My new iPad gets a lot of looks when I pull it out. Its frustrating because many people assume that I have it for entertainment purposes. But if that is all it could do, I wouldn't have bought it. If a particular appliance or gadget doesn't fit into my workflow, I don't need it. I also don't think I can explain the iPad without also explaining how I do research and why I like the particular programs that I use. The reason I bought the iPad is because it fits into my broader workflow.
When I was in High School we had this old school English teacher. She had more than one loose screw, but along with all of her craziness she had a few brilliant ideas. The big project for her class was a twenty page research paper and along with the final paper, we also needed to include our research. We had to take notes on three by five notecards, and then we were to write the topic sentence of each paragraph for our paper on a different sheet of paper. Then, we sorted our notecards by which topic sentence the card went with. It was a great exercise. One I have never followed all the way through. Although it really helps me to organize my thoughts as well as take more specific notes, I found it to be time consuming and a headache. For one, it is a lot easier to type notes into a laptop than to write them out by hand. Another thing is that I can keep much of that stuff in my head and don't need to write it all out. Also, her method assumes a static outline. But for me it usually takes some research for an outline to develop that is usable for taking more notes, then filling out the outline more, then doing more research, then taking more notes, etc. My English teacher's method is a very linear approach that I have found useful as an exercise but not in the actual writing and research process. The last problem with this approach is that it was not designed in the age when I find most of the materials I am looking for online, through digital catalogues, databases, and google searches.
Up until this past year, I have used my English teachers instructions as a kind of model that I squeezed into a couple of Word documents. It worked, I suppose. But I found myself taking notes that I didn't need, losing notes that I wanted to keep, and from time to time struggling with the outline of the paper, as it was already in progress. When one of my friends started writing a thesis, he pointed out to me that the process I was using would not work for a paper much longer than 30 pages. I think he was right. I haven't yet written anything longer than that, but after rethinking the process, I am confident the system I have now will work well for a project of any length. I should note that most of the applications I use are Mac specific. I have a couple of suggestions for the PC, but I would love to hear your thoughts on them.
Every project I have begins with finding articles and books. I use Firefox because of the great apps, especially Zotero. Zotero works great as a tool for collecting a bibliography directly from the web browser. One of the other applications that I have is Papers. Papers has what I assume to be a great web browser as well, but the problem for me is that it logs into things like JSTOR with an EZproxy and my current school uses a Samba web VPN. This makes Zotero of less value and also Papers. But I hope that soon I will be able to search for articles directly from Papers and download the pdfs inside the program along with their bibliographic information. As it is now, I have to download articles and pdfs from my laptop, and then transfer them into Papers. Papers has a great feature that can help match the bibliographic info available online. That feature still works great even if I can't yet use the EZproxy. If a book is in the Library and not digital, I import the bibliographical info into Bookends (my preferred bibliographic manager).
After collecting pdf's and Library call numbers, I can then sync my iPad and leave the laptop at home. Papers also has an iPad app that syncs over the wifi network. The iPad is so much lighter than my laptop and the screen is better designed for reading. Taking notes on a pdf in the iPad version of Papers is not as seamless as I would like and not as wonderful as the full version for OS X. But it works well. I can also take notes on library books in Evernote (which is a great program and syncs with my laptop and my iPod through the internet: it is also free). After taking notes both in Papers and in Evernote, I come home and sync my iPad with my laptop. The notes from the iPad version of Papers are uploaded to the laptop and then I can highlight the references that I want and send everything over to Bookends. This is great. My notes and the bibliography were all collected in Papers and then just transferred to Bookends. From Evernote, I select and drag the notes that I took to their corresponding bibliographic item. This ties all my notes to a specific bibliographic reference.
With all of the notes that I took tied to a bibliographic reference in Bookends, I start composing in Scrivener. The programmer designed Scrivener to write a novel, but it works great for academic writing as well. With this program, I can use a more flexible version of my crazy English teacher's method. I can drag my notes into Scrivener (and they keep their bibliographic references!) and move them around and write text and change the order or the outline. Scrivener allows for both organization and composition. I compose my rough draft in Scrivener. I also have Bookends open the entire time I am working in Scrivener, and thankfully the iPad app Air Display allows me to keep Bookends open displayed on my iPad as a separate monitor while I compose text in Scrivener.
After the draft is composed, I export my Scrivener project as a word processing document. I use Mellel because it works with Hebrew and Arabic fonts better than anything else on the market, but other word processors will also work if you don't need to worry about Hebrew or Arabic. The word processor is necessary to format the text properly. Scrivener allows you to write, but if you are going to turn this in either as a manuscript or as a term paper, it really needs to be formatted. It is also at this point that I run Bookends to put the bibliographic references into the proper citation format: Turabian, SBL, Chicago or whatever is needed.
This process is really similar to the method that my English teacher encouraged us to use, but it has definitely been streamlined by new technology. Granted, it is a little expensive. If you are on a really tight budget you could do pretty much everything with Zotero, Evernote, and NeoOffice/Open Office (all free programs, and available for PC use as well). You could even get a netbook and hack it with OS X if you want a cheap and light laptop for dragging to class. This last solution would only work if you are a little tech savvy, don't mind a few glitches, and don't care about reading pdfs on a super small screen. The netbook would work a lot better for taking notes in class and even composing a paper. But for me, I wanted something light, on which to take class notes, and to read pages and pages of pdfs. The iPad fit what I was looking for. I have some complaints. It isn't as versatile as I was hoping it would be: there is no Hebrew keyboard (though there is one on the iPod and the iPhone); I can't use some of the other diacritics I need for writing Semitic languages; and the pdf reader doesn't allow for the level of note taking that I need. This will get better with time and if you can, I would suggest waiting on purchasing the iPad. Also, the workflow that you choose may be entirely different, and something like the netbook or a laptop will work better for you. I would suggest that you download trial versions many different programs, try them out and see which ones work best for you.
I have pretty much only mentioned the programs that I use. But there are others that are worth mentioning.
Skim is a fantastic pdf reader and it is free.
DEVONthink, from what I understand, is the gold standard for organizing and doing research. It works well for sorting and searching pdfs.
VoodooPad is a localized wiki program that has this great feature of automatically linking pages together. It was a lot of fun, but ultimately I found that it didn't fit into my own research.
This website has a more complete look at a large selection of Mac Academic programs.
The Hebrew Keyboard work around for the iPad - - - I use the free app Hebrew On. It is a web browser that has a built in Hebrew Keyboard. It isn't as good as a fully functional keyboard but it works.