If someone says Tricorder....
November 2, 2012 6:32 AM   Subscribe

Researchers, Writers, Grad Students, and Professors: Tell me about your technical setup (hardware and software). What do you use, and what couldn't you live without?

My wife's boss is going back to do a PhD, and asked me to make some hardware and software recommendations. I've got my list, but I'm sure I'm leaving things off, or not up to speed on the latest and greatest. I'm intentionally leaving this field agnostic, as I'd like to see the full range of answers.
posted by NotMyselfRightNow to Technology (25 answers total) 34 users marked this as a favorite
I am a PhD student in the social sciences.

Working my way through the mountain of assigned journal literature we are assigned has been made tremendously easier with an iPad with a PDF reader (I use PDF Expert) which syncs to my Dropbox account.

I also like Mendeley for citation management.
posted by pantarei70 at 6:39 AM on November 2, 2012

The answers to this question should be helpful.
posted by ryanshepard at 6:44 AM on November 2, 2012

Citation management is the big one. I like Zotero.

If boss is writing a dissertation, learning something other than Word is essential. I recommend LaTeX to everyone, not just math/physics/engineers, mostly because BibTeX handles references so nicely. Once you get over the learning curve, compiling is so so much better to work with than WYSIWYG.

Version control and offsite backup for all code, including LaTeX code for written work. (Dropbox will work for this.)

If you're doing a lot of typing, get a decent keyboard. Being hunched over a laptop for five years isn't good for anyone.
posted by supercres at 6:51 AM on November 2, 2012 [2 favorites]

Multiple monitors. The more, the better.

I find that a lightweight laptop is essential. I supplement my MacBook Air with an inexpensive desktop PC. I use the Mac only when I'm out of the house.

A data phone is great for keeping on top of email. It is really a big help at conferences, too - I use it to find my way around and to network on Twitter. It's especially great when the conference wifi isn't working well.

A good printer comes in handy, as does a scanner. I have to send reimbursement forms in for my grant and they usually need to be signed and scanned. The scanner is nice for copying bits of library books for research, too.
posted by sockermom at 7:05 AM on November 2, 2012 [2 favorites]

Hardware: computational power doesn't matter in any field I know of -- if you need to do big computations, the university should provide big fast machines for them. At least two monitors and a decent keyboard and mouse for actually working on.

Dropbox for syncing work and home computers.

Zotero for citation management.

emacs + auctex + latex + bibtex for writing things. This is much better than Word. Seriously, so much better. I was horrified when I realised that all the biologists that I know use Word regularly for writing all their important documents.

Git/Mercurial for versioning big documents. (You can "commit" changes, roll back to any commit, "branch" a separate copy of the document if you want e.g. to experiment with rewiring the chapters, and so on.)
posted by katrielalex at 7:07 AM on November 2, 2012 [2 favorites]

Zotero has made my life so much better, I absolutely adore it. There are some extensions that are worth setting up - zotfile will rename pdf files and keep them organized in a folder. Autozotbib will sync the library to a bibtex file, also a lifesaver.

Latex and bibtex are definitely the way to go.
posted by medusa at 7:12 AM on November 2, 2012

I also like Mendeley for citation management.

I use Zotero (as well as old-fashioned typed out bibliographies) for citation management, but I love Mendeley for annotating PDFs.
posted by audi alteram partem at 7:19 AM on November 2, 2012

Zotero for citation managment and managing all the attached pdfs. Calibre for converting pdfs to docs or mobi files. Kindle for reading, notetaking, and generating citations. Kindle Clippings Converter to turn notes from kindle into an Excel sheet or into Evernotes.

From there I would sort my notes by keywords and had all my citations available without having to relook things up.

Also, a big white board to brainstorm and write the main topics you want to cover in each chapter and how they all link together. It was really helpful to look up and see the check marks beside what I had covered and know what was next. And when I thought of new ideas I could just write them down in a central place.

I also used a couple of apps on my iphone to take quick pictures of text from library books or archival materials that I couldn't take home. ImageToText was awesome because I could grab a paragraph or two by taking a picture and it would convert the image to text. This meant less typing, less handwritten notes and less liklihood of error on my part. Plus you can send it directly to Evernote.

Also, Carbonite as a backup. I had a friend in our phd program who lost her entire dissertation and all her research because she had been keeping everything backed up to a portable harddrive that was stolen out of the back of her car. With carbonite I had all my backups online and available from any computer if something horrible happened and I lost everything.
posted by teleri025 at 7:21 AM on November 2, 2012

I find Papers to be close to essential for my work nowadays. Everything else is kind of field-specific -- if the boss in question is in a numerically-oriented field, there'll be some piece of computational or statistical software that everybody in that field uses. In my field, it's MATLAB, which is horrifyingly expensive for regular folks but is site-licensed by most universities. It's also got a student discount which is worth snagging while still eligible.
posted by irrelephant at 7:35 AM on November 2, 2012

Genetic epidemiologist / academic gynaecologist here. Agree with almost everything above, including that hardware doesn't matter much except for having big displays. Really I just use mostly the same software that my collaborators use. Latex and bibtex really wouldn't fly in my field.

MacBook Air and Thunderbolt Display
High performance cluster

Dropbox AND CrashPlan AND Time Machine AND extreme paranoia


Data manipulation and analysis:
Various highly specific command line tools

PDF management:
EndNote (only for systematic reviews)
Papers (for actual citations, I have been around the block with Sente, Zotero,and Mendeley, and Papers is king as far as I am concerned)
posted by roofus at 7:39 AM on November 2, 2012 [1 favorite]

If your wife's boss is interested in building a personal digital repository of PDFs or other file formats, try out Mendeley. Then, if s/he likes it, graduate up to more powerful software like Papers (Mac/Win) or Sente (Mac only). There are features of Papers--like the ability to add keywords--that my girlfriend (working on History dissertation) just loves. It also scales well; my girlfriend has digitized more than 30,000 documents from various archives, and Papers on her Macbook Air handles them easily.

I'm a librarian, and I just did a workshop for humanities and social sciences scholars on how to work with digital files (e.g. using a camera to capture sources, manipulating images into PDFs, etc) and build a personal digital repository. A few tips I gave them:
  • Keep a folder marked "Originals" on your computer where you save the raw, unaltered versions of every file you gather. Then have a separate folder where you do the renaming, batch editing, combining to PDFs, etc. If something goes wrong, you can always go back and re-copy the originals.
  • If you use a digital camera to reproduce source documents, Picasa is helpful for batch edits. The "auto contrast" and "copy/paste all effects" feature is great for making images taken with a digital camera easier to read.
  • Develop a naming convention for your files that at least incorporates the source archive and collection number in the title. AntRenamer is very helpful for renaming many files.
  • Use print-to-PDF software like doPDF to combine files into single documents. This makes them much easier to work with later.
  • Have a robust backup system in place now, and stick to it. Use Crashplan if you have no idea what you're doing.
  • Multiple monitors can be extremely helpful.

posted by arco at 7:47 AM on November 2, 2012 [3 favorites]

You might find some inspiration from the interviews on The Setup.
posted by samhyland at 7:52 AM on November 2, 2012

The new changes to Pages in OS X Lion to add versioning make it really, really helpful for working on a dissertation. Being able to go back and recover things that you'd foolishly removed from your dissertation months ago because you thought they weren't quite right is invaluable. OS X Mountain Lion has expanded its utility, as you can now save documents to iCloud which adds a layer of backup (oh for the love of god just set up a backup first thing—do not leave that one for later) and also allows you to access the documents to keep working on it from any iOS device (I sometimes pull up my dissertation on my iPhone and make changes while I'm grabbing a coffee).

Citation management software is really, really handy, be it Zotero, Mendeley, or, if you must, Endnote. It can be really easy to let this slide, and the last thing you want to have happen is have your final draft due in a week and realise that you need to completely rebuild your bibliography because you haven't been keeping track of everything in it. If your wife's boss's department is anything like mine, they'll also ask for you to include pretty much anything you've read that might influence your writing (not just the stuff you've cited), which is much easier to do if you can just click a button and add a citation to your bibliography list.

You might also want to look into something like Evernote for the note-taking portion of research, as it allows you to tag all your notes, making them easily searchable at a later date. It can be a pain in the ass at times to keep all your metadata in good shape, but it's worth it for those moments when you remember that you read something really important but can't remember the author(s), title, or where it was published. Good metadata can also help you find things you didn't realise were relevant until they all came up when you were searching for something else. Anything that can help you pull information together is worth the time and effort.
posted by sadmarvin at 7:52 AM on November 2, 2012

Oh, and lots of people really love Scrivener.
posted by arco at 7:54 AM on November 2, 2012 [1 favorite]

I personally do most of what is said above. Everything is in Dropbox. Nothing important is not on dropbox. There's always the worry that Dropbox decides to nuke everything, but I have enough computers synched that if ever that happens you can just unplug the network cable from the wall and move the files to a hard drive.

Mendeley + a 5$ Mendeley account for storing PDFs to the cloud and synching between Mendeley. Synching PDFs between computers has been a huge plus for me. Add it at work, read it at home. You could do the same with a folder and dropbox, but once you get over 100 PDFs that can become unwieldy fast. Synching annotations to the cloud = also good. Concerning what arco said above, mendeley supports tags which I'm guessing is the same as keywords in papers. Also Mendeley gives you 1 gig of online cloud space free (I pay 5$/month because I need more). And it's multi-platform (I use PC and linux).

For writing I'm stuck in Zotero and word. Collaborators don't use latex, no way I can get them to switch. Alas. And endnote can burn in hell. Zotero syncs across computers and makes importing citations as easy as googling the title and hitting a button.

For writing large works (dissertation and chapters) to be honest I've done better spending less time organizing (annotating PDFs, evernote, etc. I tried them all) and instead just bloody write already. This won't work for everyone, but for me the process is to write and research at the same time. If I need to take notes, they go in the manuscript I'm writing as bullets that I need to cover later. Too many times I've gotten lost in the note-taking hole.
posted by Smegoid at 8:19 AM on November 2, 2012 [2 favorites]

Linguist here.

Hardware: A crappy old Thinkpad. If I need to do computational heavy lifting I borrow time on a friend's machine.
Backup: Dropbox.
Writing: LaTeX, with vim as my source code editor. (I'd recommend LaTeX highly for anyone; I wouldn't necessarily recommend vim to anyone who doesn't already know and love it.)
PDF management: Everything thrown in one big directory, with a consistent naming scheme for files.
Citation management: BibTeX, with all the data in one big .bib file, using the same scheme for citation keys that I use for .pdf filenames.
Data manipulation: Python for crunching text, R for crunching numbers.
Other useful: tmux is basically indispensable for me but YMMV. If you spend a lot of time at the command line you want it; if not, you don't.

Honestly, the most important thing is to find a setup that feels natural and familiar enough to use, and then ignore it. Don't mess with it. Don't worry about whether it's optimal. Spend your time thinking about your research, not elaborate schemes for "increasing productivity" by re-organizing your PDF library for the umpteenth time.
posted by nebulawindphone at 8:55 AM on November 2, 2012

Devonthink saved my book. It's a bit like Evernote, but more versatile.

The drawbacks: Doesn't sync online (yet). No citation mode, at least not that I'm aware of, but it allows you to categorize, sort, and search basically any kind of information.
posted by vecchio at 9:26 AM on November 2, 2012

By nice keyboard, I mean something like this, or in a similar range. You'd be amazed what a difference it can make over a low-profile laptop-ish keyboard.
posted by supercres at 9:37 AM on November 2, 2012

I love my iPad, for reading pdf documents (which is most of my reading for grad school). I got it about a month ago and have hardly had to print anything off since then. No longer drowning in paper!
posted by Rinoia at 9:59 AM on November 2, 2012

Environmental chemistry/physics

Hardware: Toshiba laptop, formerly Thinkpads. Would buy either again. An SSD has made a huge difference to how nice the system is to use. Light and small is really important. I travel with it a lot, and even the journey home and back is easier with a small system.

Docking station and external display. Gives me portability without a lot of compromise. At the beginning of the day I just drop the laptop on the cradle and I'm on. Leaving, I just pick it up. Five seconds to go, no wires to fiddle with, printers, network, headphones, etc... are all automagic. I love my Logitech Illuminated keyboard, and Razer mouse.

Software: Windows 7, which is good mostly because it gets the hell out of my way. Write in Word, excel and powerpoint. Track changes mode is really key to our workflow. Papers are typically drafted by the first author, but others may contribute large sections too. Working with external collaborators is important as well---least common denominator approaches work best. Posters in Coreldraw (which is not optimal, but what I'm stuck with). I've used LaTeX/svn and like it, but I'm pretty unique in that respect.

References managed by hand. Much easier to work with collaborators, editors and translators this way. I've tried Endnote and Mandeley and been really happy with neither---with collaborators in particular, this is a huge problem. PDFs by common naming scheme in standardized directories: I share these with my group on a network drive. We have someone whose job it is to do this (for about a dozen researchers).

In a data-intensive field, beyond knowing the usual R/Excel/Statistica/Systat candidates, knowing a scripting language is invaluable for data clean-up and off-the-cuff tasks. Right now I use Python, mostly, but I've had to do this with everything from FORTRAN-77, unix scripts, and VB for applications. Good to learn one at least. Scripting languages have saved my day more than a few times.
posted by bonehead at 10:05 AM on November 2, 2012

I can technically claim to be a grad student, though I am less so than many previous posters. I'll add just one idea for taking notes and writing first drafts of papers: Google Docs + an Android device for dictation. It’s not really a specialized workflow for academics, it’s just a great way to take notes and write drafts. I use it heavily for school - I do all my notes and drafts this way. Google Docs means you can access your work from any internet-connected device - PC, Mac, Linux, iOS, Android. So your notes are everywhere, and if something comes to you out of the blue it’s easy to jot them down (electronically, where you can’t lose them). And it’s easy to share if need be.

Android comes with some pretty awesome dictation software built-in (I disliked it in 2.3, but now I have 4.0 and it’s excellent). I also like Swype Beta (from Nuance) because it’s extremely accurate and supports more commands (quotes, parentheses). This means you can dictate every note and even dictate entire paragraphs all at once. Let me reiterate: she can save endless amounts of typing and just speak it instead. There's a reason that dictation is the standard for physicians documenting charts: it's fast. I find dication much easier than typing when I’m writing a draft and just trying to get words out. Phone/tablet dictation + Google Docs is like having a personal assistant who will write down what I say and file it for me. Then I just have to go back and make corrections later, and with the recent improvements in speech recognition corrections are becoming less common.

She probably won’t want to directly print things from Google Docs – its formatting isn’t the most attractive. But once it’s written (or at least the draft is written) it’s easy to paste into another program that will make it look much more professional.
posted by Tehhund at 10:45 AM on November 2, 2012

For data analysis, I prefer Prism GraphPad. More powerful stats and nicer graphs than Excel, and it's much more user friendly than STATA.
posted by emd3737 at 1:30 PM on November 2, 2012

Programs that I use every day: Papers, Latex, TexShop, Rstudio, R, Dropbox, Preview, Safari, iTunes, Keepass. Programs that I use on some days: Skype, Word, Wunderlist. Next time I'll have to make a nice presentation I'll buy Keynote. I tried Scrivener but it cannot deal well with tables and figures, and it doesn't work for collaborating. For writing, I also visit thesaurus.com a lot. I have an old macbook hooked up to a big screen and an ergonomic keyboard. If I run analyses that need computational power, I do it on the institute's computer cluster.
posted by Okapi at 2:29 PM on November 2, 2012

Biology grad student - absolutely can't imagine life without OneNote. Yes it is a Microsoft Office product but it's amazing. I use it as an electronic lab notebook to organize my experiments and projects, as well as to scrapbook everything else related to the PhD (meeting notes, ideas, to-do lists, timelines). The organizational hierarchy is: Notebooks > Section groups > Sections > Pages. Every single experiment I do, or every single meeting I have with my advisor, gets its own page under the appropriate section (one of several ongoing projects).

Some useful features: good sync; auto save; excellent screen clip/web capture; auto time stamping; decent search; can click anywhere on the screen and enter text; and (probably my favorite feature) type some text then press the Tab key to make a table! I have converted many a labmate to OneNote.
posted by nemutdero at 2:46 PM on November 3, 2012

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