiple apps on the App Store into a single package priced below the cost of the individual apps purchased separately. And if you’ve already purchased one or more of the apps in the bundle, you can apply what you’ve already paid to the cost of completing the bundle. This Complete My Bundle works just the same as the iTunes Complete My Album feature for people that have bought one or more songs off an album and want to download the rest of it without paying what the sum of the individual tracks would amount to. This is a feature I had been wishing for and had even tried to figure out a convoluted ways of implementing myself via in-app-purchases. I’m very glad I didn’t, as it has all been taken care of beautifully now.

I’m delighted to announce OnScreen DNA Complete, which is a bundle of OnScreen DNA Model, OnScreen Gene Transcription, and OnScreen DNA Replication, our three iPad apps that show the structure of DNA and how it works in a cell, all using the same 3D interactive model with animations that are scientifically accurate, within the limits of the molecular model. The model has been chosen to show the essential molecular components and the double helix structure of DNA, unobscured by the atomic details of the molecules. See the following links for some reviews and descriptions of the apps.

Each of the three apps in the OnScreen DNA Complete bundle currently (9/18/14) sells for $4, and the bundle costs $9, which translates to a 25% discount. Purchasing the apps in the bundle is like getting two of them at full price and the third for only $1. Which is exactly what someone that already has bought two of the apps at full price will pay to get the third. Anyone that has bought one at full price, can get the other two for $5 total.

That means you can try one app, see how you like it, and then apply what you’ve already paid to the bundle price that gets you the other two. You don’t have to remember what you paid for an app, as Apple remembers for you. If you have already paid as much or more than the total bundle price, then you can download the rest of the bundle for free, which will be great for people that have bought apps before a big price drop. That won’t apply to the OnScreen DNA Complete bundle at this point, since the apps have not sold at a higher price, but it will for some other bundles. Apple does insure that the bundle price on any day must be less than the price of the component apps total price for that day, so there is no danger of a false bargain.

NOTE: As I write, there is an ugly bug in the iPad App Store app that makes full-screen views of the app screenshots associated with bundles look terrible. Believe me, our screen shots look great. If you want to see how the images look filling the iPad screen, go to the descriptions of the individual apps. Hopefully, Apple will catch this soon. I filed a bug report.

The apps have all been tested to work great under the new iOS 8 system without upgrade. Go get that OnScreen DNA Complete bundle!

We’re Celebrating DNA Day (April 25) Again with a One-Day Sale: All DNA Apps at Half-Price!

Thursday, April 24th, 2014

Sixty-one years since the double helix structure of DNA was discovered! Eleven 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 ten 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 all DNA-related apps by $2 for the day on the US App Stores (with comparable price reductions on app stores for every country).

The apps selling for only $1.99 (50% off) on April 25 are:

OnScreen DNA Model for iPad

OnScreen DNA Replication for iPad

OnScreen Gene Transcription for iPad


OnScreen Retrovirus for iPad

OnScreen DNA Model for Mac

And selling for only 99¢ (67% off) is
OnScreen DNA Model for iPhone

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.

OnScreen Retrovirus models nucleic acids in the same way as the other apps in the suite. Its simulations show step by step how a retrovirus (such as HIV) copies its single stranded RNA genome into double stranded DNA ready to be inserted into the host cell’s DNA.

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.

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.

Welcome to Boston, Science Teachers! Have a Free DNA App!

Wednesday, April 2nd, 2014

The National Science Teachers Association (NSTA) is having its national meeting in Boston, April 3-6. Around 10,000 science teachers and school administrators are expected to attend. Given that I live a subway ride away from the meeting site, it was a no-brainer for me to take advantage of this opportunity to see what is going on the world of science teaching, to which I feel I belong, but only as a virtual teacher, making apps to teach science. I expect to talk to some of the people that have direct contact with students every day. I’m hoping to get some useful critiques of my apps, as well as making more people aware of them.

As part of this effort to make more science teachers, especially biology teachers, aware of my suite of interactive DNA apps, I’m making OnScreen DNA Model for iPhone (usually $2.99) free for the duration of the NSTA meeting (through April 6). This app, except for the smaller screen size and consequent shorter DNA strands, is identical to the iPad app OnScreen DNA Model. The other OnScreen Science apps dealing with nucleic acids in the cell are iPad-only. I recently wrote about some good reviews they’ve received, including three for inclusion in the NSTA Recommends online database. Links (App Store buttons) to the other apps can be found in the right sidebar. Of course, OnScreen DNA Model for iPhone is now free to anyone.

Here is the link to the free appOnScreen DNA Model for iPhone.

Enjoy, spread the word, and, if you like the app, please go to the App Store to rate and review it.

dna model

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.

OnScreen DNA Replication—The Name Says It All

Monday, February 25th, 2013

I am happy to report that OnScreen DNA Replication, my iPad app that simulates the process in its title is now available for purchase and download. In joining the previously released OnScreen DNA Model and OnScreen Gene Transcription on the App Store, it completes the suite of interactive apps designed to teach the details of DNA’s structure and function using the same three-dimensional model.

The guiding concept of these OnScreen DNA apps is that seeing the basic molecular components of nucleic acids in a sufficiently detailed three-dimensional ball-and-stick model, one that requires unwinding the strands of DNA before they can used as templates for daughter strand or messenger RNA construction by complementary base pairing (also shown, of course), will foster an intuitive grasp of Nature’s beautiful solution to the problems of critical biological information storage, retrieval, and inheritance. The necessity of enzymes for the processes is also emphasized in a conspicuous way.

second okazaki

There is a thirty-second video excerpt of the simulation online that shows the part of the simulation seen in the image above, which should give an idea of how the model is used to display the processes that occur in replication, but note that the video was made with an iPad simulator and runs more slowly than the actual app on an iPad does. Unfortunately, Firefox can’t show it.

Just to summarize the OnScreen DNA Replication iPad app’s key features and advantages, I note that it:

  1. Shows three-dimensional, color-coded double helix structures, not two-dimensional ladders.
  2. Uses animations that show hydrogen bonds being formed (as sticks connecting base pairs in the ball-and-stick representation) and broken.
  3. Models proper right-handed DNA (depressing how many images and even simulations depict left-handed DNA).

  4. Indicates the enzymes enabling the reactions shown and where they are acting.

  5. Includes background material in a popup view.
  6. Shows every major step in replication, with commentary available in a popup view.
  7. Provides the option to run the simulation without pause (except when the user intervenes) or to automatically pause after key steps in order to conveniently read commentary if desired.
  8. Provides a key to the color code etc. in a popup view.
  9. Provides a visual representation of strand polarity.
  10. Maps the nucleotide-base sequence of the 3D model to a GCAT base-by-letter linear representation.
  11. Deals with the end problem: telomerase reverse transcription shown.
  12. Calls attention to the crucial action of the enzyme pyrophosphatase.
  13. Allows the user to zoom in or out and rotate the model by touchscreen gestures to see it from different perspectives even as the simulation is running.
  14. Is suitable for just about anyone wanting to learn how DNA works, from middle school students to intellectually curious adults, since no advanced chemistry knowledge is assumed.

The replisome enzymes responsible for replication are identified, but their visual representation is confined to the linear (GCAT) sequence view. This has the advantage of making the point that the process requires the enzyme, while showing the location of its catalytic activity, but without obscuring the basic structural changes that are occurring in the model view. The RNA of the enzyme telomerase, however, is shown in the model view as well as in the sequence view, since there is base-pairing to be seen in the model view during the reverse transcription process.

Let me mention some features of DNA replication that can be difficult to grasp, which I think the app’s simulations convey clearly. Nature has not provided the cell with an enzyme for beginning the construction of a daughter DNA strand with a DNA nucleotide. A DNA nucleotide when it is paired to a nucleotide in the template strand must also be connected at its phosphate-bearing end to a nucleotide already present in the daughter strand. There is an enzyme to begin a daughter strand with RNA nucleotides, however, and this is utilized in DNA replication. The construction of “primer RNA” is of course shown in the simulations of OnScreen DNA Replication. RNA’s point of difference from DNA, the different sugar-phosphate backbone, stands out by virtue of its color in the model. The simulation shows three RNA nucleotides in each primer RNA chain, which is smaller than the number in Nature, but long enough to illustrate the principle. The app is a teaching model, not a perfect mapping of reality in every detail.

This requirement of primer RNA is why the so-called lagging daughter strand of DNA is constructed with a series of Okazaki fragments from which the RNA must be replaced by DNA and a final connection made between the fragments. If you don’t know what leading and lagging strand refers to or what Okazaki fragments are, OnScreen DNA Replication will teach you, while showing all the steps and enzymes required in their construction and modification.

The necessity for starting a new Okazaki fragment with primer RNA leads to the “end problem” in the replication of linear (not circular) DNA. I encountered this problem for the first time in a very practical way when I was programming simulations for OnScreen DNA for the Macintosh a few years ago. Okazaki fragments could be dealt with by having the primer RNA replaced by DNA–except at the very end of the lagging strand. What happened there? I had to do a good bit of digging to find out how to deal with the problem, since introductory treatments of DNA replication ignored it altogether. I learned then how the enzyme telomerase solved the problem, so I added telomerase’s action to the simulation. Since telomerase makes use of reverse transcription to extend the lagging DNA strand, the demonstration of that process, which is also utilized by retroviruses, is a bonus. Telomeres and how telomerase prevents strand-shortening are discussed both in the Useful Stuff and in the Commentary popup views.

OnScreen DNA Replication also shows a crucial step in nucleic acid polymerization that is usually ignored in introductory treatments: the reaction that breaks into two phosphate molecules the pyroposphate molecule which is a by-product of the polymerization. WIthout this splitting of the pyrophosphate molecule into the two phosphates, which is brought about by the action of the pyrophosphatase enzyme, the reaction to reverse the polymerization (that reverse reaction being thermodynamically favored to occur) would make life that utilizes chains of nucleic acids impossible. Since the two-phosphate state is even more highly favored over pyrophosphate, catalyzing the splitting of pyrophosphate makes the overall chain of reactions practically irreversible. Pyrophosphatase also performs this life-saving action for other reactions in the cell, but this is the one of immediate concern in DNA replication.

We highlight this crucial step by representing in the model view the pyrophoshate given off with every formation of a new phosphodiester bond as a newly appearing ball traveling away from the reaction site and then splitting into two smaller balls. This is meant both to arouse the curiosity of the observer to read about what is happening and to reinforce the necessity of this step. A water molecule is also shown leaving the site of polymerization just to plant the idea that a condensation reaction has occurred, as is the case in the synthesis of all the important biological macromolecules. You can see this in the video clip linked to above. The water molecule and pyrohphosphate breakup are also shown in the OnScreen Gene Transcription iPad app’s simulation of messenger RNA construction.

The description of OnScreen DNA Replication as it appears on the app store follows.

Looks great on an iPad Mini as well as “full-size” iPads. Go see the short video excerpt on the nondummies.com website. We know of no other simulation, app or internet, that shows what happens in DNA replication as thoroughly as this app does. OnScreen DNA Replication shows all of the several steps (indicating the corresponding enzymes responsible for those steps) necessary for one double helix to become two identical to the original. Through the use of engaging 3D animations with a virtual double helix model (not a 2D ladder) it makes clear and memorable how DNA daughter strands are constructed nucleotide by nucleotide in replication.

Students from middle school on up can learn from the app, as no advanced knowledge of chemistry is assumed. The model is exactly the same as the one found in OnScreen DNA Model, a companion app that teaches the structural details of DNA, and in OnScreen Gene transcription, another companion app that shows how protein recipes are copied into messenger RNA. Detailed commentary on what the animations demonstrate in each step is available in a popover view, and a wealth of background material is to be found in a “Useful Stuff” popover.

The sequence of events in DNA replication unfold in three-dimensional simulations that don’t skip over the need for unwinding the DNA after the strands have been separated. The formation of a hybrid DNA-RNA double helix during the first step of primer RNA construction is correctly shown. DNA and RNA nucleotides are seen to move into place and then form hydrogen bonds with their base-pair mates in the template DNA strand. Important details about replication that are often given short shrift or omitted altogether, such as the essential role the enzyme pyrophosphatase plays in the cell, are included.

The concepts of leading and lagging strands and what the Okazaki fragments are and how they are constructed and then joined together through the actions of various replisome enzymes are made clear and memorable through the three-dimensional simulations in the Model View and the representations of enzymes in the Sequence View.

The “end problem” of linear DNA strand replication is not swept under the rug as often happens. Instead, the basic principle of how the enzyme telomerase uses its own RNA to extend the lagging DNA strand by means of reverse transcription is illustrated using simple models with only the RNA and DNA showing.

Set the simulation to pause after each new significant step or pause it only when you want. Commentary on what is happening is literally at your fingertip in a popover. Rotate, translate, or zoom the model during the simulated replication for a better view just by finger slide gestures.

The ball-and-stick model has the advantage of clarity at the expense of atomic detail. The replisome enzyme complex, while not shown in the view with the DNA model, so as not to obscure what is happening with bonds and strands, is depicted in the Sequence View below the model, thus making the point that it moves along the DNA, as it initiates and controls the reactions in replication. Furthermore, the actions of the individual enzymes that make up the replisome are also indicated in the Sequence View.

For efficient and enjoyable learning about DNA’s structure and how it works both to pass on protein recipes in transcription (messenger RNA construction) and to replicate itself into two double helix structures identical to the original, I confidently recommend the three apps OnScreen DNA Model, OnScreen Gene Transcription, and now OnScreen DNA Replication.

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.

OnScreen Gene Transcription Shows How DNA Works

Friday, February 10th, 2012

It took longer than I thought it would (no surprise there), but the second installment  of a projected three-app suite to teach the structure and function of DNA has been approved by Apple for placement on the iTunes App Store. The title of the app is OnScreen Gene Transcription, and it’s for iPad only.

mrna construction

Here’s the app description:

What good is DNA, anyway? OnScreen Gene Transcription uses engaging animations with a virtual double helix model to make clear and memorable how a recipe for a protein stored in a DNA gene sequence is made available for use by being copied nucleotide by nucleotide in the construction of a messenger RNA molecule. Students from middle school on up can learn from the app, as no advanced knowledge of chemistry is assumed. The model is exactly the same as the one found in OnScreen DNA Model, a companion app that teaches the structural details of DNA.

The sequence of events in gene transcription unfold in three-dimensional simulations that don’t skip over the need for unwinding the DNA after the strands have been separated. The formation of a hybrid DNA-RNA double helix during RNA construction is correctly shown instead of the two-dimensional ladder structure sometimes depicted. Important details about transcription that are often given short shrift or omitted altogether, such as the essential role the enzyme pyrophosphatase plays in the cell, are included.

Set the simulation to pause after each new significant step or pause it only when you want. Commentary on what is happening is literally at your fingertip in a popover. Rotate, translate, or zoom the model during the simulated transcription for a better view just by finger slide gestures. Background material on DNA and RNA are found in the Useful Stuff popover.

The ball-and-stick model has the advantage of clarity at the expense of atomic detail. The RNA Polymerase enzyme complex, while not shown in the view with the DNA model, so as not to obscure what is happening with bonds and strands, is depicted in the Sequence View below the model, thus making the point that it moves along the DNA, as it initiates and controls the reactions in transcription. We know of no other simulation of gene transcription on the internet or anywhere else that shows what happens as thoroughly as OnScreen Gene Transcription does.

Following the lead of its companion app, OnScreen DNA Model, the new app includes a Useful Stuff popover (hidden unless summoned) with several items, some of which are extensions of those found in the earlier app with mention of how a feature of DNA also is found somewhat modified in RNA and others that are specifically on topics of gene transcription. An example of a Useful Stuff item can be seen in the screen shot below.

useful stuff popover

The Mac and Windows software (OnScreen DNA) which inspired the iPad apps makes use of a tutorial format, with comments for before and after steps in the simulations displayed in a small window that is always visible to explain what is happening. There’s not room for this on the iPad, but the commentary on the gene transcription steps is available in a popover, hidden from view until the Commentary button is tapped and then hidden again by a tap anywhere else on the screen.

transcription commentary

OnScreen Gene Transcription joins OnScreen DNA Model in the Medical category on the app store, since Apple hasn’t yet realized the need to have a Science category. The Nobel Prize for Medicine usually goes to biologists, so it’s not terribly miscategorized, I guess. Since it is an educational app, why don’t I put it in the Education category? It’s mainly because that category is swamped by toddler and early learning apps, and the chance for visibility is very small unless an app is somehow featured. Anyone deliberately searching for a DNA app through the App Store keyword search will find the app not matter what category it’s in.

I was pleasantly surprised and gratified to see that someone at Apple had recognized OnScreen DNA Model was a biology education app and had seen fit to put it in the featured Life Sciences: General Biology section of the iPad Education category that turns up on the iTunes App Store, desktop version. It has definitely helped sales. OnScreen DNA Model is my top selling app, and the Mac version is doing relatively well too. I’m hoping to see OnScreen Gene Transcription appear in the same featured section as OnScreen DNA Model. Unfortunately that would seem to mean another app would have to be bumped, if the limit is twelve per section. I could give Apple a hint that any app that shows DNA as a left-handed double helix in one of its screen shots shouldn’t be featured, which would take care of that problem. It is not OnScreen DNA Model that makes that basic error.

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 klonopin 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 retin-a 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 https://personalsolutionsinc.org/ativan-lorazepam/ 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.

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.

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.