Facilitating the academic workflow: Tools I use to be productive

This blog-post lists a number of applications, tools and utilities I use regularly and might be of use to others. This is Windows and free software mostly, although Firefox Plugins should be also available on other platforms. For those that are not available on the Mac or Linux similar solutions should be available, i.e. I hope so.

The tools and applications listed below are to point you in the right direction. Most applications have clear installation and help instructions or even instructional videos. Also, these are my personal favorite tools. If you have your own, perfect.


Zotero is my main software cq plugin package to manage my literature and web archiving. Once you’ve found a publication you press an icon that stores it in a folder on your drive and in the Zotero-cloud (or a local (NAS)-server with WebDav) so you can access it also on you other computers. Cloud storage is for free for the first 300MB.

Zotero can generate many references style lists. You can tag and annotate the articles on the desktop or laptop, or use Zotfile (a Firefox plugin) to transfer it to your tablet, annotate the pdf, sync it back to the desktop and extract the annotations for later reference. To me this is the best option for moving to the paperless office. Zotero also can create webpage-archives. Screen-clippers only copy the actual visible page on the screen. Zotero captures the entire page, and retains the original URL for later reference. There are other options for managing your references such as Endnoteweb and Mendeley, but I find these less adequate.

For word processing I use MS Office 365 which works perfectly. Although it syncs to One Drive by Microsoft, but I do not use it (see the later section on cloud storage). There are other packages such as Open Office (open source) . For the more technically inclined you could use LaTeX for scientific writing. I have the plugin for Zotero installed in MS Word so I can write manuscripts directly connected to Zotero for the references and create the reference list automatically. If you delete or add one reference in the text, it will be updated in the reference list. Great tool, Zotero.

Microsoft came with the Start menu for decades. However with Windows 8 Microsoft removed the start menu in favor of the tiles, even though people liked it (even without knowing it). So third-party apps stepped in to create small apps that did the same as the original start menu. In the next version of Windows 9 the start menu is expected to re-appear. However, since a number of years I use the Start menu less. Instead, I use a small application called Launchy which can be called by the keyboard shortcut Alt-Spacebar ( which can be changed to your liking). A small window pops up where you can type in the first letters of the application you want to start, and then shows the applications that fit best. Subsequently enter and the application starts. The good thing about Launchy is that it remembers the most frequently used applications so often the application you want to use pops up with only entering the first two letters.

Browsing to many folders on your hard drive to search certain files can be a real hassle. Creating shortcuts, or favoriting certain folders is an option. But for me not anymore: my folder structure is too complex. I used to use Google Desktop but is was discontinued. Now I use Listary. It indexes the folders on your hard drive and once you have opened windows Explorer and just start typing it pops up with some suggestions that fit the typed word, pick the folder or file you want and ready you are.

Data collection, cleaning, inspection and statistical computing

For web questionnaires and coding I advise my students to use Limesurvey (open source). Limesurvey is for free and easy to use. Particularly for students doing their thesis research it is a versatile, easy to learn software package. Because it is for free, they can use it at a later date in their professional career, without needing to buy an expensive license. This also holds for statistical software: SPSS is basically too expensive for small businesses whereas R is available for free. The waiting is for the statistics departments to adapt their courseware transferring it from SPSS to R. This is really made easy when I realized that the very popular book by Andy Field Discovering Statistics using IBM SPSS Statistics is also available for R: Discovering Statistics Using R. So, there’s no excuse to change to R and in the process save a lot of money on license fees to IBM.

I use SPSS version 21 (at this time, Version 22 is already available), which serves me just fine right now. It is still maintained at a regular level. Since some years SPSS has become more flexible regarding adding new statistical tool and models, using extensions, for instance to create dummies without syntax using a menu or regression modeling with obscure distributions.  This change of SPSS’s strategy is most likely due to the increased popularity of the statistical application R. SPSS now even provides tools to actually interface with R, use its functionality and echo the results in the SPSS-output. The user never sees R.

A very active discussion list about SPSS is SPSSX-L. If you’re stuck in an analysis while using syntax, you can post the problem on the list and most likely someone will help you. However, be sure it’s not a silly question because you will certainly be redirected to your statistics professor, the library, or suggested to RTFM. As for R, a very interesting blog on all sorts of applications in R is R-Bloggers.

I am slowly transferring my work from SPSS to R where possible. R can do everything SPSS can do, and much much more. A very nice feature of R is that its graphics are better looking than those of SPSS. They are also easier to modify. Although the options can be somewhat overwhelming. However, for the time being I am still too dependent on SPSS for data cleaning and processing right now. Using a lot of unstructured web data it often takes quite some time to get it in the rectangular shape for the actual analysis. Read this NY Times article about data science that sort of explains what the issues are.

When you need to clean and inspect raw data you can use SPSS to do so, see the aforementioned remarks about data cleaning. However, some time ago Google launched Google Refine. Google has abandoned the project already but decided to donate the code to the open source community.  It is a helpful tool for software and visually assisted data cleaning and data inspection.   I have used it sporadically, but because SPSS is my main tool it does not belong to make first choice.

Every now and then I need to work on HTML or CSV files. Mostly these types of files come as downloadable ones from the web. While you can import these into MSWord or MSExcel, I prefer to use a dedicated text editor. For some time I’ve been using Notepad++ which is awesome. Very powerful, tabs available. Still, now I bought a license for Ultraedit. It has more features that suit my needs, such as column selection.

Web tools

Firefox and its tools

For a number of years I’ve been using Firefox. The memory management  – that was not so good at the beginning – has improved very much over the last few years. Particularly now you can have open many tabs that do not load until you actually open them. Also you can group tabs together, for instance, when they belong to a similar project. An important feature is that when you’re working on different computers, Firefox allows you to sync all your settings and plugins across computers. So the user experience is identical with all your computers. These plugins are a major feature of Firefox. They are basically tools to facilitate web surfing but also for collecting data from the Web. Some of the main Firefox plug-ins I use are listed below:

I use Autopager occasionally: search results and articles are often spread out over many web pages. This plugin makes one single long page of it.

Greasemonkey is an plugin that hosts many scripts to change the way web-pages look esthetically. For instance you can change how YouTube looks by using YouTube Center.

If you use, let’s say, Firefox, you can use keyboard shortcuts to navigate (back: backspace), create new tabs (Ctrl-t) and close tabs (Ctrl-F4) (see this page for more keystrokes). But if you are more of a mouse user there´s an add-on called Firegestures  that lets you navigate using gestures with the mouse. For instance right-mouse-button-leftswipe navigates back, or right-button-swip-up creates a new tab. It’s getting used to it but it works quite well.

Imagine, you found a website with all the chapter of a book in separate PDFs? Normally you would save them one by one. Tedious, not to say the least. With Downloadthemall you can download them in one go. You can (de)select additional files as well. It of course also works with other file types than only PDFs.

As for YouTube videos, it’s easy to “save” YouTube video’s into categories on your Google account. However, for those video’s that might be deleted in the future, or for teaching when there’s no Internet connection, you can actually download the video’s onto your hard drive by using Firefox plugins. I use YouTube Downloader

If there’s a table on a web page and you want to copy this to a text editor or Excel, you’d normally drag the mouse pointer and copy-paste it. However, this is somewhat difficult with larger tables. With Table2clipboard you right click the table, choose Table2clipboard and choose either copy the row, column or entire table and you’re done.

Session Manager allows you to safe browsing sessions to the hard drive. When the computer crashes orWindows suddenly decides to update, you can always retrieve your sessions with your websites in the tabs restored.

Publishers will hate me for this, but I also use an ad blocker. It makes Web surfing so much more focused. I use the plugin AdBlockPlus.

For email I use Gmail, particularly because (a) my university’s web-mail is not adequate, and (b) Gmail is very flexible. The good thing about it is that it can be even made better by scripts and plugins. I use Active Inbox for Gmail for some time now. It allows you to flag emails to take action, set deadlines on emails, flag emails that require a response from another person. You can also attach emails to projects. It’s very versatile.

Other web tools

To make screen shots I basically use a few tools. I use Evernote because it is so easy to use and you can sync across computers because it stores in the cloud. I also use Snagit which has some nice features as well.

Many web apps have shortened URL generators built in (Twitter, Hootsuite). However sometimes you want to generate them yourself. Tinyurlgenerator is an add-on in Firefox that takes care of it. Click the appropriate icon and the shortened URL is copied to the clipboard to be pasted wherever you want.

To get informed on the latest publications in academic journals, I use RSS feeds for my most read academic journals and search for new journal articles. Because RSS-feeds strip the web layout of of websites you are receiving mainly textual information and some pictures and videos. This makes it more easy to get the core information without any distractions.

Some time ago Google Reader was discontinued. Many on the Web were very annoyed by Google’s decision. Still, other parties gladly stepped in to take over these subscriptions. I remember Feedly being popular, but was not to my liking. I opted for Inoreader which is available on the Web and as an Android app.

For the work of authors I am interested in I use Google Scholar to be notified whenever they published new articles or are being cited by others. Remember this is a tool that always should be complemented by searching Web of Science or Scopus (very unfortunately discontinued at my university). Also, if your university does not subscribe to a particular journal, just email the author(s) to receive a copy of the manuscript. They’ll be happy to send you one.

I am sure this happens to you occasionally: browsing the Web to find information, when you come across an unrelated article that is also very interesting. What to do! Interrupt your initial search and read it, and thus forgetting why you went onto the Web in the first place. Or save it for later and first finish your initial search. To do the latter, I save Web articles for later with Instaper that allows you to save the Web article onto their service stripped of any distracting graphics (e.g. advertisements). I find it very useful for reading the Instapaper saved articles on a tables or even your smart-phone..

Auto Hot Key is a scripting software package that allows you to automate many tedious tasks on the PC: from auto-correction, text-expanding, to creating tailor-made data-extraction. For archiving websites there are several options. I have used HTTrack and Teleport Pro, but there are many more. They all sort of perform similar. They all are not able to capture streaming audio or video. If you browse the archived website, it still will play the online video. But when that is removed from YouTube, it’s gone. So, it’s best to archive the videos separately.

To be able to access my computer remotely I use Teamviewer. It shares my remote desktop to my laptop, smart-phone or tablet. I can also use it to transfer files, although I hardly do that.


Concerned about covering your tracks on the Web, use Donottrackme. In Firefox there´s also an option for private browsing. However this option only ensures that information is not stored on the pC itself. Logs on servers of your employer and on Facebook and Google, but to name a few, are still registering your Web activities. So this is mainly important to use on shared computers.

To learn what cookies are place on your hard drive during your web surfing, use Cookies Manager+. It allows you to see, and delete cookies from websites you visited.

The keep my accounts safe I use Keepass to generate and safe my passwords and usernames. There are other solutions, such as Lastpass. But because that’s an online service I don’t use it.

Cloud options

For sharing files between my phone, tablet, desktop or laptop I use Bittorrent Sync. After all the disclosures about backdoors and security breaching brought upon us by the NSA I wanted to remove cloud storage that uses severs in the US. I choose Bittorrent Sync. As you may know the bittorrent protocol uses a peer2peer network and does not use centralized servers. The only drawback security-wise yet is that the source code is not public. But then again that of Google Drive, Dropbox, Sugarsync, One Drive is neither. Bittorrent sync uses 128bit-aes-encryption which is safe enough. Also, if you have a NAS-server many brands have an app for Bittorrent Sync. Another option for setting up your own private cloud is Owncloud, but I have too little experience with that.

To backup data I use Syncback. The free version is more than adequate.


I have a two monitor setup of 24 inch monitors mounted on an Ergotron monitor stand, keeping the desk spacious. I also have a Corsair keyboard with mechanical keys (K90). No, I´m not a gamer, but the keys are so responsive and have the traditional keyboard sound that rubber dome keyboards do not have.
I do not use a mouse but a track ball. I used Logitech ones which worked fine. I didn’t like the Microsoft trackball. For over two years I predominantly use the Kensington slimblade trackball, and I love it. For my laptop (Lenovo y500 16GB) I use a Logitech Performance Mouse.

I use QNAP NAS (Network Attached Storage) to store important files: work files, music files to stream audio and movies to my living room. Synology is also a major brand that has a user-friendly interface and many capabilities. A NAS is a small computer often running on Linux with a number of hard drives. The number of hard drives is not only to expand the physical memory but also to create redundancy using RAID. This means in my case running RAID 5, one of the four disks can crash without losing any of my data. But remember, a NAS is not a backup option. For backup, always use an off-site option, so that even if your house burns down you still have a recent copy of all your files. For instance if you backup on a weekly basis, you will only loose one week’s worth of work. That is better than losing all data. Your university should be able to offer a backup facility. But particularly when using a laptop setting up a systematic backup is often forgotten. Having no backup arranged, it will go wrong eventually. I’ve had hard drive crashes a couple of times over the last 15 years and basically had everything in order. No need for expensive solutions for recovering data by specialized companies that some people or organizations have to result to.

In conclusion

So, this post turn out longer than I expected. And I still have the feeling I didn’t cover everything. I hope you benefit from these suggestions.




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Presentation at RC33 conference on social media

Last week I attended the RC33 conference of the ISA in Sydney, Australia. I participated in two events: a session on social media and a panel session on computational social science, both organized and chaired by Robert Ackland. In the session on social media I talked about my experiences working with Twitter data and the problems, solutions and opportunities involved in using these data. Below are the slides.

The panel session on computational social science we discussed about what it is, what we can do with it as well as computational social science in the era of Big Data. As for the latter part, I do think we gain using the Big Data, although we must acknowledge their limitations. However, I also think that Small Data still has the preference for now. Whereas the use of Big Data particularly involves the analyses of large systems, but still results in fairly descriptive analysis, small data allows for the analysis of specific cases. The benefit of the use of specific cases is that particularly social media data, that are limited when downloaded from SNS’s API’s, can be augmented / enriched by added additional data. If you read our work on social media and web campaigning in general, these analyses always use additional data about parties and their candidates. This way we can move beyond the descriptive analyses of social media.
Of course, computational social science is much more than using large amounts of data. Simulating behavior according to specific rules is also part of it. Still, computer simulation has been around for some decades already and – from my perspective – they still are not widely used. At least not being published about in academic communication journals. An exception in the field I am interested in (political campaigning) is Gulati et al. on modelling voting behavior.

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To free data or not to …

In some countries downloaders and uploaders are regarded as criminals: in the US you can expect litigation by record companies and artists when you share your music. In France your Internet connection wil be cut off when you’ve been downloading music and/or video’s. This shows that the Internet isn’t a safe haven for people that want to freely share information.

This is totally opposite to what the founding father of the World Wide Web Tim Berners-Lee thinks it should be. Berners-Lee is the advocate for free data. Organizations, in particular governments, should open their databases on-line, creating a level playing field for all. It also allows for members of the general public to contribute to datasets. Also, people can, if they have the expertise, to analyse these data and share the results in a numerical or visual style. This can be risky because as is possible with numerical information, visualizations can be deceiving. The proverb “there are lies, damn lies and statistics” should be “there are lies, damn lies, statistics and visualizations”.

A few initiatives are the US government, the UK government, and the Guardian. The sharing of data is, or it should be, common practice in scientific circles. In the Netherlands DANS archives scientific data and grants access (however, not for all). In academics, unfortunately, it doesn’t always pay to share your data for an important reason. Increasingly academics are told by university management to publish in ISI-ranked journals. That’s OK. But archiving data, which is important for secondary analyses and enabling others to check your work, takes a lot of time but is not rewarded by management. The time it takes to prepare the data and report for archiving could also be spent on new research articles and data collection. So, given the choice between a time consuming unrewarded archiving and writing new manuscripts, the choice will often be the latter. Unfortunately, this can only change when universities reward archiving the same as journal publications. I feel this is unlikely to happen in the foreseeable future.

Below are two videos where Tim Berners-Lee explains the idea and shows some examples.

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