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I'm a second year PhD student. In general I love my advisor, but recently we've run into some small bumps in the road while working on a paper together. He's controlling the "master" copy and I send most of my contributions and comments through email for him to incorporate.

A few days into the process, we had a conversation that went something like this...

Me: "Hey, so I cited a few papers you might not have seen. How do you keep track of your references? I use JabRef to keep up with BibTex entries, but I can export those citations to a bunch of different formats..."

Advisor: "What are you talking about?"

Me: "Like, when you need to make your references section... how do you keep track of all the papers you've cited in the text? Refworks? Endnote? Zotero?"

Advisor: "What? ...I use the 'copy/paste' method."

I was baffled by that answer. I know he's been doing this for a long time with good success, but I cannot fathom someone who has been collaborating with so many people for so many years is still at the level of manually formatting each entry in a Microsoft Word document and then copying/pasting over whenever that reference is needed elsewhere.

Any suggestions on how I can help bring this faculty member into the 21st century without seeming presumptuous?

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    maybe it's a topic for a new question, but why using endnote etc? Copy/paste from a (paper-specific) bibtex sounds quite simple to use.. – Ran G. Jul 8 '12 at 17:22
  • Ran G, he isn't using bibtex (I wish!). He's got a giant Word file of manually formatted bibliography entries that have to be individually copied out and reformatted for each submission. – jurassic Jul 8 '12 at 21:58
  • To ease the transition, try 'Google Docs' - you can always 'format' the paper later – PhD Jul 9 '12 at 1:12
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    You are presumptuous by thinking that you 'need to bring the faculty member' into the 20th century. Everyone works differently, and as a PhD student its important for you to realise this earlier rather than later and respect/learn to adapt to these differences. – awsoci Apr 12 '15 at 3:49
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    Actually, very few of my colleagues use a bib manager, even recent Ph.D's. I find it unbelievable but this is up to them. I am now refusing to to work with one group as the manuscript management is so poor and wastes months of time and errors never get fixed. For example, I just got a paper after a year and every reference with more than one author is still incorrect. I would say manuscript management in a team tends to default to the least proficient member and I am finally starting to take a stand against this (waster your time but not mine kind of approach). – If you do not know- just GIS Jul 5 '16 at 14:56
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Turn the tables. For your next paper, you maintain the master copy. Make sure all the infrastructure is in place, including a fairly solid draft of the paper, before you involve your advisor in the writing process at all. Use whatever version control and reference system you find most useful.

Your advisor may simply refuse to use your tools; fine, you can still incorporate their emailed inputs. Or they may just need someone else to figure out the infrastructure and teach them how to use the tools, instead of figuring it out themselves from the manuals. Either way, you'll have some extra work to bring your inexperienced (and possibly resistant) coauthor up to speed, but that's a standard part of the student-advisor relationship.

In the worst case, your advisor may simply refuse to give up control of the master copy. (Never mind that it's already too late.) In that case, you may need to encourage them to look for another student.

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    +1, except for the last part. In my opinion, this is not a big enough issue to merit changing advisors. – David Ketcheson Jul 8 '12 at 18:37
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    I agree with Jeff, take control of the master copy, and demonstrate for the next paper how easier it is with your technique, and I agree with David, if you can't get the control of the master copy, as long as your advisor's technique is somehow working, it might not be worth changing advisor only for that reason. – user102 Jul 8 '12 at 19:06
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    @DavidKetcheson: That was half-joking, but only half. An advisor that refuses to let students take control of their work is doing the students an immense disservice. At least in my own subfield, I would definitely warn students away from such an advisor. – JeffE Jul 8 '12 at 22:01
  • Thanks, JeffE. I will definitely keep this in mind next go-around. I think this prof is amenable to change but afraid of the technology (as SteveP suggested.) After posing this question here, I offered to handle the bibliography because I already have most of the references in my system and it would be easy for me to do put it all together quickly. He seems interested. – jurassic Jul 9 '12 at 6:28
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    I disagree only in that your method may not actually be regarded as 'easier' than what your advisor is doing. You're making assumptions about how someone should work. – awsoci Apr 12 '15 at 3:50
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This probably sounds defeatist, but you might just have to accept the fact that some people would rather do things the hard way because they fear that the technology will eat up more time than it's worth. Maybe after building more rapport with him, you will have an opportunity to demonstrate the value of your method...for example, if a paper gets rejected from one journal and you can reformat the references in a few minutes, whereas it would have taken him much longer.

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    Once I tried to get my team to use Zotero for biblipgraphic citations. It worked except for one instance of one reference. That one instance of failure was enough to convince the advisor to never give it a second chance. – Irwin Nov 27 '13 at 21:05
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Endnote doesn't work on linux. Refworks came into existence in 2001 and is a website, it could disappear any time. Zotero is only 6 years old.

Programs come and go, websites come and go. Text files keep working. They are easy to search, easy to maintain, easy to move between operating systems.

Your supervisor has been around a lot longer than you. Perhaps they have discovered that fancy databases are not worth the extra work they involve, particularly if (like me), they've had a couple of products they love get discontinued over the years.

  • Endnote isn't just a website, it is also a downloaded software that can also be incorporated into word. But I agree, systems change/operating systems change, and in this day and age it's quite rapid there's sometimes no point in trying to keep up. – awsoci Apr 12 '15 at 3:32
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Maybe you should get your advisor to use something like svn or cvs with the ability for anyone to edit the "master copy". Then you can slip in your refs as you see fit.

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    Getting him to use version control is probably going to be harder than getting him to use bibtex. If you you try, you might as well go for Mercurial or Git while you're at it. – David Ketcheson Jul 8 '12 at 18:37
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    @DavidKetcheson I actually found Mercurial harder to learn than svn, mostly due to the distributed repository architecture: at first, people can forget to push after committing, or forget to update before committing (thus leading to potential conflict). Also, the graphical interface for Windows (we're talking about Word documents here, I'm not going to assume they use Linux) is not so good (SourceTree on Mac is quite good though). They should come up with a "dummy" mode for Mercurial (at least for the start) :) – user102 Jul 8 '12 at 19:11
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    @CharlesMorisset Yes, Mercurial and Git are harder than SVN in the same way that Bibtex is harder than copy/paste. The up-front investment is more substantial, but the long-term payoff is substantial (all of this is IMHO, of course). – David Ketcheson Jul 8 '12 at 21:10
  • @DavidKetcheson Although I completely agree with the long-term payoff of Mercurial/Git w.r.t. Word, I'm not so sure about the payoff w.r.t. SVN. I've been using Bitbucket/Mercurial for about a year, and I love the fact it's in the cloud, but in practice, I'm using it as SVN (always pull-update, and commit-push together). Maybe the distributed repo is great for writing code, but when it comes to papers, I haven't seen the interest yet (but maybe it's just because I'm using it wrong :)). – user102 Jul 8 '12 at 22:28
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    While I haven't switched from SVN (and this thread is getting dangerously off-topic), one potential advantage of Git is that it encourages micro-commits - these are handy when doing lots of edits. – Suresh Jul 8 '12 at 22:35
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Any suggestions on how I can help bring this faculty member into the 21st century without seeming presumptuous?

You can't. Your attitude is presumptuous.

I, for one, still live in the 20th century. I personally prefer the copy-paste method to BibTeX, despite having used BibTeX for multiple different projects. This is on the grounds that it doesn't give me additional files to juggle, and if I have weird references I can easily put them into the bibliography as I think they should look without having to look up the BibTeX documentation.

I'm happy to use BibTeX in my joint papers whenever my collaborators prefer. Typically, when it was `their turn' to handle the document they separated out the bibliography into a BibTeX file, and then I followed suit by adding to it whenever I had additional references to cite. Sometimes my collaborators stopped to ask my permission, which I've always cheerfully given.

I also used a more sophisticated online collaboration tool once when another one of my collaborators set up our document using it. Once again, I prefer to do things the old-fashioned (i.e. ten years ago) way but I was happy to adapt to my collaborator's preference.

Can you "fathom" my preference? Whether you do or not, I concur with JeffE -- if you want things done your way, ask to be in charge, set things up yourself, and then let your advisor know what you've done. Maybe your advisor will adopt your tools permanently if he/she ends up liking them, maybe not.

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I'd like to give the opposite answer than JaffE's. You can't, give up.

unfortunately, the relationship between you and your advisor is not symmetrical. You can try to make him/her change his/her ways, but if s/he is not willing to change (and habits are difficult to change), you'll end up just fighting windmills

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    [blank stare] Oy. – JeffE Jul 8 '12 at 17:13
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    Advisors are often just busy. And they'd be quite happy to give up control of it saves time. – Suresh Jul 8 '12 at 19:43
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I agree with anonymous.

I'm a young academic but I actually prefer the old copy and paste/formatting by hand over a program that will do it automatically. For me, I've found that generally, the copy and paste format helps in catching errors and is easier to use than an embedded software program that has the potential to crash/become buggy.

I've found that with a variety of those bibliographic programs, they are great for data-basing your entries but not very intuitive or easy to use when it comes to actually writing papers in programs like Word or OpenOffice. They don't always do well in crossing other computers depending on the programs various individuals use (i.e. some might have a mac and use OpenOffice, while the other author has windows and uses Microsoft). The compatibility can cause issues, and many academics use different programs (for example, you use BibTex, my university uses Endnote, my undergraduate uni uses Refworks).

I've also found that while programs such as Endnote can 'technically' adopt styles for a specific journal, the output is never 100% to what the journal requires. It's just easier to type it in right the first time for me, than to try and use a finicky program that can actually cause more, rather than less problems.

You should not rely on these programs to provide you the EXACT formatting required for a journal, in many cases you need to go back and fine-tune. For example, I recently submitted a paper to a journal that wanted a particular style, my referencing program was able to 'output' to this style for the journal, but it wasn't exact even though it had the journal listed as a type of output format. I had to go back and manually format each entry to ensure consistency with the latest printed issues. As I was hand-typing my in-text citations in the exact way as the journal wanted, it wasn't much formatting that needed to be done for the end.

I don't have any issues in keeping track since I use a bibliography program for a database, but tend to add the entries in after the journal article is submitted for review. I just keep track using a plain old word doc, and part of my revision strategy is to go through the paper and find every reference and cross match to make sure I haven't missed any. This also allows me another chance to see any language etc issues that might need fixing up.

I think you need to take a step back and consider that not everyone works in the same way and what you might consider as 'easy' could actually be more difficult for someone else who may have a different way of thinking. Some academics use a multitude of programs, some still prefer more traditional methods and some might jump on board with innovation, and this isn't necessarily a generational gap either.

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