Tag Archives: Research Computing

The Productive Scholar: Risk in Media Discourse: An Introduction to Topic Modeling with R and Python

Topic: Risk in Media Discourse: An Introduction to Topic Modeling with R and Python461972367(1)
Speaker: Manish Nag

Time: Thursday, April 10, 12:00pm – 1:00pm
Location: New Media Center (NMC), 130 Lewis Library, First Floor

Lunch will be provided. To register for this session: http://bit.ly/Risk-TM
(Registration is not required for attendance, however refreshments may be limited.)

Amidst global concerns over financial markets, terrorism, and outbreaks of disease, the term “risk” pervades contemporary Western media discourse. Manish Nag’s dissertation is interested in the overall landscape of risk in contemporary news media discourse, using the full text of the New York Times from 1987-2006. What are the predominant threads of discourse related to risk, how does this discourse grow and change over time?  Manish’s presentation presents how topic modeling can be used to help answer these questions.

Manish Nag is a Doctoral Candidate in Sociology. His research seeks to understand the global landscape of media discourse on global risk, as well as change and resilience in global networks of people, goods and ideas. His research utilizes mapping, data visualization, the analysis of text, and social network analysis. Manish received his BA in Computer Science from Brown University, and has worked as a software engineer, entrepreneur, and manger prior to his graduate work.

Presentation co-sponsored with Digital Humanities Initiative at Princeton (DHI).

NEW! Workshop Series: Statistical Computing with R

R is the de facto standard for statistical analysis in a wide range of disciplines such as computational biology, finance, sociology, political science and digital humanities. This two-part workshop will help participants to get started with R’s abilities, ranging from data structure to visualization. Designed for students without any programming experience, this course will better prepare you for introductory statistics courses and quantitative research at Princeton.

Dates10/9  Part 1: Introductory Workshop in Statistical Computing with R
            11/13 – Part 2: Intermediate Workshop in Statistical Computing with R
Time: Wednesdays, 7pm – 9pm
Location: New Media Center (NMC), 1st Floor, Lewis Science Library

To Register for the workshop series, please fill out the registration form here. Or access the form via the QR code to the right. Limited space available.qrfree.kaywa.com


Continue reading

Lunch & Learn: The “Mapping Globalization” Project with Miguel Centeno and Manish Nag



Detail from “Steamship routes of the World” circa 1900, the American Express Company.

“Mapping Globalization” was the topic of today’s Lunch ‘n Learn featuring Professor Miguel Centeno and graduate student, Manish Nag, both of the Department of Sociology at Princeton.

Centeno began the talk by describing the origins of his interest in globalization, about 11 years ago, about the time of Thomas L. Friedman’s first publications on his theories about the relationships between nations (The Lexus and the Olive Tree, 2000 and The World is Flat, 2004). Centeno said it occurred to him that there were many ways to frame the subject of globalization, and that the process, in fact, had been going on for thousands of years. How, he wondered, was the best approach to grasp the complexity of the concept without resorting to banalities–and what was the best way to diagram information as complex as that describing global trade?

The International Networks Archive

Centeno’s first attempt to answer that question was to develop the International Networks Archive, (INA), where he used graphic arts, among other things, to try to depict complex relationships in easy-to-understand ways. Using some common reports published by the United Nations, he used trade data to support the generation of diagrams that showed some stunning conclusions about global transactions.  Centeno calls these images “infographics.” An example, The Magic Bean Shop and The Fries that Bind Us, are two of the diagrams in the INA collection. They show the effects of McDonalds and Starbuck’s franchises on global trade. This diagram, he noted has been the most popular on the site, having been reprinted multiple times as an example of the sort of trends the INA is best at describing.



The fries that bind us? A diagram showing the effects of Starbuck’s coffee shops and McDonald’s restaurants on world trade. Image copyright 2003, INA.


“Globalization is nothing more than a complex series of transactions across the planet,” said Centeno, alluding to the strong connections that can be made by analyzing trade data. “Most of these data sets are available publicly,” he noted, showing a table that tracks the annual number of minutes spent in phone communications between countries. Data about the imports of movies, books, as well as trade data, are among the many other ways to show how these transactions take place through what seems like simple exchanges.

The INA project was followed by the “Mapping Globalization,” where data was visualized in three distinct ways.

Mapping Globalization

The first section of the Mapping Globalization site contains a collection of maps, and links to maps of various kinds: these include historic maps, interactive maps, and modern satellite imagery that help to convey the notion of geographic location as a critical, but often overlooked aspect of globalization. “Globalization involves connections between at least two places,” the website explains, “and the first step in our understanding must be an appreciation of what this means in a concrete sense of place.”

The second, and least developed, section of the “Mapping Globalization” site is the “Narratives” section, a series of animated movies that show general trends in globalization over time, such as “Migrations” and “Empires.”

Finally, the “Data and Analysis” section uses diagrams generated by technology from NetMap Analytics, which creates diagrams showing the density of trade between nations. Using data from GKG trade statistics, NetMaps are circular diagrams that show relationships between various countries, grouped by continent. Thresholds can be set on the data depicted to clarify the diagrams. For instance, setting a threshold of f “0.3%” means that links corresponding to a trade share less than 0.3% of the total dollar value in the category are not shown in the diagram.


Thumbnail image for ApparalandAccessories1980_2001.png

Trade in Apparel and Accessories in 1980 and 2001 with a 0.3% threshold. From “Brief Introduction to the Data and Selected Images from the GKG Project” by Miguel Centeno and Abigail Cook.

Despite best efforts at the time, there was no way for the NetMaps to be generated dynamically on the website, however images of several of the most interesting patterns can be found in the section of the site called “NetMap Combined Studies.”


The talk next focused on a project undertaken by Manish Nag, a graduate student in the Department of Sociology at Princeton who now studies with Centeno. Nag explained his past career as an IT consultant, and his first interest in studying globalization at Harvard, studying with Jason Beckfield. At Harvard, Nag worked on a project called Sonoma, as a way to visualize statistical data using maps. When he came to Princeton to continue his studies, he began to work with Centeno on making an interactive database that would allow anyone to diagram world trade relationships. The result was the MapTrade project.

MapTrade, still in beta, shows various projections of a world map (Robinson, Winkel Trippel, Gall-Peters, or equirectangular are the map views that the interface supports). Trade flows can be diagrammed on top of the world projections, showing trade between selected nations, based on specific commodities, or all trade between all nations. Trade data is available for 1980, 1990, 2000 and 2009.

Using the interface, it is possible to save generated maps, so that comparisons can be drawn, and the results saved for use in research and presentation. As with the earlier NetMaps projects, filters can be applied to clarify the data by setting thresholds, or by limiting the transactions by their total percentage of world trade.

Centeno and Nag used the MapTrade interface to generate a series of maps, showing the shift in trade centers over time.



A diagram showing the top 75% of trade in wheat among all nations, 1980. Image generated by MapTrade.


A diagram showing the top 75% of trade in wheat among all nations, 2009. Image generated by MapTrade

The audience then requested several maps showing various commodities, countries and time periods.


Who knew so many fish sticks were traded between the U.S. and China in 2009? That the top 50% of word trade involves only 10 countries? You may have suspected these things; MapTrade can draw you the picture to prove it!

A future phase of Centeno and Nag’s collaboration will include making the NetMaps data interactive, much in the way that MapTrade currently is, so that users can generate and save their own diagrams.


Links to all three of the projects discussed in today’s talk can be found at:



A podcast of the talk can be found here.


Enhanced by Zemanta

Lunch & Learn: Collaboration tools for scholars with Angel Brady


Photo credit: Johann Larrson, via Flickr. CC license, 2010.

Today’s Lunch ‘n Learn, presented by Angel Brady of Princeton’s Humanities Resource Center considered the topic of “Collaboration Tools for Scholars.”

Brady demonstrated several free tools that facilitate scholarly collaboration. Most were on sites external to the Princeton computing environment, one, WebSpace, is a Princeton-only resource.

Brady explained that these new tools are popular because they are stored on external servers that keep shared resources up to date, and ensure that collaborators are always working on the latest versions.Most of the tools also include social media features that allow further communication and sharing.

Formerly, trying to share, write, or gather research materials while working collaboratively relied upon repeated email exchanges, possible mis-matches between software versions, cross-platform issues, email boxes going over quota, and various versions of a file being in circulation at the same time. A major advantage to these new cloud-based services is that they are browser-based, are cross-platform, and that they allow multiple editors to work simultaneously.

Many of the functions performed by these tools can be replicated by other applications at Princeton– often more securely. However the ease of use, the fact that these tools are in common use among scholars, that students have equal access to them, and the advantage of synchronous editing make them very attractive for the types of collaborative documents and resources  that require medium security, and that need to be shared with people from all over the word. For university business that requires the transmission of sensitive information, web-based external services should NOT be used.

The tools discussed today were Mendeley and Zotero, tools for amassing an online research collection, bubbl.us, a mind-mapping service, Posterous Groups, a sub-function of a popular micro-blogging site, Google Documents an online office suite of applications, Dropbox and WebSpace, two file-sharing services, and Diigo, a social bookmarking tool.

Mendeley and Zotero

Medeley and Zotero perform very similar functions in that they organize reference and research materials found online, and also have social-media functions. These tools can be used to gather links to resources such as journal articles and web pages, bookmark, and annotate them. Downloading similar documents and links to one’s desktop can result in file names that don’t reveal the actual content of the downloaded file, and these “mystery PDFs” can be difficult to share. Mendeley and Zotero allow you to make online folders of documents, and automatically download the metadata associated with files, including titles, abstracts, and tags, listing them in a clear library-like format. You can also alter and add to the metadata. Notes, highlighting, and organization within groups and folders can be accomplished in either application. Reference collections can be make public or private, and both tools have the ability to find other public libraries organized by people who share your research interests,

Mendeley is a desktop client originally designed as a PDF annotation tool (it also supports .txt files). It also has app versions for the iPhone, iPad and iPodTouch. Mendelay works with bibliographic citation formats such as BibTeX, Research Info Systems (RIS), Zotero Library and Endnote XML. A free account in Mendeley allows for 500MB of personal storage space, as well as 500MB of shared space. Both private and public groups are supported, but the free account limits private groups to 5; with each group having a maximum of 10 members. Group folder track all group activity, and it is possible for the original group owner to reassign ownership to another user if necessary, so that existing group work does not have to be recreated in a new account. There is a bookmarklet tool to make it easy to import sources found on the web.

Mendeley platforms:

Cloud-based, with desktop apps for MacOS, Windows and Linux.

Zotero Groups is part of Zotero, a Firefox add-in that works with Mac, Windows and Linux (a stand-alone version of Zotero for Chrome and Safari users is available in alpha). Group Libraries, both public and private can be created. The Firefox plugin can capture journal and book information with one click. Highlights and notes can be added to content. Library ownership can be transferred to another user. Zotero can also be used as a bibliographic tool, with a drag and drop feature to MS Word (Zotero export bibliographic information in the RIS format, which EndNote can import.). Your Zotero library has an RSS feed that can be followed by group members, to notify them of updates. Zotero was designed for academics, and was originally created at George Mason University. Storage space for a free account is 100MB.

Zotero platforms:

Cloud-based, and a Firefox add-in compatible with MacOS, Windows and Linux versions of Firefox; a client for Chrome and Safari is in the works.


For the visually minded, Bubbl.us is a tool that allows collaborative mind-mapping via a series of connected bubbles that diagram related concepts. The free version of the cloud service allows 3 “sheets” of mind-maps to be created; more are available with a paid upgrade. Groups can be made for editing (read/write/delete) or read-only access to Bubbl.us mind maps, but group members must join Bubbl.us to participate.

Finished mind-maps can be exported as .jpg or .png image files, but the application itself uses Adobe Flash to create the interactive maps. Maps can also be embedded in an external web page as a way to share them with others. Although the tool is very simple, as mind-mapping tools go, it also has a very minimal learning curve. Most similar tools are fee-based.

Bubbl.us platforms:


Posterus Groups

Posterus, a popular micro-blogging site (think “Twitter,” but with the ability to make groups) also has the ability to make simple collaborative websites for blogging among group members or multiple groups. Posterous posts can include both text, images (with automatic slide shows for posts with multiple images), links and PDFs with a 100MB upload limit per post. Posterous sites can be private (password-protected) or public, and posting is possible using a number of devices, including mobile phones, emails or bookmarklets. Responding to or adding to posts is also possible via email. For a researcher in the field or on the go, it can be an invaluable tool to share information with group members almost instantly. Groups are private by default, and have no limits on the number of members. Posterous can be linked to existing sites on social networks such as Facebook or Twitter.

Posterous platforms:

Cloud-based, works on mobile browsers as well as desktop ones.

Google Docs

Google Docs is a great tool to use for real-time or asynchronous collaboration with colleagues; several users can be working on a document at any given time (with visual hints to other editors as to what parts of the document other users are editing, and almost instant updating of new content.) The Google Docs include familiar office-type applications including a word processor, a spreadsheet tool, a slide show creator, and a tool for building forms. Documents created in Google Docs are compatible with other similar desktop based applications, such as Open Office, Microsoft Office, and iWorks, and files can be imported and exported from one to the other.

Collaborators all need a Google account to use Google Docs, but it does not need to be a Gmail account — any email address can be registered with a Google account. Various saved states of a documents are stored and can be reviewed and reverted to when needed. Ownership of various shared documents can be reassigned to another group member, and colleagues can be invited to edit as a private group, or be completely public.

Google Docs is very popular with Princeton students, but should not be used to share secure course information that would be better put into Blackboard or another Princeton-managed storage space, however for casual collaboration, particularly outside Princeton, it’s a great tool.

Google Docs platforms:


WebSpace and Dropbox

WebSpace is a file-sharing platform that Princeton has licensed from a company called Xythos, a subsidiary of the Blackboard Learning Management System. Xythos is an enterprise-level document management system that allows for users to set up workflows, retention strategies, and enter metadata for stored documents. Everyone at Princeton with a valid netid has 5GB of storage on WebSpace.

WebSpace has built-in integration with Blackboard course websites, allowing shared storage for course participants. A popular feature of the Blackboard component is the drop box, which allows students to share work with each other, and another feature that allows instructors to post links to files stored in WebSpace directly to one, or more, Blackboard sites.

WebSpace can also do simple file sharing on a file-by-file or folder level. WebSpace integrates with the University LDAP, so it is easy to make groups within the Princeton community. A “ticket” to a file or folder can also be shared with anyone in the world with an email address. Tickets contain a specific URL to the shared material that sets editing permissions, the duration of these permissions, and shares the file directly via WebSpace rather than sending it as an email attachment. In all cases, users can “subscribe” to a folder or file that is shared with them to receive notification of changes. Files in WebSpace can also be made public, and each has a unique URL so that others can link to them.

A desktop client is available for 32-bit Windows machines. A Mac version is in beta. For those for whom the client does not work, the WebSpace drive can be mapped as a network drive.

Dropbox is the most popular of the cloud-based file sharing services as a stand-alone application, and is also used by many other applications as a storage mechanism. Dropbox allows for public or private file sharing among groups and individuals. Dropbox group members must also be members of Dropbox.

Dropbox can be mounted as a web drive on Mac and Windows, and also has a desktop client for Mac, Windows and Linux. Dropbox is used for many mobile applications, and automatically syncs all versions to the web. Dropbox free accounts have 2GB of storage, and can track changes, for some level of document versioning control.


Cloud-based, Mac, Windows, and Linux. Both tools can be used for file sharing, and collaboration, and while Dropbox is the easier tool to use, WebSpace has integration with Princeton-specific resources that can aid collaboration.


Diigo is a social bookmarking tool that allows you to bookmark web pages, annotate and highlight them, and then share your marks publicly or privately. You can create groups for gathering and sharing bookmarks. Bookmarks are organized by tags, and group ownership can be transferred to another user. Diigo, and Diigolet, the Diigo bookmarklet tool, work with Firefox and Chrome. For fans of Delicious, a popular social bookmarking among scholars that has been around for years, Diigo is a good alternative. (Delicious’s new owner, Yahoo!, has announced that it will soon “sunset” Delicious.) Diigo has an import tool that will ingest your existing Delicious bookmarks, and at lest for now, has a setting that will allow you to bookmark sites in Diigo and Delicious simultaneously.

A copy of the presentation used in the talk is visible here:

The presentation can also be viewed online here, or downloaded from this location.

A podcast will be posted here shortly.

Lunch & Learn: Research and Writing on the iPad with Will Howarth

iPadHowarth.jpgImage courtesy remiforal, Flickr. Licence: CC.

Will Howarth, Professor Emeritus of English at Princeton, spoke to a large Lunch ‘n Learn audience on February 16 about how he uses his iPad as an essential companion to reading, writing, research and travel.

Howarth began the talk by describing his long search for a lightweight, portable device that would be convenient for use while writing and traveling. From small-format computers of various vintages, to PDAs, Howarth has found the iPad to be the best solution to date. Its light weight (24 ounces), long battery life (approximately 10 hours), responsiveness, and the availability of useful applications have made it one of his favorite tools for productivity.

Howarth showed the basic mechanics of navigating several iPad screens, and using the screens to organize applications by function. He also demonstrated how to customize the persistent tool “dock” that appears on all screens, useful for storing one’s most commonly used applications.

Howarth’s preferred layout is to have news and information applications on the first screen of his device, writing tools on the second, and on the third screen, a miscellaneous assortment of apps that are either not fully tested, or exiled as being of secondary importance.

Citing the limitations of the virtual keyboard on the iPad’s touch screen for someone with larger hands, Howarth showed his solutions in the form of two Bluetooth keyboards that can be synced to the device to allow typing on a more conventional set of keys. One of the keyboards was integrated into a small carrying case. The other, more suited for desktop use, was a compact stand-alone keypad that allowed for typing on full-sized keys. Another limitation to the iPad is the lack of a USB or other data port that would allow for easy file transfer via portable storage media. However, since several of the applications that Howarth customarily uses have mechanisms to sync and share files among several machines, this shortcoming has been largely overcome by application developers. Howarth proceeded to describe and share his favorite iPad applications for writing and research with his audience.

Howarth’s talk was divided into eight general categories of iPad applications. Reference tools, Database applications for storing and organizing, Readers for books and periodicals, Note-taking tools, Notebooks that sync files between applications, tools for working with PDF files, Storage on Cloud servers, and a Productivity suite with familiar office tools, formed the outline of Howarth’s talk. Each of these categories is discussed separately below.

Author’s note: Although the talk was cut short owing to time constraints, Professor Howarth was kind enough to share his notes with me. This post contains material that may not have been presented in the talk, or was mentioned only briefly last Wednesday.

Reference tools:


Safari (included with the iPad) is the browser included on all machines using the Apple iOS. Safari on mobile devices can be customized for fast browsing, for bookmarking popular destinations, and customized to take advantage of the highly portable nature of the iPad. Howarth demonstrated how he has tailored his particular Safari toolbar so that he has research tools, particularly remote access to scholarly research collections including Princeton’s Library, available at his fingertips. Among the headings in Howarth’s customized list of bookmarks are Reference tools, Authors, and Libraries.


Wikipanion (free in the app store) is a tool designed to optimize searching, navigation, and display of entries in Wikipedia. The tool’s graphical display of a Wikipedia entry includes a sidebar outline of main headings in a Wikipedia entry to facilitate navigation and exploration, as well as contextual links to related topics.

Google Earth

Google Earth (free in the app store) is a portable version of the popular desktop application, made even more stunning by the iPad’s high resolution screen. The application includes all of the features and imagery of the desktop version, with the added ability to find your own location on the globe using the built-in GPS features of the iPad. A good companion to travel, Google Earth, like Google Maps (included with the iPad) can help to find local landmarks, businesses and cultural locations.

National Geographic World Atlas

The National Geographic World Atlas ($1.99 in the app store) is another application for maps, this time featuring high-resolution images of National Geographic’s own distinctive cartography. The app features 3 different styles of maps, and can be zoomed down to the granularity of a satellite image focusing on a particular street or building. (Street-level maps are drawn from Bing satellite imagery.)


The Safari browser should be the first point of departure as a source for reference materials, as the bookmarks can be customized to point to many excellent online tools. Howarth recommends not buying too many reference apps until the potential of Safari is exhausted.

Database Applications:

Things for iPad

Things for iPad ($19.99 in the app store), also available in a desktop version for Macs, is a task manager that fits with the category known as “todo” apps. The app allows you to enter notes, projects, and due dates, in an easy-to-use interface that syncs with the desktop version of the application. Since Howarth uses both versions, he finds it easy to set up lists at home, and have them automatically updated on the iPad. He uses the Categories to set up priorities and to schedule tasks, and uses the built-in lists for “Today,” “Next,” “Scheduled,” and “Someday” to help keep him on track with deadlines.

DEVONthink To Go

DEVONthink To Go ($14.99 in the app store) is a companion program to DEVONthink and DEVONnote, both desktop applications for the Mac. The program can be used on its own, but according to the manufacturer “unfolds its full potential ONLY when used in conjunction with these applications. Howarth uses DEVONthink Pro Office and DEVONnote, and uses the applications together to save web clips, bookmarks, files for courses, notes on alumni trips he has led, and writing projects. A sync folder in the applications keeps the iPad version updated; conversely any changes on the iPad are reflected in the desktop versions at the next synchronization.

Bento for iPad

Bento for iPad ($4.99 in the app store) is a personal database program made by FileMaker Pro. It comes in a desktop version as well, and can sync with Bento 3 for the Mac. The database includes templates for many sorts of organizational tasks, from to do lists, to events, to household inventories, to expenses–even logs for diet and exercise. Howarth uses Bento at home on his computer, and uses the program mostly for listing addresses, book
inventories, lists of films. The application, Howarth notes, can export and import spreadsheets in various formats.


These apps, Howarth noted, are best suited to those who are enthusiastic users of their desktop counte parts. For those who don’t own, or intend to own the companion programs, similar functionality can be found in the Note-Taking applications, described below.

One major lack in this category of applications is one for organizing bibliographic references. Howarth told the audience he has been in contact with the makers of EndNote, a popular bibliography program among scholars at Princeton. They report that an iPad version of their database is currently in the works.


Writing begins with reading, according to Howarth–here are his favorite tools:


iBooks (free in the app store) is Apple’s own e-book reader, with content purchased from iTunes. iBooks also has the ability to read PDF documents, which can be included in the library from email attachments sent to the iPad. Items in one’s library can be viewed as book covers on a virtual bookshelf, or in list view, and it is possible to arrange collections within one’s library. Howarth showed an 8-page PDF report written by one of his students that is now part of his iBooks library. The interface controls include adjustments for screen brightness, a search feature, and bookmarks. The interface also has an animated page turn feature, and a “scrubbing” progress bar to slide rapidly from one section of the book to another. Books can be annotated, but PDFs cannot. Although iTunes sells many popular current books, it also has many free offerings, mostly for books in the public domain.


Kindle, (free in the app store) an app that share the name of Amazon’s popular e-reader, allows Kindle books to be read on the iPad and the iPhone. There are numerous versions of the Kindle reader, available for most portable devices, desktops, and a web-based version. Content for the app is purchased from Amazon.com, or uploaded by the user. The reader accepts .azw files, .mobi files, .rtf and text files, as well as PDFs. Howarth showed how to navigate his Kindle edition of Deep Creek, a novel he co-authored with Anne Matthews under the pseudonym Dana Hand. The Kindle interface turns pages with a swipe or a tap, and tapping on a word will simultaneously offer the options to highlight the word, make a note about the text, and , and to display the entry for the word in a built-in dictionary,–with links to related entries on Wikipedia and Google. Notes bookmarks and highlights are stored on Amazon cloud servers, and can be referenced and printed through the online interface. The Amazon Kindle bookstore has the most titles of any digital bookstore, including more than 25,000 free titles from Project Gutenberg.


Stanza by Lexcycle (free in the app store) is one of the first e-readers ever made, and has been recently acquired by Amazon. Less sophisticated than the other two readers mentioned in this section, it offers annotations, bookmarks, search, and reverse black/white screen view. Stanza is backed by a library of more than 100,000 books, all of them free.


Working across e-readers can be problematic owing to the fact that formats, citations, annotations, and page numbering are not standard, which as Howarth notes, is a major headache for scholars. One bright note on this topic is the recent announcement that Amazon will include references to the pagination of the print edition on which the Kindle edition is based, which will allow more accurate citations and place finding for readers who are using both paper and digital editions of books. Apple’s threatened restrictions on books purchased from non-Apple apps also has caused some worry among consumers.

Among the three readers discussed here, Howarth declares Kindle the winner, because it is the most affordable and flexible platform for reading.

Note-Taking applications

These applications are ideal for taking, sharing and synching notes with other machines. In some cases, they can provide an alternative for the Database applications listed above. There are hundreds of such apps available for the iPad; here is Howarth’s selected list. Some of these applications have a browser interface that will update information on your mobile device.

Index Card

Index Card ($4.99 in the app store) is a simple non-linear writing tool for the iPad. It allows notes to be captured in an interface that resembles index cards pinned to a corkboard. Notes can be reordered, recolored, written, edited, and “stacked” into projects. Index Card exports a text file of your notes that can be read by most word processors. Howarth finds this a favorite tool for brainstorming, organizing, categorizing by color, and for organizing projects. He shares his cards via email, or using Dropbox.


PlainText (free in the app store) is a simple app for editing text on the iPad. It looks much simpler than Index Card, and does many of the same things. Sharing and syncing is done via a Dropbox interface. Howarth and other writers like it because it is simple, elegant, and has a very “paper-like” interface.


SimpleNote (free in the app store) is a note-taking app, that despite its name, is a little more complex than the other apps mentioned in this section. Howarth uses SimpleNote in conjunction with a Mac iOS application called Notational Velocity (a free, open-source download) that stores and retrieves notes. Howarth finds it a great way to type up quick or related ideas, which auto-sync to SimpleNote. There is also a browser application for SimpleNote that can be used to share ideas with others. There is no choice of font, and the user interface is less attractive than the other two options.


All three of these note-taking applications have unique strengths, but of the three, SimpleNote is the most versatile.


Notebook apps group items, sync them to cloud servers, allow for exports into various word processors, and allow entry of data either via a web browser or a desktop application.


Springpad (free in the app store) is an application that allows you to save notes, tasks, links, images, nearby places, barcode scans (from products, books or media), lists of things (movies, books, wines) in virtual notebooks that organize your materials by topic. It syncs via Springpadit.com to a browser interface that includes a web-clipping tool. Your notebooks can be shared with family and friends using Facebook or Twitter. Howarth likes the application for its organization and synchronization, and notes that it is a very good tool for working with groups. His notebooks, containing items related to Teaching, Writing, Travel, and Local topics were displayed against a background of a favorite picture.


Evernote (free in the app store) is probably the most popular notebook app for Apple devices. It stores many kinds of files including webpages, PDFs, text, links, audio files and images, and organizes them into notebooks based on project type. Each media type can also be geo-referenced for mapping and searching.  Evernote syncs to Mac, PC, and web interfaces, and the desktop versions are also a free download. The “todo” functions of Evernote are quite good, and works best when used in conjunction with one of the desktop versions (also free). Monthly uploads of up to 60MB per month are free on Evernote; the premium version ($45/annum) allows for monthly uploads of up to 1 GB. The premium version also allows for read/ write notebook sharing with colleagues, whereas the free version is read-only for those you share with.


Howarth notes that other notebook applications allow writing and drawing and speaking instead of typing, but his recommendation is Evernote as the best notebook app.

PDF Tools

PDF documents are part of the lingua franca of scholarly documents. There are several apps that allow PDFs to be read, annotated and shared on the iPad. Getting PDFs into your iPad can either be via a server, download, file-sharing via iTunes, or as an e-mail attachment


iAnnotate ($9.99 in the app store) as the name suggests is a tool made for annotating PDF documents ( PDF readers are more numerous.) The tool allows highlights, notes, freehand drawing or writing, bookmarks, stamps, underscoring, strike-through, and tabbed reading of multiple documents. The standard toolbars can be customized with a wide range of possible commands, and the program allows display through VGA out. Search is possible at the document level, or full-library. Markups can be “flattened” for printing and sharing in a way that preserves annotation as an image, or emailed “as is.” Sync is possible through iTunes, Safari, email and Dropbox. The same company makes a desktop PDF companion for iAnnotate calld Aji PDF Service. Using the desktop program in conjunction with iAnnotate makes it easy to manage large libraries of PDF documents.


GoodReader ($2.99 in the app store) is another PDF reader/annotation tool. It allows sticky notes, highlighting, freehand drawing and writing, rubber stamps, underlining, strike-through, and shapes such as arrows, boxes, ovals, and others that can be used to draw attention to sections of a document. Transfer and sync can be done via MobileMe, iDisk, Google Docs, Dropbox, SugarSync, box.net, and WebDAV and FTP services. The application is most versatile in the document types it can read: not only PDF, but MS Office, iWork, HTML, image and audio and video files can be used with this application.

Papers for iPad

Papers for iPad ($14.99 in the app store) is mainly for scholars of science. Although the app is a PDF  markup tool, allowing highlighting and notes, and emailing annotations, the chief benefit of the app is the built-in search engine that allows you to find and download PDF articles in the following databases: CM, NASA-ADS, arXiv, Google Scholar, IEEE Xplore, JSTOR, Pubmed, and Web of Science. There is a desktop version for the Mac that can be used for synchronization, but it also works with Dropbox, iDisk, iTunes and email. PDFs are stored on your iPad, so you need at least 100MB of free space. A limitation in the current version is that although documents are synced between the mobile and desktop versions of the app, your annotations are not.


GoodReader is a good value for most PDF use, and also works with other document types. iAnnotate has more markup features, and the advantage of VGA-out. Papers is invaluable for a researcher who commonly uses the scholarly databases supported by the application.

Storage on Cloud Servers

Getting documents on and off the iPad, keeping them up to date, and sharing them with people, other applications, and devices relies mostly on wireless forms of document transfer. Cloud servers perform an important function in achieving this goal.


From the numerous times that Dropbox (free in the app store) is mentioned in other entries, you may have concluded that it is a very popular program for file sharing. Dropbox is available for desktop and mobile devices, has a built-in public html file for sharing, and a photo file for making automated slide shows you can send to other people. Using any of the Dropbox interfaces syncs to all others. The free service is up to 2 GB, and the next upgrade takes you to 50 GB for $99/ year.

MobileMe iDisk

MobileMe iDisk (app is free in the app store, but a MobileMe subscription is required) is a popular Apple service that allows you to view and share files from a number of devices. File types from iWork, Microsoft Office, PDFs, QuickTime movies, JPEGs and more, are supported, however files larger than 20MB may not be viewable on all devices. The iDisk has both public and private folders to facilitate sharing. Paid subscribers of MobileMe who have legacy iPhones can subscribe to a service on MobileMe that will find their lost or stolen iPhone.  Owners of the iPhone 4, iPad, or fourth generation iPod touch with iOS 4.2 or higher can get this service with a free account, but storage space still costs money.

Air Sharing HD

Air Sharing ($0.99 in the app store) allows you to mount your iPhone, iPad or iPodTouch as a wifi drive on your computer. It works with Mac, PC or Linux. Mounting your mobile device as a remote drive allows you to drag and drop files between devices for syncing and sharing. Documents can be viewed and emailed. The app also allows you to mount other web-based servers such as MobileMe iDisk, Dropbox, Box.net, WebDAV, FTP, FTPS, and SSH/SFTP, and allows downloads of files from the web. Air Sharing can zip and unzip files, print to printers shared by Mac OS X 10.5 and above or Linux. It has an advanced image viewer for hi-res images, and an PDF viewer that supports large, structured PDF files. There’s a long list of viewable file types that includes most office applications and media files. The HD version is made especially for the large display of the iPad; the same company also makes a fun app that allows you to turn your Apple device into an extra computer monitor.


Dropbox is the Esperanto of file sharing apps, and you should have this one. Other cloud services can provide extra features.


iWork for mobile devices started a revolutionary trend in office-type applications. Rather than buying bundled software that includes a word processor, a spreadsheet program, and a presentation program, as is typical, Apple decided to market these applications separately for the iPad. Each app costs $9.99. The unbundled desktop version costs $19.99 each for the same three apps.

On the iPad, files can be shared using email, iWork.com, iTunes, MobileMe iDisk, or WebDAV.. There is one-tap AirPrint available on all three apps that allo
ws for automatic printing on any AirPrint-enabled printer.


Howarth describes Pages as his favorite word processor, one he customarily uses on both the iPad and his Mac to share files with MS Word users. The iPad interface is described by Apple as “the most beautiful word processor ever designed for a mobile device.” They may be right.


Keynote is Apple’s version of PowerPoint, and in Howarth’s opinion, is in many ways better. Presentations are easy to build, and sync between devices (although fonts can be an issue). Keynote is one of the few Apple apps that works with the VGA-out feature of the dock connector on the iPad, which makes it possible to use the iPad as a display, as well as editing, device for Keynote presentations.


Apple’s spreadsheet app, which Howarth says he uses mostly for grade sheets, and built-in formulas to make calculations easy. The app has many built in design features so that spreadsheets look less like boring tables, and much more like a polished publication.


These apps make the iPad a viable laptop replacement. An external keyboard is almost required to get the most out of them, but the applications cost so much less than expected, you can use the money you save  to get a fancy iPad case with an integrated keyboard that makes typing a breeze.


According to Howarth, the iPad is a lot more than entertainment — the constant evolution of apps have made it into a valuable tool for writing and research. New, useful apps are emerging everyday to extend the usefulness of this device.

Howarth concluded his presentation with this video, which he said, makes it clear that research is “the coolest, sexiest work on the planet.”

The podcast for this talk is available here.

The handout for this talk is available here.

Enhanced by Zemanta