For storing, cross-referencing notes on papers etc. the wiki is the best tool I've used. <div><br class="webkit-block-placeholder"></div><div>Tom's suggestion of Papers for the Mac is a good one. Bibdesk (<a href="http://bibdesk.sourceforge.net/">
http://bibdesk.sourceforge.net/</a>) 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.
<br><br><div><span class="gmail_quote">On 1/5/08, <b class="gmail_sendername">Tom Knight</b> <<a href="mailto:tk@csail.mit.edu">tk@csail.mit.edu</a>> wrote:</span><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">
Some things to think about:<br>* spotlight in Mac OSX 10.4+ will index pdf files, so if you have<br>text-under-pdf documents, you can retrieve the information using a<br>spotlight search.<br>* Papers, a program for the Mac. I haven't tried this, but it sounds
<br>good: <a href="http://mekentosj.com/papers/">http://mekentosj.com/papers/</a><br><br>I've given up entirely on paper. I print papers to read them, and view<br>the printed version as completely disposable.<br><br>
You need a way to scan and OCR documents into PDF format if they are<br>not already there. Scanning is relatively easy. Our new Xerox copiers<br>will OCR documents as they are scanned, and then email the result to<br>you.
<br>The HP "Digital Sender" was, prior to this, my favorite scanner, which<br>also emailed.<br>The OCR program which works is the (Windows) Abbyy Finereader.<br>If you use a Mac, you also need a copy of PDFLAB (free) which is very
<br>useful to "adjust" PDF permissions.<br><br><br><br>On Jan 5, 2008, at 6:04 PM, John Cumbers wrote:<br><br>> Hi all,<br>> So I'm halfway through my PhD and I'm just launching into some updated<br>
> reading for an old project and I'm looking at a better way to collect<br>> my notes together. I'm hoping that there is a great new tool<br>> available that someone can tell me about to make my life easier... or
<br>> at least a better strategy that someone has found to do this sort of<br>> research by...<br>><br>> I want something to collect notes from meetings with my supervisor,<br>> experiments I plan to do, notes from reading, diagrams, references.
<br>> Ideally something that would show me a list of notes I've taken, in<br>> chronological order and also searchable via tags.<br>><br>> Here are a few strategies that have not worked that well in the past.
<br>> Find papers via pubmed/hubmed/scholar<br>> add papers to citeulike, many never end up getting read.<br>> print out a few key pdf's on paper<br>> go through these, make notes on the paper itself, make notes on
<br>> scratch paper<br>> Write up key things on more scratch paper.<br>> File some of the PDF's via citeulike ID number in filing cabinet...<br>> never to be looked at again.. get on with lab work<br>> or... create stack of unsortable papers, get on with lab work
<br>> Lose papers in mass of other papers. lose notes.<br>> repeat.<br>><br>> Next best thing might be a paper notebook like a lab book. But this<br>> gets equally as messy, although I could repeat this with an index to
<br>> be move successful. But a paper book is not easily searchable. What<br>> about a word doc... argh... can you imagine... maybe there are better<br>> tools for Mac or Unix, but I'm currently mostly on a PC.
<br>><br>> Can you help? Do you have a better strategy, or tool to recommend?<br>> I've googled a few times for things like this but never found anything<br>> satisfactory.<br>><br>> Cheers,<br>> John
<br>><br>><br>><br>><br>><br>><br>> --<br>> John Cumbers, Graduate Student<br>> Biology and Medicine<br>> Brown University, Box G-W<br>> Providence, Rhode Island, 02912, USA<br>> Tel USA: +1 401 523 8190, Fax: +1 401 863-2166
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