I keep all my reference articles as PDFs attached to their Endnote entry - this makes them easy to find by author / title / journal / topic. When I read an article, I take my notes on a sheet (or two) of my homemade Cornell notes paper. Then I file these notes in chronological order by topic, and add a note to the Endnote entry (Research Notes field) on the location of my handwritten notes.

Each sheet of notes is titled with the citation of the paper it refers to, so it's easy to go into Endnote and find the PDF they refer to.

I know it's not entirely paperless, but I'm good at keeping my notes down to one page, so it does significantly cut down on the amount of paper... and it prevents me from using my bad highlighting and underlining habits to make a paper copy completely illegible.

As for annotating the digital copy, Preview has annotation tools, but I've never played with them.

Scanr is the answer. Then you get PDF's and cheap "photocopying." Using EndNote for PDF storage is good, but I would rather use something like DEVONthink Pro because of its AI bits.

Oh, I didn't really cover filing my handwritten notes as well as I meant to. When I say I file them by topic, it's done very broadly. i.e. my file on atrophy will have notes from papers on the ubiquitin ligases, the proteasome, autophagy, and anything else I particlarly think is relevant to atrophy.

This way, when I thumb through my notes on a topic, I can get a broader view and still access the original papers easily.

Berko: I was hoping for something that could then search the annotations I make on the file, not just a replacement of the original PDF. And I do like DEVONthink pro - but its a little much for me, I think. So far I've been pretty happy with a combination of Papers for quick reference, and Bookends for reference management.

GeekLady: I played with Preview annotation a little - and it probably isn't bad to add a quick note here and there - or to highlight the occasional figure. But I'm getting progressively more convinced I will need to have some sort of more organized note taking system that's paper based. Could you speak a little more to your system/workflow? Can you get good enough notes on your Cornell sheets that you don't usually need to pull up the paper itself as well? How many broad topics do you have - and do you base it around projects, or concepts? Do you integrate seminar lectures as well, and do you use Cornell notes for that too? (I've been using a bound notebook - which doesn't lend itself to filing very easily...)

Sorry for all the questions - but my graduate studies just recently outgrew my previous system, and I can't seem to keep all that noise under control.

I think this is where DEVONthink would excel. You could create notes/annotations in DTP and then explicitly link them to the articles they references. In this regard, I think creating very short notes like Steven Berlin Johnson will aid your information synthesis and connection.

Hi Crazymke. Sorry to join the party late but hopefully this will still be of value to you.

I've been paperless in academia now for over a year and a key component that has helped to stay paperless is a TabletPC. I'm sure you're already aware of what a TabletPC is but you may not know just invaluable they are to the paperless operative in academia. Inking and annotation is a breeze and all of your handwritten notes, in applications such as GoBinder. are completely searchable. Sorted!! :)
Hope that helps
Robert Burdock
'waving goodbye to paper'

Very interesting discussion. I can describe my set-up as a university professor, but its mainly a big mess, so its a do-not-do-like-me warning more than anything.

My scientific papers are mostly on paper, because when I started grad school in 1994, less than 50% of interesting articles were online in PDF format or my poor university did not subscribe to the online version. And if they were, I took the habit of printing them anyway to read on the bus, at my desk, outside on the grass, etc. I stayed with paper out of habit. I started my master in 1994, added a PhD over that and a 4 year post doc, so now I have about 20 legal size boxes of reference material I cannot bring in my new office. They are sitting in my basement since I started as a faculty back in June 06, and I still haven't figured out what to do with them. The irony is that I kept to paper for now, which makes my problem bigger and bigger, but at least I resist the urge to print much more since I apply GTD, because if I print, I decided I must assign it to a next action or file it in a project reference material box (the kind of cutted halfway boxes to hold magazines you get at IKEA) which get reviewed weekly (they are like super inboxes). I presently have 8 boxes like these on my desk, labelled with my main current research projects or class I teach. These boxes MUST be part of the weekly review, because if not, I would end up dumping papers in them and not doing anything about them (reading and note taking) and not moving the project forward.

My seminar notes are in small Clairefontaine books (aaaah silky smooth writing) that also act as brain dumps. I keep them on a shelve but they are very very hard to sift for interesting information or project idea I had while I was not listening to a speaker or riding the metro or waiting in line at the post office. I moved to 3*5 cards when implementing GTD last summer, so the 1-card-for1-talk is much easier to file as general reference material in one of my 8 desk inboxes or the general inbox for later processing during the weekly review.

I am very interested by Devonthink after seeing the Steven Johnson example that Berko gave, because the 8 boxes I have definitely overlap in topics (a paper on aggressive behaviour or hormone X or changes in gene expression with Y variable could be interesting for 3 of them), so all this clunky filing may change, except that I will still have the equivalent of 5 mature trees in my basement in the form of research papers on subjects I do not work on anymore. I like geeklady's advice of having broad topics (if you go for paper notes) because some things do not seem to have an interest for a given part of your thesis up until you come across it and read it again 2 months later (or read teh note syou took on it) and see how relevant it really is for your fourth chapter.

So the short answer is: don't do like me and take the good advices of the smart people here, which you are obvioulsy already doing since you started this thread.

I am going to research devonthink right now

This is somewhat on topic, but has anyone experimented with the ScanSoft OmniPage Search Indexer plugin for Google Desktop Search? It's supposed to allow searching of image files and scanned-image PDFs using OCR. For those of us with a lot of PDFs, or those looking to scan a large number of paper files, this might be a nice (and free) solution.

CrazyMike:
Bear in mind, I'm only a technician, but I'm working with an aim of going back to school, so when I started building my organizational system, I tried to take that into account. Also, my PI expects much of the same of me as he does of any other student or postdoc in his lab - I have to go to the local seminars, know about all the labs projects, etc. I'm also taking free courses for a Masters in Clinical Research (free because I work for the medical school, and I can only earn a maximum of 10 hours credit in 2 years, so it's not THAT great). So you can probably glean something useful out of it.

I made my Cornell Notes pdfs myself, I have lined, gridded, and blank pages, depending on what kind of notes I'm taking. The top margin covers the entire width of the paper, and is 1 inch deep. The next 8 inches is divided into 3 columns: 2.5 inches for writing review questions, 5 inches for my main note taking area, and a 1 inch gutter on the right for random crap, like "I need more ink". The bottom row is the last two inches of the paper and the entire width, I write a summary of my notes here. I print these pages up at home on decent paper - I write with a fountain pen and I like an extra fine nib, so I want to be sure my pen won't bleed. It's not 60 lb. Levenger paper, but it's better than copier paper.

Each paper, lecture, or seminar gets a 1 page sheet of notes, even if I don't fill it up completely. Longer papers and review articles, I let myself use a couple, but I haven't been to a seminar or lecture yet that requires more than 1 page of notes.

I put as much metadata as I can think up in the top margin. The entire reference information of a book or journal article. Name of a lecturer, and biosketch notes. Date & Location. That kind of stuff.
Notes go in the big 8"x5" box (and I write tiny!) I try not to reguritate powerpoint slides, but to write consisely about what is presented. Frequently I write specific information I want to remember: statistics, biochemical pathways, references.
Stuff like "what does Smad stand for" goes in the right gutter, along with doodles, comments on my need of a beer, and theraputic swearing.
After a lecture, sometimes a day, but I try to do it while my memory is fresh, I summarize into the bottom box. If they're notes for a class, I write review questions in the left column. Otherwise, I write research questions in it during a talk - it lets me save my ideas out to one side from my notes.

If the notes are for a class, they're filed by class - this means all the information for studying is under one file. If they're notes on a seminar or paper, they're filed by topic. And by this, I mean they're filed by where they fit into my world. It's broader than specific projects. I suppose you could say they're filed by area of research. When I get enough, I give the area of research subtopics. Because the complete reference to any paper is in the metadata of the notes, I can access it easily, and associate a paper with an area of research that might not be an obvious choice. And because it's just 1 sheet, if it's really, really pertinent to another area of research, I can make a copy of it and file it under 2 different topics. Kind of an analog version of tagging.

My notes are good enough that I get a good overview of what the paper/lecture was about, what was done, what general results were observed. But for any writing exercise, you have to pull up the actual paper, it's just a fact of existence. You'll need it to double check facts/results, and to look through the bibliography for more papers to read.

If and when I get richer, these notes will probably be transferred from file folders to Levenger Circa notebooks.

I also, and I consider this very important, I keep 2 lab method books in addition to my lab notebook. My methods book and lab notebook belong to the lab, I cannot take them when I leave. But I don't want to leave my methods behind, so I keep a second, personal, methods book in a regular sized gridded Moleskine. This requires more work, because I need to keep them synced, but my personal methods book allows me to track the progress I make in refining a new bench technique, while the methods book that will remain in the lab will recieve the fully refined technique, fleshed out and written as legibly as I can. Future members of the lab will look up methods from this book - asking them to interpret my chicken scratching as I work up an immunoprecipitation method is a hard lot.

Moleskine's are ideal as method books, in my opinion, because the water resistant covers and elastic bands makes them slightly more damage resistant than the normal soft bendy posterboard variety.

I also keep a separate Endnote library for the downloaded PDFs of kit protocols - I don't need this stuff cluttering up my main bibliography.

I keep extensive paper files too, but these are generally data sheets for things I purchase, printed protocols, takeout menus, vendor quotes, etc.

I hope I answered your questions, but if there's anything you want me to elaborate on, just ask.

I haven't collected a paper article in about three years. I actually use the comments/annotation feature in Adobe Acrobat. You can make a comment and later Adobe will go through and create a document of just the comments or annotations (which you can then feed into DevonThink if you're using it). It's great for articles that you teach from regularly. I used to make the same notes on the same articles because I'd misplaced the one I used the last time. Now, it's all electronic and with me all the time. I've also been using Spotlight Comments and Smart Folders to keep articles that pertain to particular projects together. It's not perfect, but it's been working pretty well.

Does anyone else use Adobe this way?

I also keep the .pdfs themselves linked to an Endnote database

Sorry to jump into this discussion late. It's a treasure trove of helpful tips and advice. Especially learning that ScanR now accepts emailed jpegs. Wow! How do they do it for free?

I did a bunch of research in historical archives in Europe in 2000. At that time, I used a digital camera to take pictures of archival sources. I used batch file renames to number them by their correct pages and organized them in folders by source. I had also used the camera to "photocopy" important secondary sources before heading to Europe; thus, I had immediate access to a lot of secondary literature on the computer. There was a lot of manual labor--but the pay-off was unbelievable. I took notes on the sources directly on my computer with FileMaker Pro. If only DevonThink had existed then...

At that time, I felt a little ahead of the curve with digitized images. None of my fellow students were using a digital camera.

Ironically, the relative success of my digital regime led me to become something of a digital pack rat, snapping up anything and everything I could. This habit grew worse with the arrival of DevonThink; I clipped anything and everything I could from the internet. The danger with such paperless solutions, however, is that they can tempt one to eliminate the all-important "processing" step--reading, thinking, writing. During a trip to the library, I might copy dozens of items without actually reading them. Yet alas, even DT, as powerful as it is, will not think for me.

Interestingly, it was the hipster PDA and index cards that helped me establish a system for "processing" (i.e., digesting) new material. Rather than copying an article, I jotted down notes and a bibliographical reference on index cards. Then, the second step was to type these notes into my computer system. Even if I don't have time to read something, I try to garner a quick impression of its argument and/or value and note that on an index card. If I need it, I can always obtain the article later. Once I gave up the obsessive need to possess the whole article, I suddenly found myself with much more control of my material.

It's more work up front. But my notes are much more accessible. The key is not just to have a system for storing material, but also a system for processing and digesting it. As a rule of thumb, I would recommend only digitizing/photocopying material that is either absolutely essential or that you will not have easy access to later (archival sources, difficult-to-obtain interlibrary loan articles, etc).

Here's a late reply as I think I may have fine-tuned my system. But alas, knowing me, it may well change again and again. I do think that this is scaleable, though, which is what I wanted. It's also heavily Mac dependent, so I apologize for those PC users out there.

1) Papers: I already mentioned, but I love this program - it really fills a niche in my work flow. I use it for the majority of my pubmed searching, as well as viewing and organizing my entire library - I'm sure you End Note users can use it as well. This is really my front end for the most part - I keep track of authors and journals here, as well as sorting out papers of relevance. In the notes section I have a direct link to the Journler entry. . .

2) Journler: A great donationware journaling and note-taking program for Mac users. This is where I keep most of my typed up notes. In case I want to search for papers through Journler itself I title the entry with the name of the paper I've read, and set the creation date to the date of publication. The category is "Paper" so I can have a smart folder with all of my notes on the side bar. For Tags I include First author, last author, journal, and usually one other (Methods, Resource, etc). This way I can create nested smart folders if I want to pull up my notes on a single author or from a single year/time period. At the top of the entry I include a link to the Papers entry (could work just as well directly to the PDF, but this is a more elegant solution for me). Then I take notes from every subsection of the papers (intro, various results areas, conclusion), or based on the figures themselves - whichever is most appropriate.

3) Articles: Now I have two stacks of papers - Papers to be read, and Papers to have notes taken. The to be read pile travels with me (if its small enough) for when I have a few minutes to take a peek at. The To have notes taken pile is usually all marked up from my read through. Once it moves out of the second pile it either gets filed if its really critical to hold on to, or tossed in the recycling bin.

I'm really happy with this solution since everything is indexed for ready searching, and I can harness both programs readily for searching what I'm looking for. Journler has several powerful export options too, so it is easily moved to another platform (even paper!).

I hope you guys like it - and that it helps someone out there - even if it is a niche position I'm in.

Have you tried any of the on-line services such as zotero or a.nnotate? You upload the paper and annotate it from a browser. The neat thing with these is that you can get other people to annotate the same version.