Michael Hohl and I started writing notes for research students on how to set up their computer so that it works well for writing and research. I have developed these notes further, and Michael’s website has very useful advice on organising workflow, folder structures, etc. The notes below concern software and on-line tools that support writing, research and collaborative working.

Whether you’re working on a thesis for a PhD, or researching for a book or major project, you need to set up your computer in a way that makes it easy to store stuff, find stuff, and sort stuff out. If you get a system sorted right at the start, then the whole venture should work almost by itself. The specific software you need will of course depend on what research you’re doing, and your preferences. It is worth trying different things out, as what works for one individual will not necessarily work for another – we all have different ways of thinking and working. It could be that you are working on a team project, in which case you will need more tools for collaborative working. What follows below is not the one true way, but some guidelines and starting points that have been shown to work.

The software recommendations are for a Mac. We may add PC recommendations in time, but to be honest if you’re using a PC you’re only making things difficult for yourself (in our view). But as we say above, it’s all about personal preference. There are a number of sites that recommend “the best OSX freeware and shareware”, which are worth checking out. Most of what we recommend costs money, but it is money well spent, and in some cases represents a very modest cost. There are some great independent software authors out there producing some very good tools.

There are four key things that you want your computer-based tools to do:

* Organise workflow (so you need a good folder structure and file naming convention) * Do stuff at your computer (so you need the right software) * Do stuff on-line (so you need the right webapps) * Ensure you don’t lose data (we’re talking regular back-up here)

Organising workflow

Michael has developed a highly effective and robust workflow system involving folder structures and consistent file names. As he says “Its totally anal – but works. It’s a no brainer and you will find stuff under great stress and in the middle of the night.”

Michael’s workflow notes explain how he has done this. His advice on how to handle files and to keep old versions of files is absolutely essential. His notes also refer to issues below, which I have edited somewhat, added additional details and provided weblinks.

Doing stuff at the computer

You should identify a core group of applications that do the things you want to do, work well together and that you feel comfortable with. Much of what I do involves making notes, organising notes, organising ideas, writing stuff up and presenting ideas as written documents, presentations, blog entries, etc. In the past I would have used Word for much of this, but now I use a combination of tools – each of which is great for a particular task. The age of the word processor may well be past. Differentstages of the writing process (and different types of writing) require different tools.

Evernote is a great note taking tool that helps capture and organise material and enables you to sync material you’re working on across devices. Hugely flexible and adaptable, some people even succeed in using it as the principal tool for doing an entire PhD.


Voodoopad – according to its producers “is a new kind of notepad. It’s like having your own digital junk drawer where you can jot down notes, web addresses, to-do lists… Anything on your mind. VoodooPad automatically links each page together, to form a miniature world wide web, on your desktop! Type in your notes, and highlight important words or phrases to create new pages; or drag and drop folders, images, applications, or URLs into VoodooPad – they’re linked up whenever the word representing it is found.” Michael uses this wiki-authoring tool extensively in his work. I’ve found that it takes a little time to get used to using it, and to appreciate its potential, but Voodoopad is a very useful application that helps to stitch together bits of writing, references, notes, files you’re working on, and weblinks. In short, extremely useful for research and writing.


Scrivener – is a great writing tool that fits very well with the way I work and is worthy of serious attention. It is cheap, but comes with a one month free trial. I tried it, bought it, and reckon it’s the best 30 pound’s worth of software on my machine. You set up a project folder and pile in all your notes, documents, pdfs, images, etc. If you use an outliner, it’s got one of those, and a ‘corkboard’ system of organising ideas and, of course, a text editor. It provides a contained environment to think and write within. If we think that a word processor is a typewriter, then Scrivener is your whole office – in short, an ideal writing tool. At the end of a project you can export the text in a range of different formats. I’ve used this for several years, on various projects from short articles to book chapters and reports. The software has been put together by a writer, which is probably why it works so well. Brilliant, elegant and intuitive.

iA Writer is built for the mac and ipad, and costs less than $5. It is generally my first writing tool of choice for small tasks, simply because it is so cleanly designed and distraction free. It syncs across devices very well and provides an elegant and clean environment ideal for focussing on how you craft the words.

Word processor – yes you do need one of these, but I find now that I only really use it at the end of the writing process. I still use Word but Michael uses Mellel. It’s not as simple as Word, but far better than Pages (the OSX wordprocessor), and printed pages look much better than in word. According to its producers, “Designed for scholars and writers, it offers innovative page, paragraph, and character styles, outline, tables, headers and footers, citations and bibliography, tabs, and much more.”

Omnigraffle – provides a powerful tool for mindmapping (and graphics) books, concepts, ideas, website structure, and the thesis as a whole. Macworld reviewed it by saying: “…this fantastic program is a revelation for anyone who needs to explain processes and concepts visually”, which makes it worth a serious look.

Keynote – the latest version is far more versatile and flexible than Powerpoint. Michael uses it “for ALL my graphic design needs, doing graphs, charts, diagrams. You can save as pdf or ppt or movie.” The advantage over Powerpoint is nothing to do with all the fancy transitions and effects, but rather its integration with other mac packages, its clear interface, and ability to produce and edit graphics.

Timeline – this software enables you to create 3D timelines that you can incorporate in Keynote presentations or use as a self-standing presentation. It’s icing on the cake stuff – but real quality icing that lifts presentations considerably whether you use iOS or OSX. Its value depends very much on how much you do presentations – but once you’ve used it once, then you’re hooked. Easy to use, and its integration with OSX is excellent – enabling you to import timelines from iCal and other applications. There’s three different versions and all are worth buying. For me the clincher is the positive and human attitude of the two person operation – BeeDocs – that produces it. Buy and download the software, then wait to see what arrives in your letterbox a couple of weeks later.

Papers – is what every researcher and student needs. It is brilliantly designed software that maintains your personal research library of PDFs. It helps you find them and download them, group them, create notes on them, and export bibliographies for End Note, etc. It costs 25 pounds, plus there is a 40% student discount. Papers and Scrivener are the two key tools that I use to pull my research material together and write it up. Like Scrivener, this is produced by people who once were researchers, and this shows in the power of the software and its ease of use. Just buy it.

Mendeleyin theory is great. Imagine Papers mashed up with Spotify so that you can link to other peoples’ PDF libraries. And the software is provided for OSX, Linux and Windows which you can download for free. The website gives you an online profile and a means of linking to all those other libraries out there, and the desktop application provides what Papers offers – but just not as well. But worth a try to see how it works for you.

MarsEdit – we encourage you to blog. It helps to make sense of your learning, it provides you with a vital sense of progress, it helps in terms of referencing stuff and it provides one way of connecting with others in your field. We suggest that WordPress offers the most flexibility in terms of a blogging service, but it is really a matter of personal preference. However, what most people agree on is that the web based interfaces for blogging services are universally fairly dire and inflexible. MarsEdit is an affordable OSx app that provides a highly useable front end to whatever blogging service you use that makes good use of the Mac operating system. Indeed this very blog is put together using it.

Freedomthe biggest barrier to doing stuff at your computer is doing stuff online. Emailing, messaging and constant online access is the enemy of concentration. This great utility simply disables all networking on your mac for up to 8 hours. Turn it on, and you get stuff done. Simple.

Doing stuff on-line

There are now many on-line tools out there to support research and to facilitate collaborative working.

Calendars and meeting scheduling

There are flexible alternatives to Outlook/Entourage that allow on-line calendars to be created and shared, like Google Calendar. Doodle “is a web-based meeting scheduler. It is used to find suitable dates for appointments with other people. No registration is necessary. This makes Doodle particularly useful for people who do not use a common calendar or groupware system. Doodle can be used to find dates for meetings, dinners, cinema, events, and so on.” I use this often. It works.

Project collaboration basecamp.jpg

Basecamp is the top dog of collaborative project management. All your notes, files, communications, timelines get put in this online tool that all your partners can have access to. It provides a clear and secure focus for all communication on a project. I have used it to co-ordinate a project with partners in a number of different Universities, while I am also a partner in another basecamp co-ordinated project with partners throughout Europe. After you’ve used it for a week you’ll wonder how you managed without it before. The downside is the cost, but it certainly does the job.

Google Apps do much the same thing, and are probably more flexible and adaptable. Using Docs, Drive and Calendar gives you the key tools you need to plan time, co-ordinate activities and share work. Zoho provides an alternative to Google Apps and indeed allows you to incorporate Google Apps in your workflow.


Editorially is a recently launched collaborative writing platform that offers some significant advantages over Google Docs. Its clean highly usable interface and easy way of documenting all changes make this worth trying out at least.

A great tool that we used to co-ordinate and plan the Global Service Jam in Dundee was Trello. It helps in terms of planning all elements of projects, identifying tasks, uploading documents linked to it, and enables sharing across the team. Try it.

Backing up data

The simple issue here is: do it. If you don’t then at some point all will end in disaster. I know. Some people backup on a nightly basis, others weekly.


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