From johncumbers at gmail.com Sat Jan 5 18:04:21 2008 From: johncumbers at gmail.com (John Cumbers) Date: Sat, 5 Jan 2008 18:04:21 -0500 Subject: [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... Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080105/1e8731ba/attachment.htm From tk at csail.mit.edu Sat Jan 5 19:34:12 2008 From: tk at csail.mit.edu (Tom Knight) Date: Sat, 5 Jan 2008 19:34:12 -0500 Subject: [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... In-Reply-To: References: Message-ID: 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3069 bytes Desc: not available Url : http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080105/d569a77b/attachment.bin From bcanton at MIT.EDU Sat Jan 5 20:37:50 2008 From: bcanton at MIT.EDU (Barry Canton) Date: Sat, 5 Jan 2008 20:37:50 -0500 Subject: [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... In-Reply-To: References: Message-ID: <52c0d2160801051737i2b9ddcd4g54f0ddda37439af0@mail.gmail.com> 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 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 > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080105/719c8f53/attachment.htm From ilyas at MIT.EDU Thu Jan 10 18:50:13 2008 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Thu, 10 Jan 2008 18:50:13 -0500 Subject: [OWW-Discuss] plugin for mediawiki Message-ID: <4786AF35.8000108@mit.edu> http://bloodgate.com/perl/graph/ some examples: http://bloodgate.com/perl/graph/screenshots.html http://bloodgate.com/perl/graph/fun.html and a live demo: http://bloodgate.com/graph-demo Would it be useful on OWW? From ilyas at MIT.EDU Sun Jan 13 15:10:35 2008 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Sun, 13 Jan 2008 15:10:35 -0500 Subject: [OWW-Discuss] From 10 Hours a Week, $10 Million a Year Message-ID: <478A703B.4010008@mit.edu> Apparently, it doesn't take much effort to keep a community website popular and even profitable: http://www.nytimes.com/2008/01/13/business/13digi.html?em&ex=1200373200&en=5b35cdd99ca4951d&ei=5087%0A From jasonk at MIT.EDU Sat Jan 19 17:56:00 2008 From: jasonk at MIT.EDU (Jason Kelly) Date: Sat, 19 Jan 2008 17:56:00 -0500 Subject: [OWW-Discuss] Collaborative Videos coming to wikipedia Message-ID: <7c085c480801191456j6fd9cd82ke126335530687b35@mail.gmail.com> http://www.downloadsquad.com/2008/01/17/wikipedia-goes-video/ from the article: "Wikimedia is partnering with the collaborative video service Kaltura to start rolling out video to Wikimedia sites. Right now, the feature is available on the WikiEducator demo site, which is not affiliated with Wikimedia. But eventually we'll start to see collaborative video hitting Wikipedia as well." Seems like this is something that might be helpful for video protocols on OWW in the future. thanks, jason From moltogatti at gmail.com Sun Jan 20 11:14:37 2008 From: moltogatti at gmail.com (Lorrie LeJeune) Date: Sun, 20 Jan 2008 11:14:37 -0500 Subject: [OWW-Discuss] Google to Become Open Source Science Repository Message-ID: <2cbee05b0801200814j146eb176m694c1410f0a9283b@mail.gmail.com> Interesting... http://www.techcrunch.com/2008/01/19/google-to-become-open-source-science-repository/ --Lorrie From ilyas at MIT.EDU Wed Jan 23 16:54:34 2008 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Wed, 23 Jan 2008 16:54:34 -0500 Subject: [OWW-Discuss] wikindex rank Message-ID: <4797B79A.1080608@mit.edu> A curious fact: on Wikindex (http://www.wikindex.com/) OpenWetWare is currently ranked #97 by daily updates (239) - just below a Star Trek wiki (http://startrek.wikia.com/) #102 by articles (7,617) - just below a Dr. Who wiki (http://tardis.wikia.com/)