Lambda the Ultimate

Perhaps you would like a combination of Wiki and issue-tracking, as in Trac, http://trac.edgewall.org/? 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.

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

http://tiddlywiki.com/

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.

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

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

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 take me some time to go through them to see which suits me. :-)

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.

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.

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...

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.

Argey

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!

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.

http://www.zotero.org/

Matt

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.