More on scientific notes

by Giles Turnbull

One of my interests is electronic notebooks, and how different kinds of note-taking and note-storing software products appeal to different kinds of users. Scientists, in particular, need something to keep track of, and possibly annotate, all the papers they need to read in the course of their work.

Flip Phillips made two posts to Apple’s Scitech mailing list today, outlining his views on a variety of note-management apps that fellow scientists might put to use.

Part 1 looks at Yep, Papers (itself the subject of intense scrutiny recently), and DEVONthink; Part 2 deals with WorkLife, BibDesk, and EndNote.

If you’re looking at note apps, especially for use in academia, Flip’s brief views are well worth a read.


William Hayes
2007-03-28 17:14:35
I'm surprised no one mentioned Quosa ( I like some of what I've seen in Sente and some of the features in Papers look pretty cool, but I have really heavy literature users where I work. I also support (I manage a biopharma library and literature informatics group) both PC's and Mac's and Quosa is multi-platform. Managing thousands of PDF's is easy, importing PDF's will (when able to match against Pubmed) automatically associate full bibliographic information for 40-70% of the PDF's I've loaded up. The built in text search engine (based on Lucene) has all of the fielded query capabilities and full-text search options, including regex, you could want with the ability to cluster based on provided gene/synonym or term lists. You can use multiple channels to search (Pubmed, USPTO, Ovid, Web of Knowledge, etc), basically providing federated search, followed up with a fully capable local search engine after you've downloaded everything available.

I've had a colleague pull down as much of 30k citations as he could grab in order to find the kinetic parameters for a set of proteins (kinetic parameters are only found in the full-text of the paper and one cannot determine if they exist based on keyword searches of the article abstracts). After a couple of days collecting :) it took him a few minutes to grab all of the kinetic parameters using the full-text search. Did he get everything available - highly doubtful as we were limited in number of journals licensed. Did he get everything super-humanly possible - oh yeah!

Virtual folders, full-text search of the localized full-text html or PDF's, ability to pull down any journal articles that you have access to (licensed or open access), ability to import/export endnote, refmgr libraries (my workflow is now to manage literature in Quosa and write with Endnote as Endnote has horrible collection mgmt capabilities), workgroup literature mgmt/sharing (in a copyright compliant manner)...

Disclaimer - I don't have any financial interest in Quosa, but I am a happy customer.

Rob Potts
2007-03-28 18:02:57
Have you looked a Circus Ponies Notebook? It may not be ideal for "reprints" but its great for taking notes, organizing data, attaching files, etc...

Its worth checking out.

2007-03-29 09:10:37
i've been using eaglefiler to store my pdfs+notes. i wish it had more fields and i wish it could export those fields to a bibtex file. since it stores the files in finder and not a big database syncing is a breeze though. its a little pokey on the old powerbook but runs pretty well on the mac pro.
Mark Bernsteiun
2007-03-29 10:55:42
We really need to separate "pdf holders" like those Flip Phillips reviews -- Papers, DevonThink, Yojimbo -- from tools for making and analyzing notes, such as Agenda, NoteBook and Tinderbox (

Storing and annotating journal articles and citations is an important application, buty it's quite distinct from making and analyzing notes. We need a better way to talk about this distinction.