Tools for (PhD) Researching

(Sorry that this is a bit off-topic...)

I'm not talking about programming tools. Instead, I need something to organize my research progress. I learnt the hard way while I was doing my Masters that when I didn't keep track of my ideas and progress on a day-to-day basis, the task of thesis-writing became almost undoable at a later stage. That convinces me I need some "tool" to build the core of my thesis on a day-to-day basis.

I can be on a very wrong track, but what I currently have in mind is a personal wiki (e.g. based on Mediawiki) which allows me to have rich cross-referencing of ideas. Come to think about it, i think what i need are:

- a place to keep a journal
- a place to keep track of all the bios and allow me to add annotations/comments/thoughts
- something allows me to keep track of branches of new ideas and backtracking.

Any suggestions?

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Perhaps you would like a combination of Wiki and issue-tracking, as in Trac, That would help you keep track of ideas and also of open problems. And Trac is also a frontend to your version control software, as long as you use svn, cvs or darcs.

some tools...

To organize your literature (collect bibtex, add tags, add comments) I can recommend CiteULike or bibsonomy or connotea.

To get your bearings in the web of scientific publications I's like to point to my own work: The citation influence browser

Have fun... Laura

CiteULike looks very

CiteULike looks very promising. But I really wish it worked *within* an idea organizer (e.g. wiki, blogger, etc) so that i can link the bios to entries of my research journal. If I have just a flat list of bios, when it comes to finalizing my papers, it'll be tedious to filter out those I need. Tagging them may help, but not ideal...

Hmm, it's always like this: some tools are good at one aspect but you have a hard time to have a nice integrated environment. It all comes down to the holy grail of software -- interoperability...

Sorry I'm whining... :-p

Your thesis is on

Your thesis is on software interoperability then, right?

My primary interest is PL.

My primary interest is PL. :-)


Very slick

I got one of those set up today, and once you figure out the interface oddities it's remarkably slick and easy to use.

I've been looking for something like this for quite a while now, actually. Many thanks.

I would recommend this as well

I would have recommended this as well. It is a really nice tool that exactly does what it should do.

At the moment there is a lot of stuff like plugins going around. I hope this will not blow everything up but keeps the core small, simple and fast.


If you have a Mac, I'd recommend taking a look at DEVONthink. It's not free, like the other options, but it can be quite useful.

Circus Ponies Notebook

If you have a mac, Notebook might be just what you're looking for.

Concept Maps

I like Cmap Tools to help organize ideas. They're easy to create and read (esp. for others if you're sharing your ideas).

Notebook and Tinderbox (with Yojimbo)

On the Mac, I would suggest looking at both Notebook and Tinderbox.

Notebook is better suited to managing PDF Files and various downloads. It has limited hypertext linking support and a delightful GUI. But if you read all of the legal boilerplate on the Notebook website, you are likely to get the sense that the lawyers are running the company and that they see their user base as potential litigants, which suggests a strong case of Not-Invented-Here syndrome and probably chokes off most user input making one wish there were an open source alternative.

The other big player would be Tinderbox which includes a license for Bare Bones' Yojimbo indexer and clipping manager (which is a Notebook equivalent that works well as a lightweight freeform ebook system for reading and full text searching all of your PDFs if you can live without Notebook's hierarchical organization facilities.

As to Tinderbox itself, before you read on, I must note that I personally know the author and have offered beta testing input in the program's development. However, I have no financial interest in its success.

Tinderbox is a proprietary semi-OO prototype-based outliner and spatial hypertext environment. It doesn't attempt to manage archiving external files like Notebook, but it is totally open ended with enough customization hooks to make it a quasi-programming environment in its own right. There is a powerful export template system, background agents, the ability to deal with recursively defined note attributes, a system of typed hypertext links, the ability to download material from the Internet, and the ability to shell out to the scripting language of your choice and pull computed results back into the program. Working with Tinderbox could give you ideas for IDE design, but most importantly, it might help you organize and structure the sea of information you pull together in your doctoral research.

It takes a lot of time to truly master the full potential of Tinderbox so you will want to try the working demo version before considering a purchase. Most users pay an annual subscription fee for a continuous stream of upgrades, but if you want to stop upgrading at any point the last version you bought will keep working. In any case, the company is very responsive to its user community and about as "nice" as can be expected of any profit making concern.

This is, of course, my personal opinion and in no way constitutes an official review or product endorsement by any organization or group with which I am affiliated.


I can't recommend Backpack highly enough. It's essentially a structured wiki on steroids. I examined a whole lot of personal wikis - tidliwiki, instiki, etc. - but none of them have the feel, polish, or ease of use of Backpack. And that means a lot, since I am much more likely to use something that is fun to use.

A free account gives you 5 pages, and paid accounts start at $5/mo. So you can try it out first, and don't need to upgrade unless you like it so much that you outgrow 5 pages.

If you want something completely free that you can host yourself, instiki is a good wiki and is easy to set up.


Personaly what I like the best to organise my ideas is tomboy. It allow you to simply take notes and words that are also the title of other notes become links. So it's kindof a wiki, without any time consummed having to change page to edit them ... etc
But you won't be able to put images in it or anything like that.

Thank you everyone. It will

Thank you everyone. It will take me some time to go through them to see which suits me. :-)

If you use Emacs...

If you use Emacs...

I keep a directory per project, with a single org-mode file of notes organized chronologically. This works well as a first draft, containing thoughts and results which can then be synthesized into conference papers and technical reports. Within each project directory I also keep a BibTeX file, adding every interesting paper as I read it, and a subdiretory containing the PDFs. With this scheme, isearch, grep and (on a mac) Spotlight are adequate for indexing and search.

freemind for mind mapping

If you like mind mapping software freemind could be a got choice for you. However it is not very well suited for creating links between ideas but more for creating hierarchies.

Writing tools

While we are on the subject of research tools...

The second kind of tools one needs are tools to help with the writing of papers. Bibliography tools (bibtex is the natural choice in these cicrles, endnote is the natural choice for those using Word) etc.

So this is a good opportunity for me to mention once more my quest for something like Sweave that would work with Scheme, not (just) R. A minimal implementation would be easy to produce, but I'd be happy to find something robust and feature rich...


How about the documentation system for PLT Scheme, Scribble? It can produce documents along with code and the results of executing that code.

Truth be told, I haven't

Truth be told, I haven't tried it yet. It seems ideal, since my code is in PLT Scheme... What I want to be able to do is easily integrate the results of running the code in the paper, not the code, I didn't notice that you can do that. (Truth be told, I really want to be able to embed graphs I currently produce from the output of the simulation using Excel..)

A tool for gathering research material

You could take a look at 3D Topicscape. Good for organizing research material as it arrives, thinking research through and outlining papers with material gathered and written - there's a user story about how someone used it as a research information organizer during their MBA studies - not a PhD, but the principles would definitely apply.


[Admin] Ads

This post is clearly an ad. It is inaapropriate to post ads to LtU discussions, which are meant to allow discussions between LtU community members.


An ad is unsolicited, this information was solicited.

If you look at the link (the user story link) I believe you will see that it is very relevant to the original question.

If you, and the person who posed question think not, I apologize, but I thought it was a focused answer.


Research Tools for the Mac

I just recently submitted my PhD and wrote a blog post about the software I used to help with my research.

Most of apps mentioned in the post do not directly address your problem of keep track of what you read and organise your thoughts apart from: BibDesk, which is great for organising your literature and annotating the papers you read, and Journler, which I've found great for writing down an organising ideas.

Since writing the post I've also discovered Skim which integrates nicely with BibDesk and allows you to annote PDF papers you read and then later search the papers by their original content or your annotations.

SlipBox is also nice for jotting down snippets like bios, quotes or short notes and organising them through tags. It also integrates with BibDesk.

To top it off, I can also vouch for TiddlyWiki which some of the earlier responses have pointed out. It's simple, effective and very portable.

Hope that helps and good luck with your PhD!

Corrected link.

The link to SlipBox duplicates that to Skim. Here's the correct link.

How about Papers?

I haven't used it myself, by Papers also sounds pretty nice for organizing and annotating literature. It's quite well integrated with article repositories used in life sciences, like PubMed, but I'm not sure if ACM is equally supported.


You might want to check out Zotero. The thing I like best about it is that it can scrape the citation information off of many online sites (i.e. ACM Digital Library) and put it right into a citation within the tool.

The beta level which I've been using also does synchronization across instances so you can have a unified view of your work regardless of what machine you are on.


Be careful: many of these

Be careful: many of these sites have incorrect citations. Had a very annoyed reviewer once because of it :)

My experiences were good.

My experiences were good. Some cites have incomplete information, but that's easy to spot. I often use google scholar, and use the import to endnote feature to grab the info into zotero.


A good outliner can give you just the right level of structure to keep your thoughts semi-organized, easy to rearrange, and quick to review. My favourite is EccoPro, an old Windows application (runs fine under Wine) that's available as a free download from its developer. Actually, it's almost like a free-form, user-friendly OODB, because it's so easy to create arbitrary attributes on items and define views and filters.

If outliners sound attractive and you have a Mac, have a look at OmniOutliner and Tinderbox, which have the advantage of being integrated into MacOS's way of doing things. The former is much simpler than Ecco, while the latter has way more features, so you might want to try both and see which one suits you better. They are not free, but there are free demo versions, and are under active development, unlike Ecco, whose most recent version is from 1997.