Software for Surviving Graduate School Part 1

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After introducing a colleague to the wonders of Dropbox today (more on that later) I realized that it might be useful to put out a list of software that is of use to graduate students. I often find that many of the software products I find indispensable are virtually unknown to many of my fellow graduate students. Certainly this is no fault of theirs–I can understand how not being a tech geek (like I am) may mean not hearing about such software, or not having time to evaluate its helpfulness.

The first part of this series focuses on general use software that just makes managing multiple tasks and projects like research papers, class notes, and thesis readings really easy. I tried to choose software that is intuitive, efficient, and accessible on a wide variety of machines. All of the software products are products I use on a regular basis or have used extensively at some point (the latter are categorized as ‘notable’ instead of essential).

The software is organized into three categories based loosely on how often I find myself using it: essential, useful, and notable. I also present some alternatives I have come across that duplicate the function of the software I choose so you can explore other options. While some of these products may seem obvious, I try to note the features that may not be obvious that graduate students should find particularly attractive.

(Sidenote: I am a Windows user though most of the software I mention here is both free and available on Mac and PC (and often Linux). If the software is not Mac compatible I will try to suggest a Mac and Linux alternative.)



What is it?:
Dropbox is a drop dead simple tool for backing up and synchronizing files across multiple computers. Dropbox sets up a new folder on your computer that is constantly synchronized (quietly in the background) with the Dropbox webserver. Every file in that folder is automatically uploaded whenever changes are made to it. Any computer you own that you link to your Dropbox account will also synchronize with this server ensuring that any changes you make to files in your Dropbox folder propagate nearly instantaneously across all machines connected.

Why do I need it?: If you are tired of using a USB stick to constantly synchronize files between two or more machines and share files with friends and colleagues (and who isn’t?) then Dropbox is for you.

Pros: Simple backup. Easy sharing. Tons of control. 2GB of storage for free (more than enough for a semester’s worth of readings/projects/data). Minimal system footprint (read: small install and no drag on your system). Makes file sharing extremely simple–you can e-mail someone a link to a file that will always be the most up to date and current version of that file (great for sharing dissertation chapters with your faculty adviser).

Cons: Requires a connection to the internet. Accessing Dropbox folder via web-interface is not as slick as using it on your machine. No intermediate paid storage option (the first tier plan is $5.99 for 50GB).

Price and Availability: Free for up to 2GB of storage and unlimited synchronized machines. Works on Windows, Linux, and Mac.

Alternatives: Paid alternatives like Mozy and Carbonite offer more comprehensive backup and online storage, but not the ease of access and simple synchronization across machines that Dropbox provides.


What is it?: Gmail is Google’s take on e-mail. It is a web-based e-mail service like Hotmail and Yahoo! Mail that is accessed through a 

Why do I need it?: Simply put, Gmail is very simple. It can manage multiple e-mail accounts easily. It is powered by Google search, making it easy to find what you are looking for, and it has an incredibly flexible sorting system, making it easy to manage your workflow by sorting e-mail into folders as it arrives (think sorting all TA related e-mail into one folder and course related e-mails into their own separate folder). It also sports a great task list that allows you to create multiple to-do lists to keep track of multiple projects.

Pros: Huge storage space for holding your thousands of attachments. Large attachment limits for sending big files. Easily searchable. Quick to access from your browser. Works on any computer anywhere (whether in the lab, in the office, or on the bus from your iPhone). Compatible with popular mail clients (Outlook, Thunderbird, etc.) if you like keeping a local copy of e-mails just in case.

Cons: If Google experiences a server outage, so too might your e-mail capabilities. Not accessible offline when flying to a conference. You won’t know what to do with all the time it saves you.

Price and Availability: Free and available from any computer and operating system that is capable of running a modern browser.

Alternatives: As mentioned, Hotmail (or Windows Live! Mail) and Yahoo! Mail. Both are serviceable alternatives but lack the sorting features mentioned above.

Google Reader

What is it?: An online RSS aggregator and reader. (Note, if you don’t know what RSS is, check out Google’s quick guide to Reader for an explanation.)

Why do I need it?:
RSS feeds allow you to monitor multiple webpages simultaneously from one single place. Just about any site you visit regularly has RSS feeds allowing you to quickly and easily scan for new content and either read the whole article or flip quickly through headlines.

Pros: Quick and easy and accessible from any internet connected computer anywhere. Saves you lots of browsing to different sites by aggregating content. Less ads. Tons of tools for sharing content with friends via e-mail, Facebook, Twitter and more.

Cons: Not intuitive to set up (but it does offer pre-packaged groups of feeds for selection and features a great suggestion mechanism). Not accessible offline when you are on the bus on your way to class.

Price and Availability: Free and available from any computer and OS capable of running a modern browser.

Alternatives: Firefox plugins, Outlook, and several desktop clients for RSS feeds.

Google Calendar

What is it?: A web-based calendar tracking system from Google.

Why do I need it?:
To keep track of your schedule and the schedules of others. It is a great way to keep track of the different events in your life all in one easy to use place and it integrates well with GMail.

Pros: Easily accessible and always up to date anywhere you access it from. Can coordinate multiple calendars and event types, multiple notification methods to keep you from forgetting an event, and easily shared with friends and family. New improvements added all the time. Keeps track of tasks from Gmail.

Cons: Multiple calendar system is not always intuitive. Interface is not as graphically impressive as some alternatives.

Price and Availability: Free and available from any computer and OS capable of running a modern browser.

Alternatives: iCal, Outlook, Zoho Planner.


What is it?: A small utility for deleting unnecessary temporary files on your
computer that collect over time.

Why do I need it?: To keep your computer running lean and clean and prevent it from getting bogged down with unnecessary temporary files that are useless.

Pros: Small, light, fast, and easy to use. Keeps your computer in tip top shape.

Cons: Deleting browser cache may mean you have to re-login to all the websites you normally visit. Telling CCleaner which cookies to keep to avoid this nuisance is not a straightforward process.

Price and Availability: Free. Only available for Windows PCs.

Alternatives: None.

FoxIt Reader

What is it?: A lightweight PDF reader that serves as an alternative to an Adobe

Why do I need it?: In addition to being a lightweight alternative to Adobe that loads more quickly, it also allows you to annotate PDF documents for free. This can save you the hassle of printing out all of those e-reserves and simply take notes directly on the documents including highlighting, underlining, and commenting all within the document itself. It also features a tabbed browsing interface when viewing multiple documents simultaneously.

Pros: Tabbed interface keeps clutter from the taskbar when viewing multiple desktops. Small and fast to load. Commenting is free and included in the software. Can be run from a USB key if not installed on the machines in your office.

Cons: Free version occasionally asks a user to upgrade to the Pro version. When underlining and highlighting in the free version a small watermark is placed on the pages when printing.

Price and Availability: Free and available for both Windows and Linux (though with less functionality on Linux machines).

Alternatives: Adobe Acrobat Reader.

Microsoft Office 2007

What is it?: Microsoft’s ubiquitous office suite.

Why do I need it?:
This is hands down the best version of Office so far.While free alternatives may do 90-95% of the things that Microsoft’s Office can do, the parts they are missing are key. Microsoft Word and Excel are professional quality document creation programs. In a world where reading, writing, and editing research papers is the main craft you simply cannot use anything less than professional grade. If you haven’t used 2007 the new ribbon interface may throw you for a loop, but once you embrace it you will discover capabilities in this Microsoft product you never knew existed.

Pros: 100% compatible with the documents your colleagues are all using. Easy to output to multiple formats (PDF, docx, rtf, doc, etc). Can be integrated with Office Live for online backup of your files. Industry standard software.

Cons: It is not free. It can be a bit of a resource hog especially if you only need to make minor edits to a document. Track changes is not an ideal editing system.

Price and Availability: Available for Windows (Mac users get Office 2008). Students with a valid .edu address can get Microsoft Office 2007 Ultimate for only $59.95.

Alternatives: OpenOffice, GoogleDocs, Zoho, and Writeboard.



What is it?: Evernote’s goal is to be a more efficient version of your brain. It is a web-based storage and organization system for keeping track of anything you
want to remember in virtually any format you need to remember it in. Evernote allows you to drop any document/picture/note into it, tag it for organization, and store it to look at later.

Why do I need it?: Evernote is a quick and easy way to keep track of research ideas, data sources, and bibliography entries that you don’t want to forget on the go. By tagging items you upload into Evernote you can easily keep track of why you stored them there and deal with them later. The range of uses for Evernote is virtually infinite, but two of my personal favorites are uploading pictures of books I want to buy or read (from my mobile phone) while at a bookstore or using Evernote to convert a handwritten note (again uploaded via a picture from my phone) into editable text.

Pros: Accessible from anywhere using your cell phone or a PC with an internet connection. Virtually unlimited possible uses for organizing. Free. Updated frequently. Loads of tips and tricks made freely available by its active fanbase. Super secure.

Cons: Like any organization system it takes some getting used to.

Price and Availability: Free and available from any computer (via a desktop application or the web browser) or any mobile phone (through an application or via SMS).

Alternatives: Microsoft Office OneNote,  Zoho Notebook, Various Firefox extensions including Zotero.


What is it?: Google’s online answer to the Microsoft Office suite including word
processor, spreadsheet, and presentation building utilities.

Why do I need it?: For collaborating on documents with multiple authors Google Docs is a huge step up from spawning several clones of a file and trying to coordinate them by e-mailing them back and forth. Also, as a quick and easy way to edit files on a machine that is not your own, Google Docs is more than capable of quickly editing a file and doing 75-80% of the tasks capable in Microsoft Word. It also allows you to upload a large amount of files and store them online as another source of backup for your important documents.

Pros: Easy to use. Integrates beautifully with GMail allowing you to click on an attachment to an e-mail and edit it directly in GoogleDocs and e-mail right back without ever leaving your browser. Lots of room to share and store documents online. Offline access possible with Google Gears. No set up required, you can start using Google Docs the minute you set up a Google Account.

Cons: Not so great with very large documents. Formatting and printing are not as straightforward as in a desktop office suite. Cannot batch upload files, meaning if you want to migrate to Google Docs you’ll have to do it , uploading a few files at a time.

Price and Availability: Free and available from any computer and OS capable of running a modern browser.

Alternatives: Microsoft Office 2007,, iWork, Zoho, Microsoft Office Web Applications.

Google Groups

What is it?: An online tool for collaboration on documents, sharing content, and coordinating activities and events. It includes an ability to create
custom pages, set up an e-mail listserv, share files, and share news quickly and easily.

Why do I need it?: Have you ever had a group project where everything the group needed to read, create, and revise was all in one easy to access place? Didn’t think so. Google Groups allows you to create just such a place so quickly and easily it is feasible to set up a group for even a short term project. Just a few clicks and the group is set up and then you can e-mail invites to everyone on the project and get to work. The e-mail list feature alone is worth the price of admission (free, by the way) because it allows you to be sure everyone on the group is on the same page and avoid miscommunication (“You brought the CD right? No? I must have forgotten to CC you on that e-mail”). The ability to create ad hoc mailing list-servs outside of the constraints of the university makes your life a thousand times easier and your group more efficient.

Pros: Easy to set up. E-mail lists are a snap. Pages can be added for all group members to see and edit. Lots of control over user permissions, allowing you to share your work without being afraid of someone changing it and/or destroying it.

Cons: Not completely intuitive to some users at first. Relatively small online storage space for files. Cannot collaborate on uploaded files or simultaneously edit pages within the group.

Price and Availability: Free and available from any computer and OS capable of running a modern browser. Not available offline.

Alternatives: Yahoo! Groups is a serviceable alternative. For collaboration and group workflow see Google Docs, Google Wave, Zoho collaboration tools and the wikispaces option listed below.

Google Chrome

What is it?: The next generation browser from Google that is lightweight and incredibly fast.

Why do I need it?:
If you use some of the online web applications mentioned in this post you will see a noticeable increase in speed and rendering fidelity. If you are working on a lightweight machine (like a netbook) you will also see a dramatic increase in load times for your browser as well.  It also allows you to create application shortcuts (on the desktop or in the start menu)  to many web applications (like Facebook, Gmail, etc.) which allows you to load these pages more quickly and without the clutter of the rest of the browser interface.

Pros: Lightweight and incredibly fast. Clean interface that feels refreshingly simple. Just works.

Cons: Not compatible with some websites optimized for Internet Explorer (such as many of Microsoft’s own web pages). No ad blocking plugins or plugins of any kind. Bookmarking system not as sophisticated as that found in Firefox.

Price and Availability: Free. Officially only available on Windows, but betas of versions for both Linux and Mac are also available.

Alternatives: Mozilla Firefox. Safari. Opera.


What is it?: CutePDF is a simple utility that allows you to turn any document
into a PDF file that is easily readable on any machine.

Why do I need it?: CutePDF allows you to take any file on your computer that is normally printable (a Word document, Excel spreadsheet, web page, etc.) and instead turn it into a professional quality PDF. It installs a simple print driver on your machine that let’s you “print” any page to a PDF file and then save that file and share it with others.

Pros: Works on any document type that can be printed on a computer. It is a tiny utility that stays out of your way until you need it.

Cons: Requires an install so not an option for a machine you don’t own. Some web alternatives now exist that are accessible anywhere. Interface feels old and clunky.

Price and Availability: Free and available for both Windows and Mac.

AlternativesPDF Converter Online.


Google Wave

What is it?: Google bills it as the future of e-mail, but it is better to think of it as
a tool for online collaboration both in real time and back and forth like e-mail. However, it perpetually defies description and you are probably better off just watching these videos.

Why do I need it?: For collaborating on a document or some other content with another author in real time. Google Wave gives you the ability to make simultaneous edits to a block of text, insert photos, and collaborate and share a variety of other content all within your browser. It is also highly flexible and expandable, allowing your “waves” to interact with a variety of web services you already know and love.

Pros: Real time communication. Eases collaboration. Looks incredibly cool.

Cons: You can’t get it yet. It is still in the preview (alpha) stage of development and only a very few (just over 100,000) users even have access to it yet. The user interface may not be intuitive. Doesn’t work well unless everyone on your team is familiar with it and knows how to use it.

Price and Availability: Free. Still in an invite-only preview phase of development that should expand within the next 6 months to open up more to the public.

Alternatives: wikis, Google Groups, Zoho Projects, e-mail.


What is it?: An extensible professional personal blogging platform.

Why do I need it?:
Blogs are not something all graduate students need by a long shot, however there are some really powerful potential uses if the need strikes. Blogs serve as a great way to share ideas, files, photos, and other content in a central place. They help organize thoughts and coordinate team efforts. And, they can serve as a great promotional tool when heading onto the academic job market.

Pros: Incredibly flexible. Tons of help available online for free. Powerful editing and content sharing tools. Expandable as your site grows to add multiple authors, multiple comment streams, and social media tie-ins.

Cons: Overwhelming at first. Best features require you to host the blog on your own hosting solution (costing money). Advanced editing and site design require some familiarity with HTML.

Price and Availability: Free including hosting at For self-hosted sites you will need to have a web-host that allows FTP access.

Alternatives: Movable Type, Tumblr, Posterous, Blogger.


What is it?: While it bills itself as an IM client, I like to think of Digsby as a real
time communication dashboard. Digsby has the standard features of letting you connect to all of the standard IM clients simultaneously and chat with your friends. However, more interestingly, Digsby also integrates with social media websites (like MySpace, Facebook, Twitter, and LinkedIN) as well as your POP3 compatible e-mail service (virtually any service) seamlessly.

Why do I need it?: Digsby is your one stop shop for real time communication. Whenever I have a wi-fi signal I leave Digsby open and set it up to notify me as e-mails, tweets, Facebook messages/wall posts, and IM messages come streaming in. I can choose to deal with any of these events immediately (and often from within Digsby), or I can choose to leave them for later. Digsby keeps you connected without forcing you to have several web browser tabs open, or a resource hogging IM client like MSN Live.

Pros: Another lightweight program. Twitter functionality is impressive and unparalleled in an IM client. Offers lots of connectivity for its users. It synchronizes your settings and IM credentials online across PCs, so once you set it up on one PC you simply have to log in to Digsby on another and it is pre-configured and ready to go!

Cons: Ad-supported installer can be a little confusing and trick you into installing a toolbar (but the software itself is ad-free). No Skype support.

Price and Availability: Free and available for Windows. Mac and Linux versions are in development.

Alternatives: Adium, iChat, Trillian, Pidgin.


What is it?: Wikispaces is an easy hosted wiki solution for quickly creating a wiki to coordinate collaboration among several group members.

Why do I need it?:
Like Google Groups, Wikispaces allows you to easily set up a single place for collaborators to share ideas and edit the same content. Wikispaces requires minimal start up costs and is easily accessed by everyone in your team no matter where they are. Great for a research team working together to coordinate data collection, preliminary and final results, as well as arrange meeting times and keep track of contact information.

Pros: Free. Easy to set up. Simple and intuitive interface. Lack of distracting design clutter.

Cons: Requires some planning to make efficient use of. small file sizes (10mb) on the per-file size limit. Ad-supported. Requires registration at yet another website.

Price and Availability: Free and accessible from any web browser. Paid solutions provide valuable upgrades at reasonable prices.

Alternatives: TikiWiki (a self-hosted solution), TiddlyWiki, Zoho Wiki. And for a review of other alternatives check out this review of wiki solutions (from the School Library Journal).


Mozilla Firefox Extensions

If you do choose to use some of these tools and access them from the Mozilla Firefox browser, I highly recommend a collection of Firefox plugins to make your experience faster, cleaner, and more enjoyable. Be sure to check them out here.


I find myself using the above software all the time. The best part is that most of it is free and easy to find support for online. Sometimes the startup cost of trying new software can prohibit users from finding a digital solution to a workflow problem, and the software above is no exception. However, I have found that most of the software above is well worth the minimal cost it imposes in familiarizing yourself with it, and once you pick up most of these tools you won’t ever put them down.

Look for some more software list posts in the future on general computer utilities (of interest not just to graduate students but all computer users), academic software, and self-marketing/web presence tools online.

For now, leave a comment or pass the list along to your friends.

Don’t think I gave some software a fair shake? Disagree about my choices? Think I’m a Google fan-boy? Let me know in the comments.

To leave a comment for the author, please follow the link and comment on their blog: Data, Evidence, and Policy - Jared Knowles. offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
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