Now that I have finally finished my thesis – yes, I keep repeating that, but after all, it’s a huge success for me – I want to write about the tools that I employed. Before I started my thesis I kept searching the internet for applications that would suit my needs and wouldn’t cost too much. Bringing those two factors together was no easy task, let me tell you … as my friends would tell you, I do have high expectations.
I found a number of articles and ended up downloading MB’s over MB’s of trial software, until I settled for three tools.

Since I want to do this properly, I will split my report into multiple parts. This first part will be about organizing notes and research material, the other part(s) will deal with organizing references (books, .pdf files, websites) that you will quote in your paper and which software to use to write the paper itself. The three tools I used are

• Journler
• Bookends
• Mellel

I will not compare them (too much, if at all) with other applications. I know that everyone has different preferences and I encourage you to try as many applications as you can before you make a choice. I just want to write about my own experience and hope that some of you may benefit from it.

Journler – Where your notes go

First I needed to figure out what my workflow would be. That will be different for everyone, so you really need to sit down and think about it. What works for one person doesn’t necessarily apply to another. Being clear from the beginning about how you want to tackle your paper will save you a lot of grief later on.

For me, I wanted to rely 100 percent on a digital workflow. I knew I’d be spending a lot of time in the college library, because many books are not for taking out. And making so many xerox copies would have killed my budget. I wanted to have all my notes on my Mac so I could search for them comfortably via Spotlight or from within any application. I remember that for my last paper I had to search manually through hundreds of xeroxed pages and handwritten notes. Never again!

Therefore, I needed an application that would allow me to take notes, to cross-reference notes, to link files to notes … in short: I needed some form of database where I could store my own thoughts and all the research material that I would accumulate. The application would need to be flexible so I could accustome it to my needs.

Now, for me an application is good when I can use it right after I dropped it into my application folder and I don’t need to read the manual first to get an idea of how to work it. Of course, finding out the details, the keyboard shortcuts and some really nice, handy features often requires a look into the help, but for a first impression I just want to use the app. Some of the software I downloaded failed there already. Journler, on the other hand, excelled.
I quickly looked at the screenshots on the official website and it was quite intuitive to use. And, even more importantly, there is an active community of users that exchange tips and information on the forum. The developer himself is very responsive and tries to help as fast as he can should a problem arise.
Don’t discard this point when you look into software, especially when you are about to buy it or use it for an important project. Always take into account the possibility that you might get stuck at some point or something unforseen might happen. You will need help and an active community and an attentive developer will spare you a lot of trouble.

I encourage you to take a look at the official site to get an idea of the user interface; I have tweaked mine a bit (don’t ask me why I used flag icons for the outline of my thesis, it seemed a funny idea at that time Winking ). What I did was set up a folder for all my research, named “Diplomarbeit” (that’s German, equals final thesis). It would contain all notes, links, documents that I deemed important at that time. In addition I set up sub-folders for the different parts of my thesis. Since I was writing about online communication and comparing traditional face-to-face interaction to mediated interaction I needed to separate my notes on those two subjects. Then I wanted each chapter that I’d write to have its own folder so I could store notes specific to that topic in one place. In the end, my structure turned out to be a lot different, but that’s another story.
Next to traditional folders you can also have smart folders. Much like smart playlists in iTunes you can define criteria that will help to populate your folder. Be sure to read up on inheritance in the help, it’s a really cool feature.

What I liked was that Journler offers the possibility to assign categories and tags to each entry. You can also color-code entries. I used colors to indicate to which part of my thesis the entry belonged. And it looks nice, too.

But the killer feature for me was the ability to link entries to each other. So, if I was writing down a summary of the book I had just read and in a stroke of uncommon brilliance I’d realize that the topic would tie in perfectly with another entry, I’d just link a word, a sentence or the whole paragraph to that other entry. It’s abolutely easy and it helped me tremendously to create connections between thoughts.
On the downside, you can really just link to another entry, not to a particular part of that entry. If you don’t know what I mean: On websites you sometimes have links that – upon clicking them – take you further down a longer page so you don’t have to scroll down. That technique is made possible by using “anchors”. You can jump to exactly the sentence or the word you want to go. In Journler, you can jump to another entry, but not to a particular word or sentence in that entry.
To prevent myself from getting confused later (if you read 80 or 100 books and cross-link them, you sooner or later forget what exactly you were trying to point out to yourself) I wrote in brackets to which part of an entry I was linking so I could find it more easily later on.

Another feature I used a lot (and will again, now that I have to read again to prepare for my final exams) is linking documents to entries – and websites! Yes, you rad correctly! You can link sites from the internet to entries in Journler and browse them right in the application itself! Or you can create an entry that consists just of a website. You can still link from it or to it from other entries.

The same goes for PDF files (or any text files, for that matter): Create a separate entry for them or link them into an existing entry – you can browse them from within Journler as well. I love these features!

Journler offers a lot more cool features, among them seamless integration with the iLife Suite, but I never really used it so I can’t say anything much about it. The reason I chose Journle over other application like Yojimbo or Mori was that back in the fall of 2006 Journler was free. After I really got into the app, I donated 15 dollars to the developer. Back then that was all I could afford, though the app is worth a lot more (to me, at least). In the meantime, Phil Dow – the developer – tries to make a living off the app and has started charging for it, though student disounts are available. Since I want to use the newer features as well as update my system (which I never do during an important project – Never touch a running system!) I will buy the upgrades or whatever is available for previous donators. I just love the app and couldn’t work without it anymore.

Go to the Journler Website

This was the first of three parts about scientific writing on a Mac.

Related Posts

• Convert AC3 Audio Files on a Mac
• Data migration: Get your emails and iTunes library back
• Converting .flac Files on a Mac (2)
• iFlicks – Manage your videos from within iTunes
• MacHeist Free Apps Giveaway
• Flac Files on a Mac
• Eigene Filme in iTunes – Beschreibungen bearbeiten
• iTunes und Filmverwaltung