Decaflon

Hi Andrew. I can't say I have a solution in a neat little package with a bow for you, but maybe I can help out.

Personally, I find myself unable to use only one program for all the PDFs, images, videos, references and notes. The only compact program I've found useful for keeping all of these is a wiki.

I'm currently using DokuWiki to maintain the basic skeleton of my research, but it's nowhere near perfect (I'm using folders and standard file organization to a great extent in addition to any wiki compilations).

However, a wiki is really easy to access, edit and maintain — so it might fulfill your needs. It's definitely better than using a blog platform.

I've just started using google docs for this sort of thing. I don't use it for anything important, but for todo lists and notes I find it perfect.

I like Scrivener for the Mac. It costs money, but I think it's definitely worth it if you write a lot of papers. It's geared toward the professional writer, but I could definitely see it used to write a PhD paper.

It's Mac-only, though, so that could kill the deal immediately.

Another voice here for wikis - I used one when I was planning and writing my thesis. Not only was it a great tool for dumping snippets, links etc, it was also brilliant (I found) when I was drafting chapters. Plus I had one set up on our server in the lab so instead of emailing chunks to and fro between my supervisor and myself, he could just hop on the wiki, have a read, make suggestions and so on.

A few words of caution - it's easy to get carried away with wikis, just having snips and pieces here and there with no coherent whole. It's perfect at the research and planning stage but once you get into serious 'pull it all together and write' mode you need to be really disciplined.

The beauty of wikis (to me) is, depending on your skills, you can hack one together to do pretty much what you want it to.

Other than that, if you're just looking to linkroll/comment, have you thought of del.icio.us, magnolia, or setting up a tumblr?

I'm a Yojimbo freak, personally.

Thanks all for your contributions, they've been really helpful. Unfortunately I'm not a Mac owner so that rules out Yojimbo and Scrivener (both of which look like excellent apps).

So that leaves me with the wiki option. I think the experience you describe Cas is exactly what I'm looking for. I'll have a look at docuwiki for a start and see where that leads me.

If anyone has any other suggestions for neat little apps that help organise your studies then please post them here.

Thanks again 9rulers.

I'm not very familiar with it, but Treepad might right be up your alley.

Wikis are one option. I know people who use Backpack from 37signals. I personally use a combination of del.icio.us and Google Notebook to capture research. I also know several people who are using Zotero.

I wouldn't focus too much on the software, wiki or otherwise, but try to layout an organized set of files and directories. How you choose to organize your files is up to you but I tend to rename every paper/book/note (typically a binary file) to include the last name of the author and the title. For images/drawings/plots, I use camelText to provide a descriptive name. Searching for files on any modern OS is then trivial. I write a lot of plain text files which are also easily searched; I have a file named NOTES in almost every one of my working directories.

General advice from someone who learned the hard way:
- Limit the amount of time you spend online (this includes reading 9r)
- Devise an organized folder/directory system that works for you
- Find a good bibliographic database manager; preferably one that allows you to easily export/input plain text files.
- Limit your use of software that uses proprietary formats (i.e. word/excel/etc) as these are irrecoverable when a minor glitch occurs. If you must use these programs, save unformatted text files regularly so that you don't loose the content.
- Buy yourself a large external hard disk and backup your computer every week/night. Likewise, get a DVD burner and make an effort to burn an archive of your own work/results every quarter. It is up to you whether you use software to manage this or just do it manually yourself. I know it sounds obvious, but If you own a laptop, make sure that your backup disk is never kept in your computer bag. I typically leave one copy of my current work on the group server and a second copy at home.
- If you go the wiki route, make sure your directories/databases on the server are regularly backed up, that the server is well maintained and has the ability to restrict network access to your wiki (if needed). Note that unless you maintain the server yourself, you are putting a lot of trust in someone else's abilities and hardware.

Good luck,
Mary

Mary, what a tremendous post! Thanks very much for sharing your thoughts on this. I have yet to find the solution that suits me best. I totally agree with your point of putting too much trust into an online 3rd party server and agree that limiting Internet time is fundamental to all studies. Backing up work is something I have done religiously since my undergrad years back in the 90's. I'm now searching for a bibliographic database system that will work offline.

You should talk to your supervisor and other group members before deciding on which bib software to use. In our group (physical sciences), we use TeX/LaTeX/ConTeXt for reports/papers and everything is in a bibTeX database. New grad students are usually encouraged to add to our existing .bib files instead of starting from scratch. MS Word has improved significantly since the early 90s but I still don't trust it with anything more than a 25 pages.

Good luck,
Mary

Tiddlywiki sounds like it'll do what you want. I know folks have used it for exactly what you're doing.

TiddlyWiki Web Site

It's easy to use, works on your desktop or over the web, etc..