[OWW-Discuss] I'm just launching into some updated reading for an old project and I'm looking at a better way to collect my notes together...

[Barry Canton]

For storing, cross-referencing notes on papers etc. the wiki is the best
tool I've used.
Tom's suggestion of Papers for the Mac is a good one.  Bibdesk (
http://bibdesk.sourceforge.net/) is a great free and open source alternative
to Papers.  It's especially well integrated with Bibtex if you like that
sort of thing and has been around for quite a while so the feature set is
rich.  It organizes your pdf files in a customizable manner.

On 1/5/08, Tom Knight <tk at csail.mit.edu> wrote:
>
> Some things to think about:
> * spotlight in Mac OSX 10.4+ will index pdf files, so if you have
> text-under-pdf documents, you can retrieve the information using a
> spotlight search.
> * Papers, a program for the Mac.  I haven't tried this, but it sounds
> good: http://mekentosj.com/papers/
>
> I've given up entirely on paper.  I print papers to read them, and view
> the printed version as completely disposable.
>
> You need a way to scan and OCR documents into PDF format if they are
> not already there.  Scanning is relatively easy.  Our new Xerox copiers
> will OCR documents as they are scanned, and then email the result to
> you.
> The HP "Digital Sender" was, prior to this, my favorite scanner, which
> also emailed.
> The  OCR program which works is the (Windows) Abbyy Finereader.
> If you use a Mac, you also need a copy of PDFLAB (free) which is very
> useful to "adjust" PDF permissions.
>
>
>
> On Jan 5, 2008, at 6:04 PM, John Cumbers wrote:
>
> > Hi all,
> > So I'm halfway through my PhD and I'm just launching into some updated
> > reading for an old project and I'm looking at a better way to collect
> > my notes together. I'm hoping that there is a great new tool
> > available that someone can tell me about to make my life easier... or
> > at least a better strategy that someone has found to do this sort of
> > research by...
> >
> > I want something to collect notes from meetings with my supervisor,
> > experiments I plan to do, notes from reading, diagrams, references.
> > Ideally something that would show me a list of notes I've taken, in
> > chronological order and also searchable via tags.
> >
> > Here are a few strategies that have not worked that well in the past.
> > Find papers via pubmed/hubmed/scholar
> > add papers to citeulike, many never end up getting read.
> > print out a few key pdf's on paper
> > go through these, make notes on the paper itself, make notes on
> > scratch paper
> > Write up key things on more scratch paper.
> > File some of the PDF's via citeulike ID number in filing cabinet...
> > never to be looked at again.. get on with lab work
> > or... create stack of unsortable papers, get on with lab work
> > Lose papers in mass of other papers. lose notes.
> > repeat.
> >
> > Next best thing might be a paper notebook like a lab book. But this
> > gets equally as messy, although I could repeat this with an index to
> > be move successful. But a paper book is not easily searchable. What
> > about a word doc... argh... can you imagine... maybe there are better
> > tools for Mac or Unix, but I'm currently mostly on a PC.
> >
> > Can you help? Do you have a better strategy, or tool to recommend?
> > I've googled a few times for things like this but never found anything
> > satisfactory.
> >
> > Cheers,
> > John
> >
> >
> >
> >
> >
> >
> > --
> >  John Cumbers, Graduate Student
> > Biology and Medicine
> > Brown University, Box G-W
> > Providence, Rhode Island, 02912, USA
> > Tel USA: +1 401 523 8190, Fax: +1 401 863-2166
> > UK to USA: 0207 617 7824_______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
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-- 
Barry Canton
Endy Lab
Biological Engineering Division
Massachusetts Institute of Technology

Tel.:(617) 401-7320 (Grand Central)
Email1: bcanton at mit.edu
Email2: bcanton at gmail.com
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