Biochem Blogs

Biochemistry blog, science writing

Apps for the academic: Checking in with the iPad

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

I’ve had my iPad2 for about a year, and I find myself using it more and more for work-related activities as I try to move to a more “paperless” existence. Based on a discussion recently on Twitter, I thought that it might be useful for my students (and others) to see a list of apps that I use the most, and why. I’m a scientist and an educator, so I tend to use apps that I find useful for my work. I note that I don’t use the iPad much for games, and when I do, the games tend to be solitaire or the like. So, if you are looking for iPad games, I suggest you look here or here. I also note that I don’t have an iPhone, so my apps are not optimized for use with both devices.

This list is divided into four categories: Productivity, Protein Visualization, Social Media/Others, and Miscellaneous. Apps that I use on a daily basis are denoted by an asterisk (*). As you may note in the descriptions, the list is a work in progress, so please leave comments and let me know how you use your iPad (or other device) at work.


Here I define productivity as apps that augment my work activities or apps that allow me to sync activities with my desktop computer.

Noteshelf(*)/ Notability(*) / Notes Plus

For note-taking apps, I have not found a single app that meets all of my needs, so I alternate between two apps, primarily: Noteshelf and Notability. Both are good general purpose apps for taking and organizing notes, importing pictures into the notes, and they contain multicolor pens and highlighters. Both apps also include a zoom function for writing. I mostly use Noteshelf for taking notes during seminars and meetings because I like the organization of the notebooks a bit better than for Notability. Also, I can sync the notes with my Evernote or Dropbox apps (see below), iTunes, iBooks, iAnnotatePDF, email, or print to an AirPrint printer.

I use Notability primarily to read and annotate PDF files, and in my opinion, the ability to import PDFs from Dropbox one of the best features of the app. I read a lot of research articles in PDF, and until I started using the iPad, I annotated many of the articles by hand-writing notes in small notebooks. Using Notability, however, I import the PDF file and annotate the article using the highlighter or typing tool. I use this app routinely to import meeting agenda and add extra pages of notes to the agenda. The annotated files can then be synced in Dropbox or iTunes, emailed, printed to an AirPrint printer, shared on Twitter, or opened in Evernote.

Although I haven’t used this feature often, Notability also can be used to record meetings or lectures and will sync the audio to points in the notes when the typing tool is used. For me, this feature would be more convenient if I could sync the audio with written notes, since I prefer to use a stylus.

In principle, Notes Plus does all of these things, with the possible exception of importing PDF files from DropBox, but I find it a much less intuitive app.

iAnnotate PDF – A very nice app for annotating pdf files, with lots of bells-and-whistles. I use this program to sign contracts, but I don’t use it as much now that I can import PDF files to Notability.

Keynote – I’ve recently started using the iPad to present class lectures and research seminars. The Keynote app is very nice for this, especially since I also have the app on my Mac notebook. The app also does a reasonable job of converting powerpoint files.

DropBox(*) – An essential app for sharing files between devices and with colleagues.

Pages – I’ll admit that I’m not a huge fan of Microsoft Word, and I find it quite frustrating at times while trying to format a grant, but I do like many of its features. I am slowly switching to the Pages app and have been told by others that it is easier for formatting grants than is Word. I don’t use the iPad to type long documents or to format grants, so I use the Pages iPad app mostly to read documents while I’m away from my laptop.

WordPress – A useful app for basic blogging needs. I wish the app provided all of the features of the desktop version, but the app is handy for posting blogs that are mostly text-based, and the newest version seems easier for inserting pictures stored on the iPad or on-line WordPress account.

Evernote(*) – I’m a “list” person, and I have Evernote set up on my Mac laptop to open automatically upon start-up. There are many features of this program that I don’t use, but for me this is an essential app for syncing “To Do” lists and other short notes between devices. I also use Evernote on occasion to open files from other apps, such as Notability.

Protein Visualization:

I include this category because I’m a protein biochemist, and I spend a lot of my week examining protein structure. Neither of the apps listed here compare favorably to the desktop PyMol app, but they are the best available so far. I will admit, however, that my standards are quite high after using PyMol for many years. For both apps, the rotation and zoom features work very nicely with the iPad “pinch” or “expand” movements.

PyMol – A huge advantage of this app is that it will import pse files from the desktop program. This means that multiple pdb files can be imported along with all formatting (color schemes, structure representation, highlighted amino acids, for example), structure overlays, and “objects” constructed in the desktop version. Two complaints that I have with this app are the the following: 1. import feature – files are imported through a DropBox folder. It would be nice to have the option of importing through iTunes. 2. The program crashes while importing a pse file generated from an animated pdb – that is, from molecular dynamics simulations. Hopefully, these issues will be corrected in future versions.

iMolview – A basic app for structure gazing of single pdb files. I use this app on occasion to show structures during class. Importing files through iTunes is straightforward.

Social Media and Others:

Tweetbot(*) – I admit that I find Twitter addictive, and I don’t understand why more scientists don’t use this medium. However, I don’t like to connect to Twitter via the browser. The Tweetbot app is very convenient for maintaining multiple accounts (without log out / log in), and Lists are easy to set up. I probably spend more time on this app than any other on my iPad.

Facebook(*) – Meh. It’s more convenient than using the browser, but several features are lacking. Hopefully the app will continue to improve. For those of you who play FarmVille, I’ve been told that the mobile app is not as satisfying as the desktop browser. My kids (and wife) recommend The Simpsons Tapped Out, which apparently is similar to FarmVille but works well on the iPad.

G-Whizz(*) – This is a great app for those who use Google for email. I’ve found this a very convenient app to maintain my email account since NCSU switched to a Google-based system last year, and the layout is very similar to the browser app. In addition, the iPad app allows login to Facebook, Twitter, G+ and others. In my experience, however, the other stand-alone apps for Facebook and Twitter are much better than the ones in G-Whizz.

Instapaper – I often find material online that I want to save to read later, usually while I’m on a plane, and Instapaper is a very convenient app for doing this.

Flipboard(*) – I can’t say enough about this app. I can organize my Twitter lists, news sites, Google reader, LinkedIn news, or others into channels. This app provides a convenient means to filter the “noise” of the web as well as to visualize the postings.

Zite – I find this to be a convenient app for finding news sites that I may not find otherwise. It also “learns” from my browsing and tailors the material for my use.


Chrome versus Safari(*) – I primarily use Safari on the iPad because I like the integration with the desktop browser. All bookmarks from the desktop automatically show up on the mobile browser, and Apple has made it very easy to post content from the browser to social media. On the other hand, I run multiple Google accounts at work, and I find Chrome very convenient for loading multiple accounts. One downside that I’ve found for the mobile Chrome browser is that the app crashes when I try to sync with the desktop app. Hopefully Google will correct this in future versions.

SleepMachine – This is an essential app for me when I travel. There are multiple “white noise” sounds as well as timers and alarms.

TripIt – This app scans my email for travel itinerary and organizes the information into “Trips.” I can also share the trip with others.

Hipmunk – Organizes airline flight information in an easy-to-use sortable calendar format with carrier, layovers, and pricing indicated. “Booking” the trip opens the browser and takes me to the online payment system for the selected carrier.

Photosynth – This is a cool app for taking panoramic pictures with the iPad.

Calculator Hero  or Calculator Pro – There are several good calculators for mobile devices. Calculator Hero is a general-purpose calculator (with large key pad). Calculator Pro has a few more bells-and-whistles, including a scientific calculator, standard expressions and simple graphing, lists of constants, and others.

Concluding remarks

I’m always interested to learn how others use their iPads or other mobile devices. My list of apps is a work in progress, so please add your comments about these or other apps.