Posts Tagged ‘science simulations’

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!

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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.

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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 app—OnScreen 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

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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.

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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 https://drbarletta.com/celexa-citalopram/ 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.

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OnScreen DNA Lite™ for iPhone Now Available

Tuesday, May 11th, 2010

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

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

gcat

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

grooves

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

key

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

single

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

renat

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

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An OnScreen DNA Lite™ for iPad Gallery

Tuesday, May 4th, 2010

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

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

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

double helix

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

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

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

popover

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

single strand

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

denatured

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

renaturation

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

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The Thinking Behind the OnScreen DNA Lite™ iPad App

Friday, April 2nd, 2010

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

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

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

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

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

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

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

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

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