While working on my diploma thesis, one thought recurred all the time working with a paper.
For better understanding I will first reiterate how we (well, at least me, but perhaps many other people, too) work with papers.
Sitting at your desk, you have a paper in front of you, a pen and a text marker, and a notebook. While reading the paper, you mark parts of the text and take notes either in the paper or in your notebook.
What kind of notes do you take, and which parts do you mark? Quotations you might incorporate into your own text, references (I have the pages with references printed twice so that I can always have them at the ready without breaking the reading process by switching pages.), concepts mentioned in other papers (quoted, extended or worked on), and a lot more.
After you read 10 papers or more, you have a bunch of notes. These are written down either in the notebook or on the papers or on both (perhaps complementary, perhaps scattered, perhaps [but much less probable] ‘mirrored’).
Now that you read the papers, you need to sort your notes. That includes reading your notes, re-reading some passages of the papers, looking through other papers as well to solve references and links, summarizing concepts spanning across different papers. This process is very time consuming and can lead to frustration (“Where the heck is that Meyer paper gone?!”, “I can’t find that reference again, it ought to be here somewhere…”, “Second, which David paper is that, the 2004 or the 2005?”). Of course, over time you will come up with certain tricks to help youself. Living is learning.
But.
All these papers I read are printed copies of online resources (PDF and HTML). Virtually all papers produced are accessible as online resources (paid or free), at least in technology related fields. So we do have two versions of them. One printed on our desks’, one either on the Web (Which I more and more find to be an extension to my harddrive.) or on our computer. On one half you have jotted notes, marked concepts. The others’ are untouched, not mapping your work on them. Both need to be sorted, ordered and filed - in different ways using different means. And then there is the information in your notebook, that isn’t part of any collection but is a separate isle on its own.
There are software tools to faciliate this process. But they break the process, too, because they don’t integrate all steps. There are (highly sophisticated) bibliographic tools for literature management, mindmapping tools, note management tools and of course word processors.
What is missing is a tool that helps you getting it all together. Reading, note taking, spanning concepts, references, links, quotes and all the pieces of information you as a reader create while working with texts.
Let’s think about a blank computer screen. We vertically devide it in two parts, the right one smaller then the left one. In the right part, the sidebar, you can define areas. You can give them headings like “quotes”, “references”, “concepts”, anything you like. In the left part of the screen, the content area, texts are displayed (Who the heck cares about formats when reading?, HTML, PDF, DOC, its all the same.). Your mouse is the tool you actually work with. Just mark a fews words and drag them into your “quotes” area, where you might enter a short hand. Find an interesting reference, and put it into the “references” area, entering a short hand. Mark a heading, drag it onto another heading from another paper already in the “concepts” area - and voila, they get linked to each other.
I think you can see what I mean. Of course most of the work the tools needs to do is to be done in the background. What I want is an unobstrusive UI. And I mean unobstrusive. Just pointing, clicking, dragging, a few hits on the keyboard, enter, done.
Here are some tools I discovered and tested. Unfortunatly, none fulfilled my requirements.
[Scrapbook](http://amb.vis.ne.jp/mozilla/scrapbook/), an extension for [Firefox](http://www.mozilla.com/firefox/) is en route to become such a tool. Today its UI is still to complex, needing to much attention, and to small, embedded in the browser’s window. If it could work with PDF documents and if the interface would be streamlined, offering less options but more commands, it would be great.
[Google Notebook](http://www.google.com/googlenotebook/overview.html) offers, via a browser plugin using a web interface, functionality to create notes. Notes are filed in Notebooks, which can be structured in sections. Both the web interface and the plugin are in need of refinement to make them usable. Today it is simply a sticky notes-like tool to jot down unstructered notes.
[Onfolio](http://www.heise.de/newsticker/meldung/76774)