Archive for the 'Science Tutorials' Category

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 most successful post: Paper versus Mendeley, Zotero and stuff.

I am really surprised. When I started this blog, I wanted to share my thoughts about science, about being scientific, about research… and also about Mac in research. When I began to use Mac, it was difficult to me because I didn’t knew so much about software, tools, and so. And then, once, I wrote a post, almost like a review, about software to manage papers and references.

To date, it is the most visited post. I can imagine that many people are looking for information about which software is best for their needs. I never intended to make an explicit publicity on a specific software. I just wanted to express my experience about using those softwares.

Now, I want to make some updates to that post, and about managing references in Mac.

1. About Mendeley: I consider myself a reasonable person, specially being a scientist. Therefore, when a new version of Mendeley is released, I install it and try to use it. But, a few minutes later, I send the program to the Trash. Even more, when a fellow ask me about a software to manage papers and references, I ask: “Mac or Windows?” If the response is “Windows”, then I answer: “Give a look to Mendeley. Give it a try”. Almost every time, my friend returns, days later, and say to me “I uninstalled Mendeley. It ‘s just… complicated”.

It seems that, for many people, Mendeley is slow, complicated, and inefficient. Besides, it’s a huge program, considering the lack of remarkable features inside it. I really want Mendeley being a good software, but the opinion of my friends is the same as mine.

b) About Papers: I love Papers. It’s my software to manage my articles. But I feel that, since a long time, the team behind Papers just relaxes. There is no real improvement in every new version of Papers; only the typical “a bug is fixed when you make that-thing-that-you-do once every two years”, and no real improvement in metadata retrieval. I paid for Papers, and if a new version with real improvements in metadata retrieval from the journals, a good system for managing a bibliography with integration woth Word and Pages, and with new tools for making annotations in the articles, I will be glad to pay for a new release. But, in summary, I feel that Papers just got delayed in time.

c) About Zotero: One day, I received that message: “A new version of Zotero….” Of course, as an obedient fan of Zotero, I installed the new version… And I never could use Zotero again. I needed a new version of the Word toolbar. It didn’t work. I tried to go back to the old version of Zotero. Nothing. Also, the Word for Mac is awful. Then I got a huge amount of work, and I never looked back to Zotero. I need more time to solve the problem, but my feelings about Zotero are not optimistic.

That’s all I have to say about this topic at this moment. If you want to know more about bibliographic management, you should read this post.

Quick guide to create journal-quality figures: basic protocol

I am a Mac user since almost two years. In the first months, I had to create a set of figures for submitting an article. I was lost because I didn’t knew how to create line art figures at a 1000 dpi resolution.

That’s why now I am posting a basic protocol to create quality figures for a paper, to those who are at the first steps in Mac.

Basic Protocol 1: Create a quality chart

You need to have iWork (buy it, it is worth the money) and Photoshop. Also “Preview”, included in Mac.

Step 1: Creating a chart. In Numbers, you can create the chart according to your needs. In this example, I created a bar chart, with error bars. Numbers automatically place the chart below the datasheet. Activate the “Print view” option in the “File” tab (Note: since I have Numbers in Spanish, I don’t how if the translations are correct… I include a screen capture to illustrate).

Step 2: Export as pdf. Once you created the chart, go to File>Print. In the “Print” window, go to “Open with Preview” in the “PDF” button. This step is just to check that the chart is correctly placed in the page. Once you are satisfied, in Preview go to “Save as” and save the page as a pdf.

Step 3: Open Photoshop. Go to “Open”, and select your pdf file. This will open a window, where you can select the pixels/inch that you can input to the document (see next figure). Once you have the pdf in Photoshop, you can crop the image.

In the next figure, you have a close look at the chart I created, with a 50% view, opened at 1000 pixels/inch (as many journals ask for line art). You can see how simple is this approach.

Step 4. Composition of multiple figures. For a typical journal figure (with subfigures a, b, c and so on), you can do the following: create the charts in Numbers, and make copy & paste in Keynote or Pages (I prefer Keynote). Then, print the Keynote slide as a pdf (if you need to include a photo, like an immunofluorescence or a western blot), you can obviously leave a blank space, and then import the picture into the pdf file opened in Photoshop.

You may ask: “Why not Office?”. The answer is very simple. In iWork, you can modify the charts as you like, and the font size remains the same as you modify the chart’s size. In Office, usually if you paste a chart in Word, then modifying the chart’s size can be tricky: font size change, for example. Besides, iWork do beautiful charts with a vector style.

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