Posts Tagged ‘DNA Model’

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

Thursday, September 18th, 2014


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

And the Winner for Best DNA Simulation on an iOS Device Is…

Tuesday, March 18th, 2014

No, in this imperfect world no one is going to be excited when the envelope containing the name of the winner in that sadly neglected category is opened. Still, my cell biology apps for the iPad have gotten some good reviews in the past several months in places that command respect, and I thought I’d gather links to them here to have a page that I could in turn link to whenever I wanted to make people aware of the reviews. Reviews of iPad apps to teach DNA structure and function are not to be found in highly traveled spots on the internet. Coverage of education apps is pretty thin, and what little there is mainly concentrates on very young learners, as does the Education category on Apple’s App Store, where apps with cartoon animals (goofy expressions preferred) dominate.

I keep hoping Apple will add a Science category to its App Store, but for now I have to choose Education (no chance to be visible as one of the top 200 paid apps) or Medical (slight chance to make the top 200 occasionally). I have opted for Medical, but, fortunately, someone at Apple noticed OnScreen DNA Model and selected it to get a certain amount of visibility in the Education category for iPad apps. Currently it is featured under Apps For the Classroom->Biology and Apps for High School->Biology->Cell Biology & Genetics. Of course I’d put it in Middle School also, but I’ll take whatever I can get. I’m sure it’s the main way people actually hear about OnScreen DNA Model, which can then lead to the other apps. Your health and well-being matter to us, which is why we want to provide you with all the information you need. Clomid may have some potential side effects, but understanding them can help you make informed decisions.

Although they are less likely to be seen than a mention on the App Store, detailed positive reviews from respected sources are great to receive. Just to have them all in one place, here are links to the seven reviews I’ll briefly comment on below.

Genetics Engineering & Biotechnology News

May 1, 2013 OnScreen Gene Transcription

June 1, 2013 OnScreen DNA Model

July 1, 2013 OnScreen DNA Replication

December 1, 2013 OnScreen Retrovirus

NSTA Recommends

February 21, 2014 OnScreen DNA Model

February 21, 2014 OnScreen DNA Replication

February 21, 2014 OnScreen DNA Replication

I ran across the Genetics Engineering & Biotechnology News online magazine site early last year and saw that they had a monthly Best Science Apps feature (alternating every two weeks with Best of the Web). The reviews were concise, but meaty enough to show that the reviewer was obviously spending some time with the apps and making useful observations about them, and that the reviewer was actually knowledgeable about the science. Since the section was called Best Science Apps, they weren’t publishing reviews of apps they didn’t like, but the apps weren’t all getting the four stars highest (“Excellent”) rating either. Some were as low as the two-star “Good” category. I thought my apps, dealing as they do with the basic structure and function of nucleic acids would likely be of interest to them.

In January 2013 I emailed the reviewer to suggest OnScreen DNA Model and OnScreen Gene Transcription for review, offering to provide promo codes for free download. This is not a form of bribery (apps were $3-4), but rather a courtesy to the perspective reviewer, who couldn’t be expected to buy every app that might be worth reviewing. Apple provides a certain number of these promo codes free to developers just so they can get the apps onto the devices of potential reviewers and such. Anyway, the response was positive to taking a look at the apps, sometime in the next month or so. When, in March, the reviewer gave me the go-ahead to send the promo codes (they expire four weeks after being created—the codes, not the apps downloaded with them), I sent codes for the two apps I’d mentioned plus one for OnScreen DNA Replication, which I had finished and gotten onto the App Store in the meantime.

I hoped for the best, but as with most creators awaiting judgment of their work (think of the playwright, at least in movies, awaiting the morning editions after opening night), I was a little anxious. I was 99.9% sure I didn’t have any scientific errors, but would the reviewer appreciate the things I was proud of, like the background text I had spent so much effort on? At least, if the apps weren’t even deemed “Good,” I would just get no review at all.

That would be cold comfort, but it’s more than can be said about online reviews posted by app customers on the App Store. One-star reviews there mean “hated it,” and every app developer will sooner or later gather a few nasty (sometimes plainly inaccurate) and unfair reviews, while having no way of responding to the reviews on the App Store. I keep meaning to write about that subject, but that’s not what I have in mind for this piece.

When I saw OnScreen Gene Transcription had made it to the Best Science Apps section of the May 1, 2013, issue of Genetics Engineering & Biotechnology News and had been rated a four-star Excellent app in the review, I was both gratified and relieved. As might be expected, my opinion of the reviewer rose even higher, but not just because of the overall rating. It was rewarding to see that someone knowledgeable and conscientious had appreciated my work, including parts of it I wasn’t sure would be noticed, like the background text and commentary and just the way it was designed. The short summation of the praiseworthy elements of the app (beside a check mark) was “Background section, nice simulation graphics and commentary.” In the spot for the not-so-hot attributes (beside an X) was a simple “None.”

For all I knew, that one review would be it for Genetic Engineering & Biotechnology News. Maybe they wouldn’t want to have more apps from the same developer, at least for a while. But in the very next batch of Best Science Apps (June 1, 2013), there was a review of OnScreen DNA Model, once again with the highest rating. Among other things, the reviewer noted how the simulation of denaturing and renaturing of the two DNA strands made the interaction between them intuitively clear. By the check mark was “Great 3D DNA model, great text content.” By the X: “None.”

Now I really hoped OnScreen DNA Replication would also be reviewed. And it was, in the next issue containing Best Science Apps (July 1, 2013), once again with the highest rating. By the check mark was “Great text content.” For the first time something appeared by the X: “The simulation graphics are a bit convoluted.” Within the text of the review appears “Due to the complexity of the process, the simulation is a bit difficult to follow; however, credit must be given to the attention to detail.” The ending of the review was about as complimentary as it could have been. “Just like the other apps by this developer, the OnScreen DNA Replication app is incredibly educational and fun to use.

The fourth of the OnScreen Science apps using the same basic 3D model of nucleic acids is OnScreen Retrovirus. This app made it to the App Store in June of 2013. For some reason, I didn’t send a promo code to the reviewer for the new app right away. Maybe in the back of my mind was the feeling that I shouldn’t press my luck, though I certainly hadn’t decided not to ask for a review. I was busy getting all the apps ready to run on iOS 7, which was a pretty major job that took weeks. I hadn’t even checked out the Genetic Engineering & Biotechnology News site until mid January of this year, where to my surprise I saw that OnScreen Retrovirus had been reviewed without my having provided a promo code. The review had a great beginning: “The people at OnScreen Science are at it again, this time using their 3D nucleic acid model to simulate cDNA synthesis from a viral RNA template following infection by a retrovirus.” I love that “at in again.” And the rating made my apps four-for-four in gaining the Excellent designation. By the check mark: “Great interface, easy navigation.” By the X: “None.”

Just to put the Excellent ratings in perspective, the distribution of the ratings for other apps (excluding the OnScreen apps) in the issues in which the OnScreen apps were reviewed was 6 Good, 12 Very Good, and 5 Excellent. OK, it’s not quite as impressive as an Oscar or a Nobel Prize, but it’s pretty good. I have no way of knowing if it’s actually helped sales of the apps, since I can’t tell who is buying them, never mind where they learned of them. There was no noticeable spike in sales after the publication of the reviews. Still, if nothing else, those reviews are something I can refer people to for confirmation that the apps are of a high quality. Not to be overlooked, either, is the morale boost one gets from feeling one’s work validated. The income from those apps is hardly enough to justify the effort required just to maintain them every time Apple comes out with a new iOS version or device; so recognition really helps, even if it’s recognition in an out-of-the-way niche on the internet. The apps are, after all, pretty much in the niche category. I will resist the temptation to advertise that the apps have received “prestigious” four-star awards, as one hears so often about a supposed honor, the very existence of which is known only to a few.

In case it hasn’t come through already, I recommend the Genetic Engineering & Biotechnology News site’s Best Science Apps section as a great way to find intelligent and useful evaluations of apps for biology and chemistry in particular, both for educational and research aid purposes.

The other reviews I want to mention are those recently placed online in the National Teachers Association’s data base called NSTA Recommends. Again, only reviews for apps that the NSTA reviewer, typically a science teacher, heartily recommends are included in there.

To quote from the web site:

Our panel of reviewers—top-flight teachers and other outstanding science educators—has determined that the products recommended here are among the best available supplements for science teaching.

Why no negative reviews? They can be fun to read, even to write, but teachers are pressed for time—so only products that are reviewed favorably make their way into NSTA Recommends.

I emailed NSTA with a suggestion that the three apps devoted to DNA’s structure and functioning in the cell be considered for review and got a favorable response. It took quite a while after the NSTA contact said they’d be interested in looking at the apps before they actually got to them. One set of promo codes expired and the next was getting close to its expiration date before NSTA lined up a reviewer who downloaded the apps. I was just glad it was happening, since the NSTA is a large organization, with over 55,000 members engaged in science education, spanning the whole K-College range of students. I don’t know how many teachers use the data base, but getting a spot on NSTA Recommends list with favorable reviews couldn’t hurt.

The reviews, once they had been reported and published on NSTA Recommends, were all I could have hoped for. Again I was gratified to see that my work had been appreciated by someone that obviously had the experience to make his opinion valuable. And the grade level was listed as 6-College, exactly as I would have said myself! The NSTA reviews were not only thorough and insightful; they had a very practical, classroom-oriented angle, always focused on the question of what value would these apps be to a teacher. I thought it was a very good observation by the reviewer that the apps could serve to increase the teacher’s knowledge and understanding of the material covered in the apps, not just the students’. I was delighted that the reviewer made a point one seldom hears about apps that aren’t free, when he referred to the apps as “low-cost.” The reviewer had also noticed that there is a version of OnScreen DNA Model available for the iPhone (and iPod Touch) and mentioned that the students could download that app onto their personal devices, an observation that deserves extra points, I think.

The reviews made the observation that a teacher could project the iPad screen image onto a bigger screen for all the class to see, whether because only the teacher had an iPad or to make sure certain points were getting across. All of the features of the apps, including the organization and content of the background text, the ability to pause the simulations whenever desired for making a comment or reading commentary, the multiple views of the process, with the 3D model and the linear representation of the strands’ base sequences, and the attractiveness of the apps to students, were commented on in favorable terms.

Reviewing apps for NSTA Recommends must still be quite new. Although the reviews appropriately designated the format as “App,” the menu for restricting the NSTA Recommends online database search by format didn’t include “App” as an option. I’ve pointed this out, so it may be fixed by the time anyone reads this. The time to be considered “New” on NSTA Recommends is only two weeks, during which time a new review will show up when a searcher checks the New box. After that, only apps found by word in the title, author, or word in the text show up (with the option to restrict the search by format) in a search of the database. Unfortunately, due to some glitch, for all but the last three days of the OnScreen Science Apps’ time to show up as New, their reviews appeared without images, which was about as appealing as a Facebook or LinkedIn profile without a picture, especially for apps that are, above all, graphical in nature. That’s fixed now. Check them out.

OnScreen Retrovirus Shows How the AIDS Virus Copies Its Genome

Thursday, September 12th, 2013

OnScreen Retrovirus, my latest iPad app has been on the App Store for a couple of months now, so it’s high time I said something about it. Since the new iPad & iPhone operating system iOS 7 will be available to the general public September 18 and Apple is now accepting submissions of new apps and app updates written for it, I can show what the app will look like with the new interface. Let that be a justification for the antabuse delay.

retro action

The AIDS virus is the most notorious of the retroviruses, which is why I put it in the headline, but there are many more, including some nasty ones that cause cancer. I didn’t know much about retroviruses, or any viruses for that matter, until a year or so ago, when I decided I really should learn more. The detailed knowledge of how DNA works, which I gained during the course of developing the other DNA apps (OnScreen DNA Model, OnScreen Gene Transcription, and OnScreen DNA Replication), had heightened my curiosity about viruses, while providing me with the background to make the road to understanding easier.

Viruses are very strange creatures—or should I say objects? To quote from the first paragraph of my entry on Viruses in the app (from Useful Stuff popover view in one of the images below):

Are viruses alive? Look up virus metabolism, and you’ll come to a blank page. So viruses aren’t alive in the usual sense that living cells and multicellular creatures are. Yet viruses consist of proteins and genetic material, which are crucial constituents of living creatures, and, when in the proper environment (in their “host” cell), viruses can reproduce in their own unique way. So it’s really a matter of taste whether to call them alive or not.

Just as “real” organisms do, viruses make use of nucleic acids to store instructions for making the proteins vital to their survival. These proteins are few in number since the virus doesn’t have to make a living, but only hole up safely until it can enter a cell to reproduce, making use of a cell’s protein-construction apparatus. The full set of nucleotide sequences of the virus’s nucleic acid (which may be DNA or RNA, single-stranded or double-stranded, depending on the type of virus it is) is its genome.

The genome of a retrovirus is contained in a single strand of RNA. The way in which a retrovirus uses a few enzymes (proteins) it contains to construct a double-helical-strand of DNA, which also contains its genome, the virus’s RNA serving as a template, is fascinating. Mind-blowing, I think, as it depends on there being certain sequences of nucleotides at just the right place and in just the right order to enable nucleic acid strands involved in DNA synthesis to separate and then join again at another place in order to continue the process. Anyway, the simulations of OnScreen Retrovirus show how this happens in a detailed way that I think makes it very clear. And clearly mind-blowing!

retro commentary

OnScreen Retrovirus doesn’t show either the full virus entering the cell or the completed DNA being inserted into the host cell’s DNA. There are some good animations you can find online to see, at least in a sketchy way, those events. What I have not found online is any detailed simulation of the genome replication, and that is what OnScreen Retrovirus takes care of, making use of the same three-dimensional ball-and-stick model of nucleic acids featured in the other OnScreen Science iPad simulations.

The app’s Useful Stuff items and the Commentary for each step of copying the retrovirus’s RNA genome to DNA explain what you see in the simulations, necessarily introducing several key concepts, of which the screen shots should give an idea.

retro contents

It’s a accutane bit disconcerting to think of it (like the knowledge that our bodies contain more bacteria than human cells), but our DNA, for all its stability in the context of ordinary cell metabolism, contains many short segments called transposons that either move from place to place in their chromosome or make copies of themselves to be inserted at another location. Transposons accomplish their transpositions by utilizing the cell’s machinery to produce the enzymes needed to accomplish the task. In particular, those called retrotransposons have their DNA transcribed to strands of messenger RNA, some of which are used to synthesize enzymes, which act on other strands of the RNA to make double-stranded DNA to be inserted elsewhere in the cell’s DNA. Exactly the way a retrovirus does. So the simulation of OnScreen Retrovirus provides a simulation of a retrotransposon’s DNA synthesis as a bonus.

About iOS 7, I can say that for the OnScreen Science DNA apps, the changes are basically cosmetic and, I think, all for the good. The old tool bars and buttons of previous versions of iOS seem awfully dark and gloomy compared to the new ones. The new “buttons” are really more like links on a web site, just colored text on a light background, but people are used to links, and I think that change will go over well.

I hope to have all four of the OnScreen Science iPad apps that deal with DNA and RNA ready for sale on the App Store before the public release of iOS 7. The new updates will continue to support iOS 6, though not iOS 5, which means they are saying goodbye to the original iPad. Anyone wanting to run these apps on an original iPad had better hurry to get them before the updates go through. The updated apps will run on iOS 6 and just switch over automatically to their iOS 7 versions once they are running on a device with iOS 7 installed.

Update: before I could post this, I got word that version 2.5 of OnScreen DNA Model was going live on the App Store. So it is now too late to get it for the original iPad. I think Apple has app updates for iOS 7 on the fast track for approval, since I submitted only yesterday. So, you really must hurry if you have an original iPad and want to run these apps.

FLASH! (added 9/21/13) Although Apple has not announced it yet, it is now possible (and hopefully a permanent new feature) to download earlier versions of apps that have been left behind when updates raised the minimum iOS requirement. That means it is still possible, for instance, for people using the original iPad, which can’t run any iOS version greater than 5.1, to purchase OnScreen DNA Model even though the most recent version 2.5 requires iOS 6 or greater. Version 2.4 of the app, which is virtually identical, can still be downloaded. Just proceed as if you hadn’t noticed the iOS requirement. The App Store software will detect that your device can’t support the latest version of the app and will ask if you want to get a previous one your device can run instead. If you say yes, the older version will download and install. And all is as if you had purchased the app when that version was the latest. You are entitled to free updates on other devices in the future. I verified all this myself with actual downloads, but we can’t know whether it’s a permanent feature or just a test of a possible one until Apple says something about it. So far, they have only acknowledged it for updates on older systems.

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 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.

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.
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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. Knowledge is power, and we’re here to provide you with the necessary details. From mild discomforts to rare occurrences, it’s essential to be aware of every aspect before making any decisions regarding your health. Take control and learn about Ambien side effects, so you can make informed choices in consultation with your healthcare professional.

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. While Xanax can be effective in treating anxiety and panic disorders, it may cause drowsiness or dizziness. Stay vigilant and avoid activities that require concentration until you know how this medication affects you.

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.


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 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.