On my 13"MacBookPro 8GB Ram 500GB HD backed up on WesternDigital 320GB external HD and Mozy remote backup... I use:
Sente to house journal articles I will cite. It looks and acts like Endnotes but is less expensive. In its `notes' frame next to the PDF, I'll write my summaries of the article. So all the citations sit in Sente but the citation format I use is BibTek for citation in Latex (see below). Sente is easy to populate, just needs to add the ability for its own browser to link to the University library - currently you have to go to the library website in your own browser, sign in, download the PDF, then add it to Sente. Developers have promised to add a direct connect to password protected libraries for password holders. $90 for students Mac only
Scrivener is a program for writers of big projects...even though I write small papers, I start big/global. So when starting a project, I open a project here. Into it, I drag the articles I'm going to use, the notes on the articles, my DTpro notes on anything related...and then I start outlining the project, and then within the outline, I start writing in full screen mode. I don't deal with tables and figure here, just the text. For citations, I bring in the citations from Sente in BibTek format (Bibtek is free). $45 for Mac only, PC beta. Sente DPpro and Scrivener have very good user forums.
In the parallel universe of data analysis, I use Stata11 and dream of one day mastering R and WinBugs for Mac. From Stata, my analysis is dumped elegantly into a text file to be included in the final document. The text file is written in Stata but in Latex code for output of publication quality tables (I haven't figured out how to do the same for Figures, and graphs are saved as jpgs to be included in the Latex shell below). My rule is to never cut-and-paste, and never lay out a table twice. If an analysis has to be redone, you just run it again with the new variables or estimates, and the text file is updated...no more fiddling with the layout once established. $500 student pricing for Mac and PC, R/WinBugs is opensource
My two universes of writing and analysis merge in TextMate. There are free Latex layout software such as MikTek, but TextMate has a few bells that justified the $40. Latex is a typesetting language and more biomedical journals are providing authors with their Latex shell. You download the shell and plunk your text in from your exported Scrivener project, in Latex language, include your table txt files generated from Stata, include graph jpgs, add invisible notes such as references to jog your memory where you got the info beyond the simple citation method (like the do.file used for each value or the codebook document name), and you upload to the journal two files: the Latex file and you BibTek file containing your cited references exported out of Sente in BibTek format. You can also generate a lovely, publication quality PDF to circulate to your coauthors. I'll be honest, the learning curve for Latex is massive. But I was motivated because I want to just write and analyze, and the layout and formatting is reproduced easily with your favourite Latex shell or can be adapted from one journal to the next with the journal-specific shell. Latex re-typesets the article so that things fit best, and any edits you need to make are all going to be about content...not the tedious layout stuff.
Adobe Acobat X Pro - I haven't actually started using this but it was $45 for students...and my plan is to use it instead of Microsoft Access for data entry. Adobe has a forms-creation program, and you can direct the data entry into a spread sheet such as Excel. Unlike Access, I thought that people would be able to use this for data entry using only a free downloaded version of Adobe Reader...which I thought would be more practical for remote settings +/- old PCs.
Other handy programs are:
Skim - free PDF reader for Mac with better than average annotation tools.
Microsoft Excel - I use this for my research log...it's big and old and has multiple sheets...everything is in it - the codebook, the notes on the problems & when they were solved, the meetings that took place, what I did today and last year, scratch pad, abbreviations, definitions - basically, this is the one document to pass the "hit by a bus" test...if I'm ever hit by a bus, this is where the next researcher can pick up and continue the project.
Skype - feeling like Major Tom sometimes - this free app reminds me I'm on earth...conversely, allows me to ask a question to the one person I know has the answer regardless if they're in the office or in India...hopefully will replace my cell phone plan some day
Chrome - it's free and the fastest browser, by far
TextEdit - comes with Mac (or Wordpad on PC) - I just take notes in .txt file format and throw them into DPpro, leave them on my desktop to be deleted when no longer of use, or put them in a file and add a hyperlink in my research log notes to find the extended version of that thought...anyone still have files in WordPerfect5.0? I believe you'll always be able to read a txt file...which is also the saved file format of DPpro, Scrivener and TextMate - underneath are all just .txt files, and with Reveal in Finder, you can open them using a simple text edit program.
Mindnode - a mindmapping program for splaying snippets across a page to push towards some organization...or not, $20 for Mac
Email gmail - no folders, no download and saving...if I'm feeling like I should archive an email, I throw it into DTpro but that's rare, I just assume I'll be able to find important emails with the search function
A Whitelines Squared A5 notebook (with a multipack of colour sharpie markers) - to write in, make to do lists, draw lots of diagrams, make connections of seemingly unrelated topics, and use as a mouse pad for my peripheral mouse.
