Software for research

News Chris Salter Dec 3, 2012

Researching is easier when you have the right tools for the job - Chris Salter shares a basic toolkit

One of the skills that new university students will need to learn is the ability to research information. At college and GCSE, it may have been sufficient to quote Wikipedia and rely on class handouts, but at university, a student needs to show more knowledge of their subject and related areas. Learning how to effectively research at an early stage of a course will help significantly later in the course such as at dissertation time.If you’re considering postgraduate study or a doctorate, the ability to research is a very sought after skill.

This article sets out some software that will help you as a student to become a more effective researcher. While the software alone won’t automatically make you a good researcher, like any workman, a decent set of tools will help. Where possible, software mentioned here will be displayed with cost and what platforms it’s available on to ensure that you don’t have to spend any of that hard-earned student loan.

Likewise, this article will apply to anyone that has to conduct research as part of their job. Making and recalling notes can help immensely within most lines of work, especially if you’re approaching a difficult task and think others may have come across a similar issue in the past or you think you’ll be needing information in the future.

Note taking

The aim of research is find new information. However, in this quest, very often you’ll have to record information from others as you go, so that when you get towards the end of your research and have to summarise everything, you’ll need to be able to go back over what you’ve found. Due to the differing features of each software, you might find yourself using a couple for different tasks!

Evernote

Link: www.evernote.com
Cost: Free/£4 month/£35 yearly
Platforms: Web/Windows/Mac/iOS/Android (Linux support third party)

A cross between a web service and program, Evernote allows you to write and sync notes between all devices you own. These notes can be rich text (with tables, images and check boxes) to purely text based notes. Anything you write on a device is synced to the Evernote servers and is then accessible on any device you connect to your account. Access is free but has a number of restrictions like only 60MB upload a month and no offline access on mobile devices. Premium membership extends this to 1GB uploads a month (the total amount of disk space is unlimited on all accounts, just the amount of upload per month is restricted) and adds additional features, such as the aformentioned offline sync. Indispensable for accessing your notes on whatever device you use.

Simplenote

Link: www.simplenoteapp.com
Cost: Free/$2 month/$20 yearly
Platforms: Web/Windows/Mac/iOS/Android

Simplenote is a similar service to Evernote, though it only focuses on plain text. Primarily a web service, you access Simplenote via the website to get started. As its name suggests, creating and writing a note is simple as clicking and starting writing. In a previous Micro Mart issue, I introduced Markdown. Simplenote is Markdown aware and can display any note you write in Markdown as a complete note with the formatting shown, which Evernote is not capable of. This allows you to write formatted notes without having to mess about with toolbars or formatting menus. Desktop access to Simplenote is provided via third-party applications and these sync to the service, much like Evernote. The benefit of opening the API up like Simplenote has done is that third-party developers can develop different applications, so as a user, you’ll be able to choose one that you prefer.

Tiddlywiki

Link: tiddlywiki.com
Cost: Free
Platforms: Windows/Mac/Linux/iOS/Android

Tiddlywiki is an easy-to-use wiki software. It allows you take notes and store them in a single HTML file, editable from your web browser. Just like the wiki software behind Wikipedia, it lets you easily link your notes together to reference notes within your notes. While Evernote and Tomboy allow this (and in a workaround, Simplenote can do the same), Tiddlywiki’s whole aim is to link notes together like this and it accomplishes it well. To run on Android and iOS requires an app, but it is possible. Drop the wiki file into a file syncing service and you’ll be able to access your notes wherever you are without having to rely on a webservice, like Evernote or Simplenote.

Tomboy

Link: projects.gnome.com/tomboy
Cost: Free/$1.99 month/$20 yearly
Platforms: Windows/Mac/Linux

Tomboy is a common sight on Linux machines, installed by default with the Gnome desktop usually. However, it’s a cross platform app that also runs on Windows and Mac as well as Linux. Tomboy supports wiki linking, similar to that of Tiddlywiki. Like Tiddlywiki, Tomboy notes can be synced to different machines, though like Tiddlywiki, you’ll have to use a third party to do so.

Referencing software

Tracking what you’ve read is essential when performing research, so you don’t end up duplicating your reading and to make sure that you are able to properly reference your research - something that should always been done to prevent accusations of plagiarism and to allow other to follow the steps that you made in your research. Keeping track of it as you go allows you to keep up to date and makes it easier at the end of the work to ensure that all references are in place.

Mendeley

Link: www.mendeley.com
Cost: Free/£3.99 per month/£44 per year
Platforms: Windows/Mac/Linux/iOS

Mendeley is a desktop app that combines both note taking and referencing. It allows you to import PDF documents you’ve downloaded from the web and then stores details on them in its reference database. To make it easy, the software checks the PDF for information and will autofill in the titles and journal references for you - normally fairly accurately, though sometimes it may need checking. From there you can open the file and annotate it, make notes and then it can sync these notes (and the PDF files if you want) to the web so you can access it on any of your machines that sync with the Mendeley server. It then also has a Word plug-in that you can install to make it easier to insert the references and bibliography into a document. A number of referencing styles are included. If you write using LaTeX (covered in Micro Mart 1196), Mendeley also outputs its references as a Bibtex file, allowing easy integration into your workflow. An account is free and comes with 1GB of storage for papers. Additional storage can be bought for a monthly or yearly fee.

Zotero

Link: www.zotero.org
Cost: Free
Platforms: Windows/Mac/Linux/iOS/Android

Zotero is a bibliography referencing manager that integrates with Firefox but now also comes with a stand-alone client. Like Mendeley, it is able to read the data from papers just from adding the file to the program so that reduces time needed to write it all up. It offers a few different features to Mendeley but performs the same function. Unlike Mendeley, its referencing utility only works with .rtf files, which restricts it a bit more in comparison.

Jabref

Link: jabref.sourceforge.net
Cost: Free
Platforms: Windows/Mac/Linux

Jabref is a Java-based program and will therefore run on any operating system that Java runs on. Unlike Mendeley or Zotero, the user has to manually enter data into the database, which can be time consuming but prevents errors from poor transcription. As it stores its references in a BibTeX database, ready for use with LaTeX, most journal and knowledge sites will offer downloads in BibTeX format, which can make importing articles easier.

Writing

Writing up your research is a major part of the research process; without writing down the results and conclusions, no one can follow your thought process or see how you reached your results, which is a key requirement to publishing work. Research documents can tend to be short memos all the way up to large, multi-volume reports or books. Various software exists to help make it easier to write up long research documents - Word isn’t always the best tool.

Scrivener

Link: www.literatureandlatte.com/scrivener.php
Cost: ~$45
Platforms: Windows/Mac

Scrivener is a writing software, aimed at those writing long pieces of work, although it works equally well with short reports as well. Borrowing principles from LaTeX (mainly that the content is separate from the layout), it allows you to break down your work down into different chapters, sections and subsections and easily move the work around. It’s an incredibly powerful tool but can take some learning to get used to. It does offer 30-day free trials to allow you to discover the ins and outs of the tool. It can output its writing as PDF, HTML, .doc and other formats. Scrivener also allows you to make and keep notes related to your document within the file itself, which can save having to switch between another software and Scrivener to write.

LaTeX

Link: www.latex-project.org
Cost: Free
Platforms: Windows/Mac/Linux/iOS

LaTeX is the master of academic writing. As mentioned previously, it separates the writing from the layout and makes it easier to set up everything. The downside is that it requires some learning. Also, it’s such a huge subject, as there are so many different editors (from ones such as Vim, which is basically editing in a command line, to fully featured clients that mimic Word, such as TexnicCenter) that a whole article could be written on it alone. However, it makes long-winded academic writing far easier than having to wrestle with Word’s ability to place captions and figures on different pages and other oddities.

LyX

Link: www.lyx.org
Cost: Free
Platforms: Windows/Mac/Linux

LyX is LaTeX for those that don’t want to learn LaTeX. While LaTeX is a fantastic tool for those writing long documents (anyone who has wrestled with Word’s formatting will quickly appreciate it!), it does take some learning and not everyone is comfortable writing code. Step in LyX, which aims to produce LaTeX-quality documents for those who are uncomfortable leaving behind the WYSISWYG (What You See Is What You Get) style editor of Word. Because it uses LaTeX as its basis, LyX still requires some learning, but the basics there make it easy to get going and produce decent-quality documents straight away. Like LaTeX, it can deal with mathematical formula extremely well and is ideal for students or those working in STEM subjects.

Data handling

Presenting data and manipulating data is also another key research skill. While your university may have access to software such as MATLAB and SPSS, not every department or workplace will be able to afford the licences for these. However, some alternatives do exist.

Gnuplot

Link: www.gnuplot.info
Cost: Free
Platforms: Windows/Mac/Linux

Gnuplot is graphing software that allows you to create professional graphs. While it takes some getting used to, there are some excellent guides online that will help you make the most of it. Ideally suited to processing large datasets and performing repetitive graphing tasks (due to its command-line nature), Gnuplot outputs its data ready for use in Word, LaTeX or whatever software you’re using.

PSPP

Link: www.gnu.org/software/pspp
Cost: Free
Platforms: Windows/Mac/Linux

PSPP is an open-source clone of the SPSS statistical software suite. Advanced software for those needing to perform statistical analysis on datasets, PSPP is a step up from using Excel for performing calculations. Matches the functionality of SPSS very well for free software but doesn’t look as polished.

Octave

Link: www.gnu.org/software/octave
Cost: Free
Platforms: Windows/Mac/Linux

Octave is an open-source equivalent of MATLAB. It offers some compatibility with MATLAB as well, should it be required. Designed to produce computational models and calculations, Octave takes some learning, but if you need to perform the sort of calculations that Octave is capable of, you’d have to learn either MATLAB or Octave anyhow. Octave has the benefit of being free and open source, so you’ll be able to use it wherever and whenever you want.

Remote access

You should check with your workplace or university if they have remote access to their network. Some universities have moved to web-based email systems, allowing staff and students to remain connected (Loughborough University uses Google Apps for Education, allowing students full access to all Google products within the App range - ideal for collaborating with other students, because you know everyone can access the data you send). However, other systems may be in place such as VPN access, allowing you to access restricted areas of the university network from home, file system access, allowing you to access personal files on the go and mobile access for various devices. All of these will allow you to work from wherever you want, rather than stuck in the library or computer lab.

Backup

Writing and storing notes is all well and good but what if an accident happens and that laptop of yours gets stolen or you spill wine over it? You'll want a copy of your work somewhere you can access it again in a hurry - nothing causes stress like losing your dissertation hours before hand in. Dropbox (www.dropbox.com) is well known for syncing and the fact that it has a cloud copy is great but it's not aimed at backing up. Spideroak (www.spideroak.com) offers more free space than Dropbox and if you sign up with an academic email adress (.ac.uk) it'll give you a 50% student discount. Crashplan (www.crashplan.com) offers a cheap offsite backup as well as you can use friends computers to back up work too.

Conclusions

This article has briefly detailed various programs that can make it easier for those conducting research to progress through the main stages of reading, making notes, referencing and writing up the results. As most offer a freemium model, you’ll easily be able to try them all, then stick with one you feel comfortable using.