Archive for June, 2010

References Management in Mac: new guide on using Zotero

As I mentioned before, the most successful posts on this blog (in terms of visits and comments) are those related with reference management in Mac. A long time ago, I published a post in which I wrote about the advantages of Papers, or more exactly, the disadvantages of Mendeley in Mac, and I recommended using Papers+Zotero in Mac. But I had a problem with the new versions of Zotero.

Now, I solved the problem with Zotero, and I will explain the steps to have a fully functional Zotero+Papers combination for making bibliographies in Mac.

NOTE: The following steps are valid to use the latest version of Zotero with Word 2004. Since the Office for Mac is very bad, I have no intentions to purchase the Word 2008. But plugins and instructions are available for using Zotero with Word 2008 in the official site.

Step 1. Updating.

In order to have a fully functional set up, you have to install the newest version of Firefox (3.6.6.). You also have to install the most recent version of Zotero, and the Phyton extension and the latest word plugin. The last two (PhytonExt+Word Plugin) are available in this page of Zotero, under the “Mac OSX” section. Follow all the instructions; it’s easy.

Step 2: Updating the library in Zotero.

I recommend deleting all your libraries and start from scratch. If you have Papers, take a time in updating and matching all your PDFs. Once you are ready, go to File>Export>BibTeX Library* (it’s the one that works best for me). *Caution, I have both Papers and Zotero in Spanish, so some names and menus could be different.

Once in Zotero, in the Actions menu, I go to Import. Select the *.bib library that you exported from Papers, and then wait. Depending on the size of the library, it will take a little time to have an updated library. But, when it’s finished, you will be ready to work.

Step 3. Working in Word.

You are now ready to use Zotero in Word. In Tools>Customize, select the Zotero Bar, and place it where you feel it’s more comfortable.

When you need to insert a citation, just click in the “Zotero Insert Citation” icon (the first one, from left to right) in the Zotero Bar. A window will show up. In this window, you can select the citation style. When you are ready, a new window will open, showing your library, and you can now select the reference you want to cite.  When you are finished, and need to insert the final bibliography, just click in the “Zotero Insert Bibliography” icon (the third icon), and then you are ready. You have a muanuscrpit with references and a bibliography.

Please note that in the official site in Zotero, there are full instructions in the usage of Zotero and the plugin. Instructions here.

The Node: an interesting virtual coffee break

I have been far from the blog and all the stuff unrelated with Pubmed and journals. But a few days ago I found a new feature in the Development’s journal homepage. It is called “The Node“, and its description is as follows: “We’d like you to think of the Node as a way to spend your coffee breaks“. According to The Node, more exactly, according to Earl Wilson, who (and I’m not sure because there are so many ‘Earl Wilson’s) was a famous columnist, the best place to share information and ideas is, actually, the coffee break.

The concept itself is very precise and interesting. I found myself many times, in meetings, talking with colleagues about data, experiments, ideas. Personally, I love the poster sessions, because of that sense of lack of formality, sometimes drinking beer and talking for hours about science. In an oral presentation, it’s just too short. You show up in front of the scientist, you try to explain in only 10 minutes the data gathered in months, often years of research. And, most of the time, the people in front of you are desperate to make a “smart” question (which means, 99% of the time, to try to ask something impossible to answer so they seem smart, kind of “Oh my, he must publish in Cell”). Oral presentations, specially in 10 minutes, are against the whole idea of meeting someone: to talk, to discuss, to share.

Returning to the original idea… usually, in meetings, the coffee breaks are the ideal place to share and connect. Often, coffee breaks are conducted in open spaces, but the coffee and cookies are placed in just two or three tables, and you have a little chance to came across with the keynote speaker of the day, or with that guy that you saw in the last session talking about that topic very related with your PhD research thesis. You say “Hi!” to that guy, and well, you have to leave the table because fifty other people are trying to get cookies. And then, voilá! you are talking with people about science. “How did you make the experiment with the zebrafish embryos?” “Oh, well, we discovered that adding 0.2M of ….“. I found that in these situations, colleagues are more open to share technical tips and advice. I have very good experiences in coffee breaks and poster sessions, at least here in Chile. That’s the spirit of The Node, according to the creators: to rescue that sense of sharing and talking.

Ideas like The Node and some others around the internet (like Benchfly) are very valuable. Most of the time, you can assist to one or two meetings per year, and sometimes you just can’t go, either because of funding, or time, or because you are trying to get that paper published once and for all. But virtual coffee breaks allow us to connect with people working in similar fields, and to share experiences about science and scientist’s life.


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