How do I cope with my pdf load?

Вторник, 08 Февраля 2011 г. 09:00 + в цитатник

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pdf As promised I will explain how I am strugling to keep an overview of all the references I collect during my historical research about brain stimulation in psychiatry. Ideally, with a web application I should be able to do all the things I want. But none does exactly what I want. Web applications as Mendeley or Labmeeting are great for sharing your pdf with other people and tagging your pdfs. So lets start how I work.

*) I start using Endnote. I use the online search option in Endnote to find articles about for instance transcranial magnetic stimulation. The interesting ones I add to my Endnote library. I can use them later to create references in Word.

*) Next I export my references to a text file. This text file is imported in an Access database. I created this database especially for this research. I for instance want to know the last time I opened a pdf. I also want to store quotes from the original article together with the meta information.

*) I use Adobe Pro to annnotate the pdfs. You can highlight or underline text with Abobe Pro.The underlined or highlighted text can then be copied into my Access database. I do not have to retype all the text.

*) Another thing that annoyed me was the many mouse clicks I needed to arrive at the pdf. First I click on the link in my database. Then at home I have to login to the library. Then the Pubm ed page opens and I have to click the logo of the journal (if it is electronically available). After clicking that logo I have to click again on a different page and then finally I have my pdf. This takes at least 6 clicks. To overcome this I use Greasemonkey. This is an add-on for Firefox. This add-on uses javascript and can automate things. I created several scripts and now if a pdf is available it will open automatically if I click on a Pubmed link.

*) I store my information on an external harddisk to be able to work at different places.

If you want more information about how I work or if you have ideas how I can improve my process please let me know in the comments.

Updated

An example of the Adobe Online Sharing Service.

Links:

Adobe Online Sharing Acrobat.com is a set of online services — file sharing and storage, PDF converter, online word processor, and web conferencing — you can use to create and share documents, communicate in real time, and simplify working with others. Its free, so sign up now.

Abobe Pro Pdf reader and manipulation tool

Endnote Reference management software

Greasemonkey Firefox add-on

Labmeeting Online sharing of pdfs

Mendeley Online sharing of pdfs

Related Articles at MedBlog.nl:

How do I get and store all my electronic information?||

Videos about TMS and Deep Brain Stimulation||

An example of Health 2.0||

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How do I get and store all my electronic information?

Вторник, 08 Февраля 2011 г. 09:00 + в цитатник

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Yesterday I wrote about my pdf-overload and how I am coping with that. Today I will write about other sources information that I want to store or want to be alerted to. I use:

*) Evernote to store extracts from webpages with the accompanying link. Before using Evernote I used Google Notebook. But since there are rumours that Google stops supporting Notebook I switched to Evernote. I must say that I liked Notebook better. One of the reasons for that is that I also use Google Reader. I also would like to have the opportunity to work offline, but I did not yet find a solution for that.

*) Google Reader to read my RSS-feeds. Not so long ago I had over a thousand RSS-feeds but I removed them all and started all over again. Nowadays I have approx. 25 feeds I read. I also created RSS-feeds for Pubmed for deep brain stimulation and transcranial magnetic stimulation. Below you can find a video about creating a RSS-feed for a pubmed search term.

http://www.youtube.com/watch?v=t4FKO85irvw

*) Twitter to obtain information before it is even published on one of the weblogs. Since google reader does not yet(?) support some kind of alert if a new message arrives, Twitter gives me alert if something new is posted. But I am not yet a fervent Twitterer.

*) I almost never use the favorites of my browser. Google Chrome automatically remembers the websites I visit the most. For other websites I just type the URL or I use google to find the url.

*) I installed WordPress on my Asus EEEPC with linux. I also installed a webserver with mysql. This allows me to take notes during discussions in places where no (wireless) internet is available. These spots still exist in the Netherlands.

As you can see I still use several software packages to store my information. Ideally, I want to store all the information in one place.

Related Articles at MedBlog.nl:

Store my medical data at Google or Microsoft? I dont think so!||

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Deep Brain Stimulation for OCD

Вторник, 08 Февраля 2011 г. 09:00 + в цитатник

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Belgian psychiatrist Damian Denys explains (in dutch) the use of DBS for OCD at Pauw en Witteman, a dutch talkshow. Below you can find an extensive video in which a patient treated for OCD is shown. Additional information should be found at Teleac in the course Wetenschap is beterschap, but unfortunatelly I could not find it.

The AMC, the medical centre Denys works, also interviewed him for the video series Fascinaties (Fascination).

Related Articles at MedBlog.nl:

Weblog about Deep Brain Stimulation||

Videos about TMS and Deep Brain Stimulation||

Build your own brain stimulator?||

Brain stimulant: an very interesting weblog||

How do I get and store all my electronic information?||

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Мой настрой: good
Я слушаю: nirvana

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Dr Shock’s selection of dutch medblogs

Вторник, 08 Февраля 2011 г. 09:00 + в цитатник

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Unfortunatelly we (Dr Shock and I) were not able to get a lot of input from other medbloggers for our grand rounds. Of course there were exceptions such as Laika. As a result of this Dr Shock started his monthly rounds of dutch medblogs.

The Dutch grand round had a short live. Nevertheless some medbloggers in The Netherlands produce interesting posts. Had lost track of most of them. Decided to produce a monthly selection as a kind of grand round. Choices are very biased and made by myself. If you feel left out, unappreciated or anything else please contact me [dr Shock].

I started my own weekly grand rounds (in dutch) in 2007, but it took me too much time to continue.

Related Articles at MedBlog.nl:

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Rondje langs de medblogs [11]||

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Dr. Shock vermeld tijdens de Grand Rounds||

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Greasemonkey scripts for pubmed

Вторник, 08 Февраля 2011 г. 08:59 + в цитатник

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Dr Shock asked for this. I use five Greasemonkey scripts.

*) Pubmed redirect. First of all I redirect all pubmed pages (ncbi.nlm.nih.gov) to the pubmed page (ncbi.nlm.nih.gov.proxy.library.uu.nl) of my university

*) Automatically open UBU link. If the pubmed page consists of a direct (UBU) link this script automatically opens the link to the pages of for instance a journal.

*) Resize window. For some reason I do not know a library page opens in a small windows. This scripts makes sure that the window resizes to the full screen.

*) Automatically open PDF. If the pubmed page consists of links to pdfs then this script automatically opens the pdf.

*) Redirect Springerlink. This is a redirect script for Springer pages.

You can find the scripts below. Any questions? Let me know.

Pubmed redirect

// ==UserScript==

// @name           Redirect Pubmed

// @namespace      Redirect Pubmed

// @description    Redirect Pubmed

// @include        http://*ncbi.nlm.nih.gov*/*

// ==/UserScript==

//alert(document.location.href);

var str = document.location.href; // get the hyperlink of the current page and store it in the variable str

var matchpos = str.search(/proxy.library.uu.nl/); // see if proxy.library.uu.nl occurs in the variable str

var rep = ncbi.nlm.nih.gov.proxy.library.uu.nl; // store new hyperlink in variable rep

if (matchpos ==-1){ // if str does not contain proxy.library.uu.nl then substitute links

str = str.replace(/ncbi.nlm.nih.gov/g, rep); // substitute ncbi.nlm.nih.gov with variable rep

document.location.href= str;

}

Automatically open UBU Link -

// ==UserScript==

// @name           Automatically open UBU Link

// @namespace      NLM.NIH.GOV.PROXY.LIBRARY.UU.NL

// @include        http://*ncbi.nlm.nih.gov.proxy.library.uu.nl*

// ==/UserScript==

// an UBU link is characterized by one of the following links: sfx.library.uu.nl, pubmedcentral.nih.gov/articlerender or ncbi.nlm.nih.gov.proxy.library.uu.nl/entrez/utils/fref.fcgi?PrId

var links = document.getElementsByTagName(a); // get all hyperlinks and store them in variable links

for(var i = 0; i < links.length; i++) { // loop through the hyperlinks in variable links

var url = links[i].href; // store array variable in url

var matchpos = url.search(/sfx.library.uu.nl/) // see if sfx.library.uu.nl occurs in the variable url

if (matchpos !=-1){ // if url contains sfx.library.uu.nl open url in new tab

GM_openInTab(url);

}

var matchpos1 = url.search(/pubmedcentral.nih.gov\/articlerender/); // see if pubmedcentral.nih.gov/articlerender occurs in the variable url

if (matchpos1 !=-1){ // if url contains pubmedcentral.nih.gov/articlerender open url in new tab

document.location = url;

}

var matchpos2 = url.search(/ncbi.nlm.nih.gov.proxy.library.uu.nl\/entrez\/utils\/fref.fcgi\?PrId/); // see if ncbi.nlm.nih.gov.proxy.library.uu.nl/entrez/utils/fref.fcgi?PrId occurs in the variable url

if (matchpos2 !=-1){ // if url contains ncbi.nlm.nih.gov.proxy.library.uu.nl/entrez/utils/fref.fcgi?PrId open url in new tab

GM_openInTab(url);

}

Resize window -

// ==UserScript==

// @name           Library

// @namespace      Sfx.library.uu.nl

// @include        http://sfx.library.uu.nl.proxy.library.uu.nl*

// ==/UserScript==

self.resizeTo(screen.availWidth,screen.availHeight);

Automatically open PDF -

// ==UserScript==

// @name           Automatically open PDF

// @namespace      Pubmedcentral

// @include        http://www.pubmedcentral.nih.gov.proxy.library.uu.nl/articlerender.fcgi?tool=pubmed&pubmedid=*

// ==/UserScript==

// if a hyperlink on a http://www.pubmedcentral.nih.gov.proxy.library.uu....gi?tool=pubmed&pubmedid=* page contains blobtype=pdf then it refers to a pdf. So this scripts looks for such hyperlinks and opens them if it occurs.

var found = 0;

var links = document.getElementsByTagName(a); // get all hyperlinks and store them in variable links

for(var i = 0; i < links.length; i++) { // loop through the hyperlinks in variable links

var url = links[i].href;

var matchpos = url.search(/blobtype\=pdf/); // see if blobtype=pdf occurs in the variable url

if (matchpos !=-1 && found==0){ // if url contains blobtype=pdf open url in new window

window.location = url;

//alert(url);

found = 1; // to prevent opening more than one window the variable found is set to 1

}

Redirect Springerlink

// ==UserScript==

// @name           Redirect Springerlink

// @namespace      Pubmedcentral

// @include        http://www.springerlink.com/*

// ==/UserScript==

var str = document.location.href;

var matchpos = str.search(/proxy.library.uu.nl/);

var rep = www.springerlink.com.proxy.library.uu.nl;

if (matchpos ==-1){

str = str.replace(/www.springerlink.com/g, rep);

document.location.href= str;

}