A successful PhD: software recommendations and other tips?

October 8, 2011 5:55 AM

Hacks for a Successful PhD? I'm looking for tips or software that will help me - as a new PhD student - finish successfully. Researchers: tell me your tricks!

Three days ago, I started a PhD in the humanities. It's a three-year research-based PhD (i.e. no time spent on course-based Master's work, no TAing, etc. - it's research right away). I'm obviously invested in doing a good job and am of course prepared to do the bulk of the heavy lifting on my own. However I'm curious to know any tips from those already in the trenches. I'd be interested in more general advice and strategy, as well as particular software that might make my life easier. Essentially, I'll be reading secondary sources this year (primarily books, not articles), doing archival research next year, and writing up my findings in my final year (that's the plan anyway!).

I've heard Papers for Mekentosj recommended, although looking at it, it seems it might be more helpful for those in the sciences and/or those working primarily with PDF articles rather than books. I've also heard Endnote recommended, as well as Latex/Bibtex (?), but don't know much about how good they are. I've been warned that writing up a PhD is "almost impossible" in Microsoft Word, although I have no way to assess whether or not this is true. I've always done things totally old school and low-tech, working in Word. Certainly, when I was writing my master's dissertation, I would have welcomed some software to help organize and check my footnotes, but I don't know if what's out there is suitable for my subject, or more trouble than it's worth. Basically, I'd love to hear any advice you all have, especially regarding software, that you wish you'd known about at the beginning of your PhD. And if it's applicable to my humanities subject, even better!

posted by UniversityNomad to education (22 answers total)

(I am assuming you are a Mac user because you mentioned Papers.)

Scrivener! A million times, Scrivener. It's for writing, moreso than organization (though it can be used for that). I think it takes some users a little while to get into it, but once you figure out your own workflow with it, it will become indispensable.

I use Endnote, but now it is more out of a sense of obligation than anything else: I paid for it, and by gum, I'm going to use it. It does the job but I have a lot of problems with it, not the least of which is that they release a new version almost every year and want users to pay full price to upgrade for what are ultimately pretty minor changes. Your best bet is to try a few of the bibliographical management programs out and see what works best for you, which may be just whichever one feels the least frustrating to use. Try Papers, Endnote, Sente, Zotero, and some others. Much of it really comes down to personal preference.

Instead of Word, I use Nisus Writer Pro, and love it. It is much easier, much more stable than Word on a Mac, and handled my dissertation quite well when I wanted to compile it all into one file. Word will probably do okay with individual chapters unless you start to try to do things like create tables of contents and such. The real trouble is, though, is that much of the world still uses Word and will look at you oddly for using anything else. Nisus Writer can open .doc's, but uses .rtf by default. If you need to send something to a Word user, you can just rename the file "whatever.doc" and they shouldn't flinch when they open it. The new version of Nisus Writer will also do comments and track changes, as well. You may want to give it a try.
posted by synecdoche at 6:21 AM on October 8, 2011 [1 favorite]

My PhD was in the social sciences and had to be written in Microsoft word (seriously: this was a requirement), but here are a few tips that I used.

1. Keep a notebook (electronic or otherwise) for your ideas. You will have good ideas; you will forget your good ideas.

2. Good research follows a structural formula (e.g., this literature says one thing, whereas this other literature disagrees; we know x about y, but not z; our theory about x would change if we considered y from another field). Find your formula and stick to it.

3. Learn how to write without inspiration. Writing is your job. Writing isn't something you can afford to only do when you feel like it.

4. Check in with your advisor/supervisor/chair often, even if they are busy. Not checking in means more wasted time.
posted by eisenkr at 6:26 AM on October 8, 2011 [9 favorites]

I use Latex/Bibtex, but I do math, so it's sort of necessary. If you're not doing math, you might want to try Word and Zotero or Mendeley (both free) instead. My wife finds Zotero invaluable. Writing a PhD in Word is not impossible; my wife did it just fine, while I used latex (personally, I use texworks)^*. If you decide to use latex, look on your University's website for an official class file that will automatically format your document according the University's specifications.

I'd recommend some sort of time management software, like Google Calendar or iCalendar. Email clients like Thunderbird have the capability to interface with Google Calendar, so you can view your calendar along with your email. if you need to do any stats, I'd recommend R (also free). For vector graphics, if you need to make figures, try Inkscape (free).

If you're a little techy, I'd recommend using SVN as well; see here for a guide. TortoiseSVN for Windows has the ability to track changes across image, text, and Word documents, so you can have version tracking across your whole project directory, not just your Word documents. You might also try Evernote for keeping track of stray ideas and files.

Also, do not forget, whatever you do: BACKUP YOUR WORK AT LEAST DAILY. There's lots of good backup software out there; If you're a Mac user, get a Time Capsule and backup regularly. If you're a Windows or Linux user, get a good quality harddrive (or large USB drive), and use the built-in backup programs. I'd also recommend online storage and backup. Try, for instance, JungleDisk or Dropbox. You can keep data synced and backed up across multiple computers with these services. backup backup backup.

Look into your University's licensing scheme for software. You may, for instance, be able to get free or cheap antivirus, Microsoft Office, Adobe Creative Suite, etc, directly from them.

^*(As a user of latex, however, I am required to say that Microsoft Word sucks and latex is much better.)
posted by Philosopher Dirtbike at 6:39 AM on October 8, 2011 [2 favorites]

Endnote: I use it but I'm not sure I would recommend it. See what referencing softwares your institution licences and supports. Whichever you pick use it from the start, and use the keywords element to keep track of where you are saving the pdfs of whatever you read.

I did my PhD in Word. Make sure you get a template set up first but its by no means impossible, especially if you are not using a pile of mathematical notation, which is what all the science types I know want Latex for. One of my PhD students insists on doing everything in Latex on Linux which is a pain in the arse as I don't use it and it makes giving feedback harder than it would be in Word.

How to get a PhD by Phillips and Pugh can be a useful way to get a grip in what us expected in earning your degree. (amazon.com link, its on amazon.co.uk also).
posted by biffa at 6:41 AM on October 8, 2011 [1 favorite]

I wrote my psychology PhD in Word (my supervisor did all her commenting by email using track changes in word so using anything else would have been impossible). I have to say I didn't have any problems with it, though I was very careful.

I used Endnote to generate my bibliography, though I didn't really use it to manage and organise my papers as much as I could have done. My university had a licence that covered everyone. The next university I was at used something called Reference Manager that did the same things I used Endnote for. Even if you don't use it for organising, sorting or cross-referencing I think you will thank yourself if you use something like this.

I think Word worked well for me for several reasons:
- I spent two weeks learning about styles and sections and used them religiously right from when I started writing up
- I didn't put in any diagrams or tables until the last minute
- each of my seven chapters (8-10 000 words each) was a separate file until near the end
- I allowed an entire week for putting the whole thing together at the end - tables of contents, page numbers, headers and footers, bibliography, appendices, getting everything into one file
- All my figures and tables were linked to where they were referenced in the text so when I change the order around the all magically renumbered themselves

In actual fact it took me less than 4 hours to go from making my last content revision to having a full PDF of the thesis that I had checked through. Doing everything properly from the start allowed me to just click 'Hey, make me a table of contents' and it happened, than click 'Oh yeah, and a bibliography' and suddenly 200 perfectly formatted references appeared at the end.

I agree with the advice to keep a notebook. The best way to do this will vary according to your subject and your style. I was doing experiments so every experiment (there were 5) had a methods document where I noted down choices I'd made and the rationale for these. Silly things like 'these images have left on the right hand side' were absolutely invaluable when I came back to write it up 3 years later.

Finally, start putting money aside now for when you overrun.
posted by kadia_a at 6:46 AM on October 8, 2011 [2 favorites]

Science grad student here, so I can't give specific advice on humanities research. I would highly recommend making friends with your department's IT person, because they often have extra licenses to software you will need, and that is an easy tipping point between two equivalent programs.
posted by fermezporte at 6:47 AM on October 8, 2011

I'm writing my PhD currently (as in should be doing some revisions right now). I'm admittedly not high-tech and in the social sciences. I am writing my thesis in word. I have 5 different word documents, one per chapter. I use Mendeley for journal articles. For books, I set up a wordd template of a one page summary with quotes and longer notes on 2nd + page. This wasn't the best system, but it has worked well enough. I set long term goals using google calendars. I use google tasks for a daily goal. I tried using Evernote, but it wasn't that useful. I am doing citations in Refworks. I do a folder system for my research. For each project I work on, I keep 4 folders in my main project folder on my computer - Administration, Data, Analysis, and Output. Administration includes my IRB information, Contact lists, and since I do letters for my contacts - Letters In and Letters Out. Data for me is broken down into Qualitative Data, Quantitative Data. It is further broken down, but as a humanities person it may not be relevant. Analysis is broken down into Outlines, Summaries, Drafts, and Tables/Charts - aka, anything I'm writing up but haven't finalized. Output is things in finalized form - abstract, articles, chapters.
posted by quodlibet at 6:48 AM on October 8, 2011

Choosing Your Workflow Applications (PDF)

that's more geared towards social sciences, so you can ignore the stats stuff
posted by cupcake1337 at 6:49 AM on October 8, 2011 [1 favorite]

Oh, and if you back up to an external hard drive, make sure you keep it somewhere separate from your computer. There were several very sad cases at my uni where people had all their data from the last 8 years of part-time PhD/6 months of fieldwork in remote siberia/whatever stolen along with their only backup.
posted by kadia_a at 6:49 AM on October 8, 2011

Previous posts might interest you. As well as ProfHacker.
posted by quodlibet at 6:57 AM on October 8, 2011

Definitely investigate Mendeley.
posted by bluedaisy at 7:32 AM on October 8, 2011

Besides the computer applications, which have been covered above, I want to mention some low-tech hacks. I nth the comment about keeping a notebook for your ideas, and I would also recommend taking a few minutes each day to write something. It doesn't matter how dull or underdeveleped it is; what matters is that you're developing the habit of writing regularly. 15 minutes a day will serve you well.

Also, add every article that you read, or that is mentioned in coursework, to your master bibliography. The reading you've done earlier—even in a totally different subfield—has a way of becoming relevant when you least expect it, and I would have saved hours of frustration if I just recorded the bibliographic data of everything in one place.

Finally, I'm surprised no one has mentioned DevonThink yet. It's a database application designed for you to capture your sources, notes on sources, your own notes, and more. It's not easy to explain what makes it great, but doing a Google search for research and DevonThink will show you lots of examples of people using the application in all kinds of interesting ways.
posted by philosophygeek at 8:07 AM on October 8, 2011 [4 favorites]

Not a PhD student and will never be but I do have to organize quite a bit of information. I use: Scrivener, EverNote, and TextWrangler almost exclusively.
posted by dfriedman at 8:09 AM on October 8, 2011

Why people use LaTeX.
posted by esprit de l'escalier at 8:13 AM on October 8, 2011

I got my PhD in the humanities last month. For a while I felt this pressure to buy spiffy software that would make my life easier, and I'm no lover of MS Word, but ultimately everything (even bibliographic software like Zotero) proved distracting to me. So I just used these:

Word

Dropbox for syncing and file backup

Freedom for turning off the internet all day (by far the most important)

...and a little noise machine app to drown out grad students chatting all day in the next room over.
posted by Beardman at 8:47 AM on October 8, 2011

Yup, I did mine in Word too. My advice is similar to others: organise your thoughts and your work process. Write every day. Set aside time and just write, you don't have to spend hours (twenty minutes will do), but make it part of your daily routine.
posted by ob at 8:49 AM on October 8, 2011

If you decide to use LaTeX, check out BibDesk. I've just started keeping track of everything I read in it. I already use it extensively for finding things I've read, but I'm especially looking forward to the day I first write a paper in LaTeX using citekeys and *poof* my bibliography magically appears.
posted by ootandaboot at 3:15 PM on October 8, 2011

I've begun using LaTeX and bibtex with LyX in the degree I'm doing now (a Masters) and I'm finding it a sharpish learning curve with a very good return on the investement of time and energy. On the other hand, since nobody else uses it it pretty much rules collaboration and groupwork out so I've got to use Zotero and OpenOffice as well.

I've edited a PhD written entirely in Word with citations and a bibliography done the old-fashioned one-by-one way. It's hard work but it's not impossible---of all things, page numbering turned out to be the biggest problem. (The solution was to pre-print a ream of paper with page numbers, then feed it through the printer again).

I didn't complete the (history) PhD I put four years into, so take this advice with a grain of salt. More useful than any IT solution were the paper-filing systems I made. On every sheet of paper, I put every possible bit of meta-information about the source: author(s), title, date, obviously, but also page ranges within sources, library section, call number, manuscript number, archive details, and so on. You can never know too much about something you read ages ago and when it comes time, you'll be glad you did. I used ring binders for different categories of notes and for copies of drafts. I still use those folders every now and then.

An old colleague of mine once went to an overseas archive in a very out-of-the-way city and left the handwritten notes in a taxi at the airport. If you're doing valuable work like that, put the notes through a photocopier!

I'm fascinated by the idea of doctoral students who have office space. Really?
posted by Fiasco da Gama at 3:35 PM on October 8, 2011

I wrote mine in LaTeX in a field where most people use Word. This was a problem. I recently spent three months reformatting the damn thing into Word for publication. (Yeah, I know there is software that can turn LaTeX files into Word, but they do a crappy job with glossed interlinear examples, tables, etc, of which I had hundreds.)

I recommend finding out what publishers want for book manuscripts and journal articles, and sticking to that format/software.

One other point that struck me in your post is this: "I'll be reading secondary sources this year (primarily books, not articles), doing archival research next year, and writing up my findings in my final year"

I used to think like that too. It was basically my plan for my PhD. What ACTUALLY happens is that when you start writing, you have to go back to reading secondary sources. When you start looking in archival sources, you have to go back to reading secondary sources. When you start writing, you realise you need to look at more stuff in the archives. When you start reading sources you need to write in order to get your thoughts straight. Basically it turns into one big mishmash of read-write-read-write-research-read-write-research-write, with the research only ending (if you are LUCKY) a few days before the final version of the manuscript is complete.

A better way to plan your timeline is probably to allow lots of time in your third year to go back and read more, and to start writing earlier rather than later, because it's only when you start writing that the real research begins.
posted by lollusc at 6:14 PM on October 8, 2011 [1 favorite]

Oh, and if your archival research is out of town or overseas, do anything you can to allow yourself the time and finances for a second trip about half way through your third year. You will need it.
posted by lollusc at 6:15 PM on October 8, 2011

To add an alternative to Beardman's suggestion, I use Self Control which you can use can selectively block sites (like Metafilter...) while allowing access to sites that might be necessary for your research.
posted by fermezporte at 5:21 AM on October 9, 2011

My graduate work went from terrible to passable when I started doing the following: Every Monday I would send my supervisor a list of things I would accomplish that week, and every Friday I would send an update saying what I'd accomplished. I have no idea if he even bothered to read the emails, but it really helped me focus my work.
posted by auto-correct at 9:38 PM on October 9, 2011 [1 favorite]