Archive for the 'Scientist Life' 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.

New directions and projects

The last year, and the beginning of 2011, has been full of projects, work and other stuff. All this had me away from the blog. As a scientist, sometimes things get really hard to maintain in a specific way. And the blog is the downfall of all the work that I have been doing lately.

Chapter One. Just… Research

For example, here in Chile, the spring (starting in September) becomes THE season of meetings and events. In october, I had the pleasure to participate in the European Wnt Meeting, held on the Karolinska Institutet, Stockholm. Back at home, I had now the opportunity to attend the 5th meeting of the Latin American Society of Developmental Biology (LASDB), featuring important scientists from all the world. It was an incredible experience, to participate in both events. But, as many of you probably know, you come back from these events with your head full of ideas. Translating those into a planned experiment, testing the conditions and getting results can take a lot of time. And I am still in that process.

Chapter Two. About Advocacy

I proposed to an Association of Researchers in Graduate Level” (sort of translation), an idea to promote science in the people, to reach authorities and to promote science in the media, among other things. This campaign has been difficult to develop. The lack of funding, and contacts outside the science world, makes this advocacy campaign an “impossible” plan. I really admire the strength of the “Science is Vital” initiative. But we are far from that success and resources.

Chapter Three. Related Stuff.

I collaborated with some posts on The Node, the more-than-awesome blog and community around the Development journal. I also published some letters in chilean newspapers, about the state of Science in our country. These media included El Mostrador (the first and most important digital newspaper), letters in La Tercera and El Mercurio (the two most prominent printed newspaper), and others.


It has been interesting. All this work. But I believe that, this year, I will come back to my roots at Astu’s Science Blog. But excluding more discussions regarding Mendeley, Papers and related software. Science life or, more exactly, scientist life, will be my most common topic this year (I hope).

What I have been doing lately

Well… This is my first post written from my iPad. I have been a little dissapeared from the blog lately. The last three months have been crazy: I had to go to an european meeting in Sweden (which means, exactly, to fly from the other end of the world), then back to help in the development of an international course on regeneration, then going to another international meeting, in Chile this time, then back to the lab to planning new experiments and discuss ideas with my PI, adding the comments of other researchers gathered in the two meetings, and writing some stuff for an advocacy project and also writing some post for the outstanding The Node.

After all this work, I am tired. Obviously. It is hard when you don’t see a reward for your efforts. Only a few comments in my posts regarding the “Paper versus Mendeley” battle keep this blog alive; I am pretty sure that, if I send to the trash those posts, the visits will drop to zero. I am also thinking that the advocacy project will fail, mainly becausethe lack of energy of chilean scientists to fight to change the awful scenario for science funding amd science policy. I like to write, but writing without knowing if someone is reading your work is just dissapointing. I have to manage todo all these things in a pretty much demanding lab (my PI has great expectations in his graduate students, and he also likes having his students 24/7 in the lab), and also I have a family life, and doing this stuff implies less time with them. So, I decided to leave the blog unattended for some weeks.

For those of you following the “Papers versus Mendeley” issue, I have news indeed: I wrote about Mendeley for iPad. I could not keep using Mendeley: it crashes, it is slow, downloading one paper at the time from my online account and many other little details pushed me to test Papers for iPad. And it really rocks! I will not make a review of Papers for iPad. Just use it. I believe that the iPad is one of the best news for scientists. To date, I am saving paper because I read papers only on the iPad; I give presentations with the iPad, and many other things too. The only feature missing in iPad (that makes me to not saying that the iPad is perfect for scientists) is the ability to incorporate error bars in charts.

Anyway, I need to sleep now. Best regards.

About Meetings…

I am back in Chile. I went to the European WNT2010 Meeting, held at the Karolinska Institutet, Sweden. It was a very wonderful meeting, specially to me. I don’t have so often the opportunity to go to another far country, and share my results with the authors of the papers I usually read. It is a great time also to learn, the new techniques, theories and trends in the field.

Main entrance to the Karolinska Institutet at Solna, Stockholm, Sweden.

This meeting was full of prominent researchers in the Wnt field. I presented my results from my PhD research Thesis, and it was extremely fantastic to receive the comments and suggestions from experts. And it was really cool to give a talk with my iPad. Actually, I was initially afraid to go with my iPad in the travel. But soon I realized that it was a very good choice. In the airport, I got delayed in a 4-hour delay. Most people were wondering where to plug their computers because of the small battery time they had. But my iPad had 10 hours of battery so I just used it without worries. Also, in some places the WiFi connection was paid, so I used my 3G connection. Wonderful. Once in the meeting, it was very useful to take my iPad in the conferences, take notes, review the maps of Stockholm, and other things. In this travel, I take out most of my iPad. I had an App to review the climate changes, details of my flight, how to get to some places, reviewing some papers…

And giving a presentation with the iPad is very nice. You will have a black screen showing the slide number (as far as I can remember… I was a little nervous), and the keynote presentations displays very well in the big screen. Also, if you forget your laser pointer, you have an option in the iPad: you keep pressed your finger in the screen, and a point very similar to a laser point will show up in the screen. You have to keep pressed your finger, and you can move across the screen to move the pointer.

Now we have another interesting meeting here in Chile: the meeting from the Latin American Society of Developmental Biology (, if you can review the program). I will be out some time until the “meeting season” ends. Best regards.

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.

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.

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.

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