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.

Conclusions…

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).

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.

SUMMARY

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.

Pros and cons to be a scientist in Chile

Usually, I write post about a specific topic. A paper, news from somewhere. But I have been a little busy and distracted to write something that specific. Today I have the need to talk about scientist’s life here, in Chile. Why? I am living a vocational crisis, or so. See, to be a scientist here has its disadvantages. For example, I really hate the buildings. As you may know, with so many earthquakes, and also because of a bad culture regarding constructions, the buildings are pretty ugly. I went once to US and I became crazy with the beauty of the universities. Here I have some reasons to why you shouldn’t be interested in making science in Chile.

Reasons to why I am not happy being a Scientist in Chile

a) Infrastructure: it is evident that a first disadvantage of making science, at least in the lab, is the lack of a proper and extensive infrastructure. Buildings are small, and I have witnessed some deadly fights for a small lab between colleagues. This problem is a real concern, because the scientific population in Chile is growing and the Facilities and Buildings are not growing at all. And I’m not talking about the lack of beauty and comfort of our facilities.

b) Equipment: also, the lack of cutting-edge equipment is discouraging. Even if you have a good Research grant, buying an equipment here costs several times more than in US. Hey, we are at the end of the world: we are exactly at the opposite point compared to China, and we are located at the other end compared to US and Europe. That really makes everything more expensive, including Taq Polymerase.

c) Distance: the location of Chile has another difficulty: it makes expensive to attend meetings, courses and events in US or Europe. Also, making an internship has the same obstacle.

d) Government Grants: the money that Chile expend in R&D is small, compared even with other countries of South America. Accordingly, there is a lack of good grants, and they are not enough for the scientific community in Chile.

In summary: there is few money to make science; the existing money is not enough to buy good equipment and reagents, because we are far from the producers of those reagents and equipments, and also we are not allowed to attend meetings and courses because travel expenses are huge. And you have to deal with it in your ugly building, with only one coffee shop (if you’re lucky; don’t even dream about having a Starbucks nearby).

Of course, it can’t be that bad. So when I am crying about all this stuff, I remember that being a scientist in Chile can be also very exciting and funny.

Reasons why, after all, I am very happy to be a Scientist in Chile

a) The scientists: Chile has a great number of good scientists. The PhD programs are competitive, and the Chilean meetings have a  very good level. The creativity allow us, usually, to have important guests attending the meetings in Chile, facilitating great talks and in a very nice environment (see the photo for an example). The classes are good, and in general, the formation on the PhD programs is very good.

A place called “Ojos del Caburgua” (Eyes of Caburgua), close to the town where is held the Annual Meeting of the Chilean Society of Cell Biology.

b) Publications: closely linked to the previous point. The number and level of the publications is good, specially when you compare the productivity in Chile with other countries in South America or even with other countries of similar characteristics. I am making my PhD Research Project in a lab that has publications in Nature Cell Biology, Development, Developmental Biology and Genome Biology in the last years, which is a very competitive job considering our reality.

c) The challenges: being in a country like Chile makes things harder. You have no cutting-edge equipment to make that great experiment. So you have to go back to the basics. One of our professors always ask: how would you do this experiments, if you were back in the sixties? And it really helps sometimes.

d) Chile itself: You will be working in one of the most beautiful countries in the world. Once, I worked in a side-project in an Evolutionary Biology Lab. The people went to the Atacama Desert one week, to study the reproduction of some species, and two weeks later, they went to the rain forest in the south, and so on. If you are a geologist or an astronomist, for example, you will be delighted with the beauty of our land. Also the variety of landscapes and species opens a lot of opportunities in research.

These years as a scientist have been very exciting. Sometimes I get sad about some specific issue (usually, a scientific discussion with my advisor, or the lack of a reagent to make a new experiment, or the high price of a reagent to buy it), but at the end of the day, I go happy to home.