My essential Mac research applications

A few weeks ago Mark Frauenfelder posted a list of essential mac applications. He had a bunch of great suggestions that reflected his graphics and writing needs. As a long-time Mac consultant and a grad student, I thought a similar listed aimed at the research community might be a good idea. The following applications are the go-tos for my research and content creation needs — I hope you find them useful. My apologies to Linux and Windows users — many of these don't exist for other platforms. I'm hoping that you can suggest alternatives and software that I've missed in the comments.

papers.jpg 1. Papers ($79, $49 student price, OS X). If you use journal articles in your research, you need this software. Think of it as iTunes for academic documents. It does several things for you. It organizes groups of documents, keeps a bibliographic database linked to the documents, lets you search for current articles by journal, author, or any other criteria you can think of, both in your document collection and online. And yes, it will import and export to your EndNote [bibliography management software] database. It also supports "cite anywhere" technology that lets you search for and insert styles citation in any program that supports text input. They have a 30 day trial period, so you can download and try before you buy.

pdfpen.jpg 2. PDFPen ($60, OS X). Of course having PDFs from a journal is great, but what if you need to hilite something, join together two PDF documents, or pull text out of a scanned PDF? That's where PDFPen comes in. It is similar to the free, open-source skim, but I prefer the interface. If you're working with PDFs, either of these is preferable to Acrobat. The free trial works with all features, but includes a watermark on PDFs.

PDFKey.jpg 3. PDFKey Pro ($25, OS X, Windows). Unfortunately some PDFs that you run into are locked, meaning you can't mark them up as you would a printed copy. You can print a copy and then re-scan, or you can spring for PDFKey Pro and unlock the PDF, allowing you to mark up articles as needed. Free demo available for download and evaluation.

calibre.jpg 4. Calibre (Free, OS X, Linux, Windows). When Amazon deleted copies of books people bought for their Kindle, I decided that ebooks just weren't worth the bother. That's changed recently. First I found out that Amazon has released software readers
, so you're not tied to their hardware. Then I found out that there were alternate open source ebook readers like Calibre available, which include plug-ins that let them import ebooks in formats such as Amazon's. There is also software that will let you take control of your ebook collection. Now I can use ebooks without worrying about a company pulling the plug on the content I've paid for.

graphicconverter.jpg 5. Graphic Converter ($40, OS X). This is software that's been around on the mac from back in the 90s, and it's still being maintained and updated. In terms of fuction it's similar to Photoshop, and allows you to do pretty much any kind of image manipulation you want. The big advantage for academics (aside from the price) is that it reads around 200 different graphic formats, and outputs around 80. If you've got a file that you can't open, this should solve the problem. Free download with unlimited evaluation time (shareware).

audacity.jpg 6. Audacity (Free, OS X, Linux, Windows). What Graphic Converter is for images, Audacity is for sound files. An open source sound editor that lets you record and modify sound files in non-proprietary formats such as Ogg Vorbis, MP3, WAV or AIFF and even raw. It has a generous set of features, including frequency analysis tools of interest to biologists and linguists.

eazydraw.jpg 7. EazyDraw ($95, OS X). Way back when the Mac was new, Apple included a program called MacDraw that let you put together vector graphics. This made creation of flow charts and technical diagrams a snap. These tools eventually made their way into word processors such as Word and Pages, but they never really felt right to me. EazyDraw is the closest I've found to getting back a copy of MacDraw, though the price is a bit steep. They offer an evaluation download that limits you to creation of 20 objects, and also offer a 9 month license for $20.

livecode.jpg 8. LiveCode ($99 and up, OS X, Linux, Windows). Back in the day Apple also introduced a software development kit called HyperCard. Unfortunately at the time John Sculley was in charge, and couldn't figure out how letting end users write their own applications could be a money-maker. So HyperCard died, but was followed by a series of programs that allowed users with little coding experience to create custom software. LiveCode is a descendant of the original HyperCard, and can even import HyperCard software. It is also cross-platform. Write once and compile for your platform of choice — OS X, Linux, Windows, iOS, android, or your browser. The programming language is simple to learn, object oriented, and very flexible. There are also a large collection of code libraries that allow you to add in specific functionality such as SQL or PDF support. If you need custom software and don't have a programmer, this is a solution. Free 30 day evaluation, education packages and pricing available.

You may have noticed that I left EndNote off the list. This wasn't an oversight. While it remains a popular bibliographic engine and does a good job of integrating with Word, the lack of real integration into other word processors is a big negative. In addition I'm tired of buying a new version when Apple releases a new OS or Microsoft releases a new version of Office. The new "cite anywhere" technology built into Papers means I can free myself from continued reliance on EndNote, and I'm happy to leave it and $100 upgrades behind.