Research Software and Tools

The time for Ph.D. exam preparation is fast approaching (I really should start this summer) and I have been trying to develop strategies for successful note taking, organization, research, and scheduling.

I was initially inspired by D. Travers Scott's blog courageously chronicling his exam reading. After some more searching I stumbled across David Parry's excellent blog discussing a variety of different tech tools for academics, Academhack.

So far I have gotten a hold of EndNote on the recommendation of a colleague, but have yet to really play around with it. I have been told it is incredibly helpful in terms of managing and implementing citations.

I have also started my own blog which I hope to utilize, at least until I find a better solution, as a space for venting and filing of notes.

I have taken a brief look at some other applications for note taking but none seem to be quite as functional as a basic blog. Blogs have a decent interface as well as good categorization, linking, and commenting functionality. However, I am sure there must be something better.

Are there any killer apps people would recommend for academic work? Or perhaps even general suggestions and advice for exams and dissertation?


Admittedly, I haven't tried Endnote, but Zotero has been my citation manager/note taker of choice. It works right in Firefox, so it's really convenient. It does have it's limitations, but most of those can be worked around, and it's advantages outweigh those (mostly) minor inconveniences.

I think a Blog is also a great way to keep track of stuff. I haven't updated mine that well, but I do have a dissertation blog.

The other tool I use a lot for notes and general outlining is Netvibes. I use it like a wall of sticky notes where I can tack ideas and rearrange them periodically. It's also accessible anywhere, so that doesn't confine my work to a particular box, which I like.

Finally, another tool I experimented with, but never got the hang of, is FreeMind, a "mind-mapper". I showed it to my students, and at least one really got into it, so it's useful to some people.

Anyway, hope that helps. I really like learning about productivity/research, so let us know what else you end up using.

Let me second Zach's

Let me second Zach's comment, there are a lot of advantages to choosing Zotero over Endnote.

The other application I find useful is Devon (this is Mac only). There are a lot of shoebox, organize everything, applications out there, but this is the one I prefer. Getting used to using one early certainly helps in the process.

I have been toying around

I have been toying around with Zotero today quite a bit and have been really pleased. Being able to pull things directly off the webpage I am looking at is a huge help. I also have been working on getting the folder shared so I have a unified database between my desktop and laptop.

Unfortunately, I don't have a Mac so I can't check Devon out.



I'd second a recommendation for Freemind. It's great for organising random thoughts and inserting links to stuff in a 'train of thought' way. I use it for writing and presenting lectures and wish I'd known about it when I was working on my thesis.

I used Endnote a lot with my thesis. If you maintain it and write your citations into your text using Endnote then final formatting of footnotes/endnotes and generatio of bibliography is an absolute breeze.


I have been testing EndNote and Zotero quite a bit over the past few days.

I definitely was preferring Zotero, due to its incredibly easy interface and importing of citations directly from the web. However, I cannot for the life of me get it to work in MS Word. I consistently get errors and when I browse the support forums on Zotero the fixes are very detailed and difficult to implement.

I think that is going to force me to use EndNote. It wouldn't be such a bad thing if I could just get the online periodical search functionality to work. As of now I have to manually enter all the journal articles I find on MLA Int. Bibl. for example because I cannot connect.



I don't know if this is the issue you're having, but for a while I couldn't get it to work because I had mismatched reference types in the same document. I think I was trying to switch from Fields to Bookmarks and it got all crashy.

I guess it is still in beta, after all.

No stability problems with Endnote, then?

The problem I have with

The problem I have with Zotero is more serious than that. Anything I click on causes a fatal error in Word.

As for EndNote, no issues yet other than the frustrations I mentioned with getting it to connect to my library databases.


my issue

That was my symptom too, actually, though there are probably multiple errors which could cause that behavior. It would work fine in a blank document, but when I pasted in the text of the chapter in question, it would start crashing whenever I tried doing anything with it. Turns out I had invisible reference fields, so I just had to track all those down.

A possible alternative to EndNote...

Hi Tanner,

a good friend of mine and I both struggled with the same issues - how to manage and share our research - while writing our Ph.D. theses. So we set out to develop a software ourselves, called Mendeley (

For example, when you add a research paper (in text PDF format) into Mendeley, it tries to automatically extract the metadata (authors, title, journal etc.) and the cited references without you having to type it in. Mendeley also offers superfast full-text search across all your documents, tagging/categorization, and will soon allow sharing your research library with colleages.

It's still in a closed beta test, but our website should give you a pretty good picture of what's coming up (and if you're interested, we'd be glad to have you as a beta tester).

Cheers from London,

Sounds like a promising

Sounds like a promising project. I would love to check it out. You can email me at tanner [at]


Blogs rulez

no ... i think blogs are really the best solutions for it (at time). they are free avaible, mostly up2date and easy to handle.

Try NoteScribe

If you're a window's user, I think my company's Note Software NoteScribe would be a valuable asset for you. We had quite a few graduate students beta test the program, and they loved how useful it was for keeping track of research and ideas for their dissertations. Our lead programmer was working on his MA thesis when he developed it, so I think it would be right up your alley. Let me know if you have any questions, and check us out at

Let me know if you have any questions!


I will face my dissertation

I will face my dissertation in the January so your blog helped me a lot. First of all thanks for those links to D. Travers Scott's blog and David Parry's blog. Those blogs are extremely useful for exam preparation. I see that this entry was written over a year ago, so I think that you have passed your exam and dissertation successfully because I see you are a clever one :) Thanks one more time for posting it here. I have bookmarked your blog and will be waiting for other interesting entries from you. Thanks!


Brad Kallson from software development services

I think blog are the best way

I think blog are the best way to conduct research and I guess they are the most appropriate research tools available to us. I spend most of my time reading different posts it provides me with a lot of information and knowledge. The best part it is easy to digest.
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