Archive for the 'Bioinformatics' Category

Dissapointed with Papers2

Why, on Earth, would you release an upgrade from a popular software, only for a limited number of users because your new, improved, released software supports only the last operative system? Why the people behind Papers released the long-long-long time awaited Papers2 only for Snow Leopard Users?
I was recently reading a post regarding why Mac users still use Leopard instead of Snow Leopard. Lack of time to make the upgrade, the sense of the upgrade being unnecessary, specially considering that you have to pay for the upgrade, and reports about several bugs and incompatibilities, lead users so use Leopard even today. Most of my scientists friends are Leopard users, and also Papers1.x users, and I believe that they are happy. Despite the lack of features awaited for a long time. Even considering that Mendeley is free and always improving. And considering that, for example, Mendeley Lite for iPad is free, in contrast to Papers for iPad (which, by the way, still lacks many features).
But I have been a strong supporter of Papers. I truly believed that, somehow, old Papers1.x users were going to be awarded because of their loyalty. But the upgrade price seems to be a barrier for many, specially for students (and I believe that the new Mac-Student users will turn undoubtedly to Mendeley and Endnote), and to me (and I am pretty sure that for many others too), the need of having Snow Leopard puts another big issue to deal with.
Also, some reports about missing features, bugs and others (see The only explanation I found regarding this “hard” decision is:

Unfortunately Papers2 requires 10.6. This was a hard decision, because we know we still have a small percentage of Papers1 users running OS X Leopard 10.5. However, supporting 10.5 had also a lot of technical consequences. In particular, with OS X Lion 10.7 coming soon, we might have had to cut 10.5 support later, which would have been much more difficult to do on paying costumers.

Note of course that your copy of Papers1 will still work the exact same way as it does today on 10.5 for as long as needed.

I believe that the company does not care about loyal, old users of Papers. They say the percentage of Leopard users is small. In my experience, this percentage is pretty close to 100% (maybe because I am in a small, less-developed country, I don’t know), but this only decision is enough to me to decide not to upgrade to Papers2, and I recommend to you to do the same.

In the future, I will be featuring new softwares and tools for scientists, to compensate somehow this huge turn-off.

iPad in Research 1.0

If you are a scientist doing your PhD, or at the beginning of a postdoctoral position, or if you have a family (and so on) you will find with little time to learn and investigate deeply enough before to make a decision about purchasing an iPad and taking it to the lab. Searching for experiences with iPad’s users in research is a good start. It worked a little for me. And I promised myself to keep people updated about my experience with iPad in research. Useful or useless? Free or Paid’s apps? iWork or DocsToGo?

With some weeks of use, I will give you some personal advice and comments about iPad in research.

iPad in Research: comments and advice.

1. Maybe, the first statement, is the following: iPad will change your life. Absolutely. For the basics, at least. I remember when I went once to a meeting with my old laptop, weighting almost 3 kilograms. It was awful. With the iPad, you will have a light device to check your email, send emails, reading papers, searching Pubmed, reading Nature/Science, reading a manuscript… I find myself lately going with the iPad to bed to read some paper. You will find yourself replacing the heavy laptop with the iPad to check your email, and reading papers. It’s just great for this basics. Your back will be happy when going to meetings.

2. Being said that, the iPad is not suitable to create scientific material. This only point makes the purchase of an iPad not worthwhile if you want to replace your laptop for scientific needs. Here I will tell you 3 key points.

a) It is almost impossible to create a scientific presentation on the go. Even more… It’s almost impossible to carry with you the powerpoint of your PhD defense/presentation without spend hours making conversions and adjustments. The first time I sent a powerpoint presentation to an iPad, the result was awful. The same with keynote presentations. In order to carry a presentation with you, you must insert all the images as PNGs. This is just plain stupid, and the people from Apple really need to fix this. If you are a patient scientist, you can convert and fix all your presentations. But, at this point, Keynote and DocsToGo are made for basic needs only,

b) If that was not enough reason, here is the second big problem. You can’t create charts with error bars! This one is really painful. This means two things, my fellow researcher: you can’t create scientific charts on the go, which will push you back to the laptop to analyze and plot data; and second, you can’t view charts with error bars in Keynote! One of the best things about Keynote for research in Mac is the ability to copy a chart from Numbers, and modifying the size, colors, and other features in Keynote without the need of opening Numbers over and over (I remember trying to change the font size in a chart in Powerpoint, and waiting for Excel to open, closing the window, waiting that the expected change was good enough… with iWork you can forget about that old “Window’s pain”). But with iPad, you will need to export the charts as images (again, PNG format) and inserting them in the presentations, which is a sort of “what’s the point in having iWork if it will function as an office from the 2000 year”.  Apple: you really need to fix this if you want to have the iPad going massively into the laboratories.

c) At this point, the lack of multitasking makes difficult to use iPad for serious scientific work. Also, Apple needs to work on big improvements on Safari for iPad (for example, allowing the download of PDF files -a.k.a. “papers” to us).

3. Nonetheless, the iPad is still very useful to daily needs. I read journals in the iPad (although you can’t save PDF from Safari… your best shot is having a PDF reader with a built-in browser), check my email, and carrying my presentations (I had to fix all of them). Also, if you are a traveller, you will have many apps useful for you.

4. About apps: Many apps are available to scientists. Periodic table of elements, some biological apps, even the “iPathways” (which you can use to read molecular pathways in SBML language) are available. Maybe the most important choice is what software you will use to manage your scientific papers. Before the iPad, I was a strong follower of Papers for Mac. I had many, many, many reasons to choose Papers over Mendeley. But now, I am slowly changing to Mendeley. Why? For many reasons. First, Mendeley (a “lite” version, tough) is free, and Papers exist as a “paid” version only. You will pay for a version that makes almost the same that the free Mendeley, except for highlighting. But, what’s the point on paying for highlight papers if you will not be able to export those annotations and highlights to your Mac?! Besides, what happens if you are a Windows user? In that case Mendeley is your “only” option. I see a near future where people will change to Mendeley. Half of the iPad’s users are Windows users, so they will use Mendeley soon. The other half, the Mac user, will think: “Well… I paid for the desktop version of Papers… Do I have to pay again for the iPad version (a high price, compared to other PDF readers apps with highlighting and annotation features), considering that I can export my entire library to a free account on Mendeley online and having a “lite”, free version of Mendeley?” Of course, this will change as soon as Mendeley releases a paid version (the called “Mendeley Pro“?). Then the real battle will begin. So far, I think Mendeley Lite for iPad covers most of my needs. I have to make a workaround to use it: exporting a custom collection in Papers (which I called “iPad”, jejeje) as a bib file; opening this collection in Mendeley, choosing to sync the PDF files linked to this collection onto my online account, and downloading those PDF onto Mendeley on iPad. But hey, I am already making worst workarounds to carry on my presentations.


As a normal user, I find iPad a life-changing. Really. But, as a scientists, iPad still need some improvements. Being more specific, more suitable Apps are needed to the scientific community. Allowing the creation of scientific charts (with error bars!), more flexibility in Keynote, and multitasking are extremely urgent needs. There is a niche in which companies can still work to gain more money and followers. For example, Papers could release a “lite” version of Papers for iPad, or maybe offering some kind of discount to the desktop users. Paying a total of $57 for the desktop+iPad combo, now with an improved (and improving every day), free Mendeley at $0? I would change now to Papers for iPad with a “lite” version.

The scientific websites should also work on improving accessibility for iPad. For example, journals would release versions for iPad (and tablets) of their magazines. They would gain more subscriptions. There is a lot of potential on iPad in research. I recommend having an iPad for your normal needs, but I hope and wait for improvements in iWork and other Apps.

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.

My definitive guide to manage references in Mac

One big disappointment I have is managing references in Mac. In windows, there are some programs, and Endnote seems to work fine with Word. Also, Mendeley released the new version integrated with word. But, in Mac, there are several problems using Endnote. My word (2004) crashed all the time… specially when I was writing accented characters (á, é, í, ó, ú)… and I am a Chilean guy, and I have to write my thesis, research projects, etc, in spanish.

So, I started to evaluate the options… also online options. These are my thoughts about them:

1. Connotea. It seemed fine to me…but, the problem, as well as many other web-based reference manager tools, is: integration with word. Some developers think that making an “export to word” option will be fine… but I guess these guys never used endnote and they don’t appreciate the “cite while you writing” feature. With just an export option, you have to select, make extensive copy and paste, bla bla bla. But Connotea works well. I didn’t have any problems importing a library created with Papers. And that’s something I cannot say about:

2. 2collab. The biggest disappointment. I couldn’t import any library… either created with Papers, or Endnote, or Connotea, or CiteUlike… It is just useless.

3. CiteUlike. The same as Connotea applies to this app. Also, the interface is very ugly.

And that’s about online tools. I wanted to try Sente, but I am not willing to try som trial-version, to fall in love with it and then to have to spent more than 80 USD. No. I want free applications. I already purchased Papers. There must be an option to use papers and word, at least with a “third-party”.

4. Mendeley: another BIG disappointment. Two things really bothered me.

a) Metadata annotation. I opened my “papers” folder with mendeley… waiting… hours… (while mendeley updated my online library…). And then, voilá! 800 papers… But wait! Just 200, or less, had the right metadata information. The only way to have the 800 papers with the correct metadata, was importing a library from endnote, and all this is to avoid having endnote working because it crashes my word.

b) Absolute no integration with word in the Mac version.

Well… after days surfing the web, I remembered Zotero. I tried Zotero, and bum! Finally the masterpiece missing in my pipeline to work with references in Word.

So, after this long introduction, I will describe:

My definitive Guide to Manage References in Mac

– Software needed: Papers, Zotero, Word.

Step 1: Exporting a RIS library from Papers. You can select a collection, or specific papers… but I recommend to export all your papers. You have to go to File, Export, RIS File.

Step1Export your library as RIS file using Papers.

Step 2: Download Zotero add-on for Firefox, and the Plugin for Word. Follow instructions to install them.

Step 3: You can import several file types into Zotero, to create a libary. For example, a Endnote library. If you have Mendeley (and with God’s help, you have all the metadata as you wish), you can also work with it. But most of the Mac users I know, work with Papers. You have to go to the Actions palette, and press in “Import”.

Step2I apologize… my softwares are in spanish. But you can get the idea

Step 4. Inside Word, insert citations using the button “Zotero Insert citations” in Zoreto toolbar. Once you finished, you can create your bibliography list pressing the “Zotero insert Bibliography” button. And that’s it.

Imagen 4

You can see the Zotero toolbar. And Word run as usually.

That’s it! You have your new system to manage references in Word. I have to do some notes, nonetheless:

– I have Word 2004. I don’t know if this would work with word 2008.

– Also, Zotero works in Firefox. I don’t know if you can use it in another web browser.

– I did not tested this using libraries created with other softwares as Mendeley or even Endnote.

But, it has some advantages:

– Currently, Mendeley does not support viewing pdf files. You have to open acrobat or another reader.. also endnote. But, with Papers, you can view your pdfs as you are working, exporting your selections, getting the right metadata with the fetching tool, printing, searching papers… all in one program! And also, Papers is cheap, compared with similar softwares.

– Also, about Zotero… you ALWAYS have Firefox opened, or not? So, you really don’t have to open a second software. I recommend opening a new window in Firefox, to work with Zotero.

– Finally, Zotero is free. You don’t have to purchase an expensive program.

I hope this can help you. I spent several hours trying to get with something like this. And a disclaimer: I am not part of any Company, or Business… I am just a PhD student trying to make my life (and now yours) easier.

New note added on proof: I had to update Firefox, which I hate… every new version, Firefox gets more heavy, memory-consuming and problematic. Zotero beta release seems to work only with Firefox 3.X version. So, I installed the Zotero version, and the Word plugin that I found in the forums, and I tried creating a new library, and I had problems with special characters (á, ó, ñ, ü, etc). So, I wrote a message in the forum. But, by now, I managed to create a RIS file with endnote, and it worked fine.

Papers or Mendeley?

When it comes to bioinformatics, I acknowledge that I am a naive and basic user. Nonetheless, I always try new tools and softwares. Some time ago, I became interested in tools for management of papers and data. I discovered Papers, but I was a Windows user. When I moved to Mac, the first thing I did was to try Papers. I was amazed by the software. It was very, VERY easy to use, and it was very valuable to organize my papers collection. I usually have several folders with papers, and when I want to read one, I get lost in the sea of folders. With Papers, all the papers are copied in a single folder, renamed (no more “374645432.pdf, or 1234_2323_349.pdf or names like these), and you can organize your papers into specific collections. Also, you can read the pdf file inside the Papers itself, very useful when you are looking for a lost paper… you don’t have to open every single pdf file… you are actually seeing it when you scroll over the list.

A screenshot of Papers.

A screenshot of Papers.

I felt in love with Papers. But it wasn’t free. You have to purchase. But the web page claimed that, if you are a student, you can get a discount. When I see something like that, I think “well, surely you have to send several papers, letters, signed and with the US Embassy approving..”. But this time it was easy: just to scan your student ID. In hours, I had my discount. Today, I am very happy with Papers. It is really useful to me, specially now that I am writing my PhD Research Project.

But then, Mendeley appeared. My Windows-user friends told me “Jaja, you spent money in a Mac and purchasing Papers, but Mendeley is free”… Well, after several post around there, I tried Mendeley. And I have to say, I was disappointed. My aim is not to post a negative opinion about Mendeley. Sure if you are a Windows user, you will value the existence of Mendeley, and if you are a Mac user, the chances are you have Papers. But I have to say some points:

a) Overall, if you don’t have much time to spent learning to use a program, Mendeley is not good… It is not as easy-to-use as Paper is.

b) If you have a slow Internet connection (or if you have a huge collection of papers), also Papers is your choice. I am still seeing messages with tasks being in operation with Mendeley. Mendeley allows you to have a backup of your collection in the web, but when you have a high number of documents, it becomes slow and, at least in Mac, the software shuts down.

c) You can’t read the pdf inside Mendeley (I already explained why this can be so useful).

I have a backup of my paper’s collection (in progress, though) in the web with the program Labmeeting. I think this tool is the best in the web nowadays. You can:

a) Manage a paper collection, and you also can organize it in several folders, synchronize the metadata, and share the papers.

b) Set up a Lab Page, where you can share data, protocols, notify about meetings, seminars, etc.

c) Get in touch with colleagues.

A little screenshot of the main page of Labmeeting.

A little screenshot of the main page of Labmeeting.

Labmeeting is a good combination of Social Science Networking + Paper/Data Management. I tried to get my lab’s colleagues to test Labmeeting, but I guess scientists are not so interested yet in these tools. Nonetheless, I think the use of this kind of softwares can be very useful to improve communication and performance of a lab group.

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