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Dec 2, 2013

The Best Science Apps: 12 December Picks

Make your smartphone even smarter with these useful research-aiding apps.

The Best Science Apps: 12 December Picks

The Chem3D app received four stars. Find out more about this app and others below.

  • Is there an app for that? If there is, you should check if it's in GEN's Best Science Apps first! Every month, we bring you a list of the best biotech- and biopharma-related apps we think you, GEN reader, would find useful and/or interesting. Here is our most recent list of Best Science Apps. Enjoy!

    Key:
    Four stars: Excellent
    Three stars: Very Good
    Two stars: Good
    + Strong points
    Weak points

  • Gene Tutor ★★★

    Click Image To Enlarge +

    Platform: iPad/iPhone
    Cost: Free
    + Covers a number of topics, many study questions
    Difficult navigation

    The Gene Tutor app, designed as a study aid for a genetics course at Barnard College, is a great reference app for any student of molecular genetics. The app covers a number of topics such as Mendelian genetics (including subtopics such as probability theory, pedigree analysis, and chromosomes and linkage), DNA structure and replication, gene regulation, and DNA repair/recombination. A set of study questions accompanies each topic, with each question marked as being easy, intermediate, or hard. App users can flag specific questions, and they can track their progress through the “statistics” tab. Navigation through the app is cumbersome and not very intuitive—for instance, the only way to exit a study question session (without going through all of the questions) is to rotate the iPad into landscape orientation to display the menu. (One cannot access the menu sidebar in portrait orientation.) Navigational issues aside, the app contains a lot of useful information.

  • Oligo Dilution Calculator ★★

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    Platform: iPhone
    Cost: Free
    + The oligo properties tool
    App is fairly limited in scope

    It’s a fairly straightforward app, but the Oligo Dilution Calculator app by Eurofins MWG Operon does the job it sets out to do: help you dilute your primer stocks. The dilution calculator has users input the stock and final concentrations (with unit options of molar, millimolar, and micromolar) and the final volume (most likely to be in microliters). In return, the calculator returns a text description of how much of stock and water/buffer one must combine to get the desired working solution. In addition to the dilution calculator, the app includes a useful “properties” feature. This feature displays the reverse, complement, and reverse-complement sequences for a user-inputted oligo sequence. In addition, it calculates the GC content, melting temperature, and molecular weight, as well as a few other characteristics specific to the input sequence.

  • FlyPunnett Lite ★★

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    Platform: iPad
    Cost: Free
    + Simple to use
    Graphical depictions of crosses would be nice

    Most people who have taken biology or genetics classes probably remember drawing out Punnett Squares to calculate the genotypes of the offspring from a particular genetic cross. While entertaining to a degree, Punnett Squares most certainly grow tiring after a while. This is likely to ring true for geneticists or researchers working in model organisms in which genetic crosses are very frequent, such as the fruit fly. The FlyPunnett Lite app (and the advertisement-free full version) aims to relieve Drosophila researchers of their Punnett Square burden. After simply entering the genotypes (three editable fields per parent, corresponding to the sex chromosomes and autosomes 2 and 3), app users can hit the “Breed!” button to display the corresponding offspring genotypes and frequencies. It would be nice if the information were displayed in a more Punnett Square-like format in order to graphically depict the calculation; however, the text display is clear and easy to read.

  • Molecular Biology Review ★★★

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    Platform: iPad/iPhone
    Cost: $3.99
    + Many different chapters, includes audio lectures
    Some poor graphic quality, some typos

    If you’re looking to brush up on topics such as DNA replication, protein structure, or molecular biology laboratory techniques, you’ll enjoy the Molecular Biology Review app by Lou Devlin. This app is divided into 10 chapters that include (in addition to those topics listed above): history and overview, nucleic acids, chromosomes, the genetic code, transcription, translation, and gene regulation. For each chapter, there is a lecture (with both an audio file and text/graphics), a set of flash cards, a chapter test, and a test statistics summary to track one’s progress. The app includes a significant amount of material, with each lecture ranging from 5 to 30 minutes in length. Some of the graphics are not the greatest quality, but they are still informative.

  • OnScreen Retrovirus ★★★★

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    Platform: iPad
    Cost: $1.99
    + Great interface, easy navigation

    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. Under the “useful stuff” tab, app users will find information on a variety of relevant topics such as DNA/RNA structure, reverse transcription, viruses and retroviruses, and retrotransposons. The screen can get a bit confusing, what with an RNA template strand and a growing DNA strand, but the app includes a key that is useful in clarifying which colors of the ball-and-stick model correspond to which nucleotides and bonds. As with the other apps from OnScreen Science, this app plays to the strengths of the iPad interface, with easy zoom-and-pinch and two-fingered navigation.

  • Optogenetics Pro ★★

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    Platform: iPad/iPhone
    Cost: $1.99
    + Includes many parameters, pro version includes complete brain atlas
    Methods for generating plots not given

    Optogenetics is a recently developed (and commonly employed) experimental tool in neuroscience research that allows researchers to either activate or inhibit populations of cells through the delivery of light to those cells. Of course, the efficiency with which one can activate/inhibit the target cells depends on a number of factors related to the delivery of light, such as the diameter of the optical fiber and the power of the light being applied. The success of the procedure also depends on which light-activatable proteins are being employed and which region of the brain is being targeted. Using the Optogenetics Pro app (and to a more limited extent, the free version of the app), researchers can explore the relationship between the aforementioned experimental parameters and the resulting penetration depth of illumination. Users specify the various parameters listed above, and the app generates a plot of optical power at the fiber tip versus the penetration depth of illumination. This can facilitate the design and implementation of optogenetics experiments.

  • Elemental ★★

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    Platform: iPad
    Cost: Free
    + Includes some pre-drawn functional groups
    Limits on reaction arrows, textbox not working

    The Elemental app is a free chemical drawing app that allows users to sketch benzene rings and chemical reactions with the tap of their fingers. Users select buttons along the top and the left side of the app to select the features they want to draw. These include specific atoms, lines, or other shapes. There are also buttons to select, delete, and copy/paste. The app has promise, although at the moment it also has some glitches and limitations. For one, although it touts itself as an app for drawing chemical reactions, the app (puzzlingly) limits users to a single reaction arrow per drawing. Additionally, there is also a glitch that renders the textbox tool unusable. Those limitations aside, the app still has some utility (and it will have much more once the present issues are addressed).

  • Oresome Elements ★★

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    Platform: iPad
    Cost: Free
    + Provides examples for each element, colorful
    Can’t switch between game levels

    I can certainly appreciate an app that incorporates a pun in its name (and I hope you can, too). Take, for example, the Oresome Elements app, a periodic table and game all-in-one that is aimed to teach students the atomic symbols. In addition, this particular periodic table includes the nice touch of providing examples of where one might find each element. (For instance, vanadium is found in metal springs, while germanium is used in electronics). The game component of the app is simple, as it has users simply drag floating bubbles labeled with atomic symbols onto their appropriate spots on the periodic table. There is a built-in help (or rather, answer) feature that allows users to tap on a square of the table to reveal the correct symbol corresponding to that element. The game is divided into three levels, with each level bringing in additional squares of the periodic table.

  • Open Worm Browser ★★★

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    Platform: iPad/iPhone
    Cost: $0.99
    + Multiple views, can highlight single cells
    Two-fingered drag navigation a bit difficult

    One typically requires a microscope to visualize the genetic model organism C. elegans. However, with the help of the Open Worm Browser app, anyone can take an up-close-and-personal look at these microscopic worms, in the form of a 3D animated model. This model is fully rotatable and can be enlarged via standard pinch-and-zoom iPad mechanics. Using two fingers, users can drag the model across the screen to display the specific region of interest. App users can select different views of the model–these include the cuticle view (showing only the worm’s exterior), or interior views comprised of organs, muscles, or the nervous system. One or multiple views can be selected at once. Within each view, users can choose to highlight specific cells from a drop-down menu.

  • Chem3D ★★★★

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    Platform: iPad
    Cost: Free
    + Great response times, many adjustable parameters

    The Chem3D app is an excellent (and free!) app to view the three-dimensional structures of proteins and macromolecules. The app handles conventional iPad finger navigation mechanics very well, with fast response times. App users can begin by selecting one of the sample structures included in the app, or they can search the entire Protein Data Bank from within the app to download other sample files. The settings menu allows users to toggle among four different display modes: wire frame, ball and stick, space-filling, and cartoon. Additionally, users can choose to enable “rocking mode,” which adds motion to the model. The background color can also be adjusted. Screen images can be emailed, shared via social media, or saved to the camera roll.

  • Physics Chemistry Maths Formulas: Formula MAX ★★★★

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    Platform: iPad/iPhone
    Cost: $0.99
    + Nice design, great organization
    Nothing major

    The Formula MAX app boasts a collection of 492 physics, 331 chemistry, and 370 math formulas and definitions. To do a bit of my own math here, that’s a total of 1,193 formulas/definitions…not too shabby. The app is nicely designed, with a sleek aesthetic and easy navigation. The content of the app is organized into the categories of (not surprisingly) physics, chemistry, and math. For each definition or formula, app users have the option to add it to a “favorites” list that is easily accessible from the main screen. Additional features of the app include a nicely designed, interactive periodic table, a logarithmic values calculator, and a trigonometric values calculator that gives the values for sin, cosine, etc. for a given angle.

  • Field Guide to Victorian Fauna ★★★

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    Platform: iPad/iPhone
    Cost: Free
    + Great photos, easy navigation
    Can’t pause/stop birdcall sound clips

    Myriad nature documentaries and wildlife shows have taught us that Australia is home to some of the most beautiful and exotic animals on the planet. If you’ve been wanting to get a closer look at some of the beautiful fauna that this country has to offer, but you don’t have the airfare (or vacation time) saved up, then the Field Guide to Victorian Fauna app can be a practical alternative. The app features animals specifically found in the Australian state of Victoria. It includes all types of animals, from birds, to insects, to spiders, to marine invertebrates. Each entry includes a high-resolution photo of the species, a brief description of identifying characteristics, habitat, and diet, and a distribution map. The endangered status for each species is also given (at state, country and worldwide levels). For the bird entries, there is the added auditory treat of birdcall sound clips.



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