Monday, March 30, 2009

Mendeley - Academic software for research papers

Do you hate it when Mac users brag about using Papers? Do you use a PC but also want a great reference managing software?

Mendeley is a free, award-winning, desktop and web solution designed for managing and sharing research papers, discovering research data and collaborating online. It combines Mendeley Desktop, an easy-to-use PDF and reference management application (available for Windows, Mac and Linux) with Mendeley Web, an online social network for researchers.
(From wikipedia)

I know that lots of fellow researchers/bloggers have talked about Mendeley, but I feel it deserves to be seen by everyone.
This is a great aid for managing articles and also for creating references lists, as it easily integrates with Microsoft Word. You can also just drag-n-drop a PDF article into Mendeley and it automatically extracts all the metadata (authors, pages, journal, etc.). But what if the metadata is incomplete? Well, you just enter the PMID of the article, and Mendeley will find the info and add it!!
Also it has several web-based features that deserve checking out, for example, data sharing, online networking, etc.

Test it... it's great, and it's free! Visit it's website now.

Here's a screenshot:


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Sunday, March 29, 2009

SNPs in the human genome: Hot paper in biology

The article "A second generation human haplotype map of over 3.1 million SNPs," by the International HapMap Consortium (K.A. Frazer, et al.), Nature, 449(7164): 854-61, 18 October 2007, has made it to the Hot Papers Database in the area of Biology due to its high citation rate during November-December 2008. The paper was cited 61 times in current journal articles indexed by Thomson Reuters in those months. Notably, during that period, only two other biology papers published in the last two years (aside from reviews) attracted higher citation totals.

[Source: ScienceWatch]

I normally do not encourage "excitement" about citations and journal statistics such as the Impact Factor, but I did a lot of reading on SNPs and the HapMap last year, and I thought it was interesting to highlight this article as the HapMap has important implications for the prevention, diagnosis, and treatment of human diseases.

Do you know what the HapMap is? If you don't, take a look at this site [What is the HapMap?]
It's a short (~2 pages) and very illustrative article explaining the basics about the whole project.


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Friday, March 27, 2009

PHD Comics's Jorge Cham in Science: a profile

Most of us (and by 'us' I mean grad students) are familiar with Jorge Cham's comic strip "Piled Higher and Deeper" or just "PHD" where he illustrates the everyday frustrations and experiences of life in a lab from a hilarious point of view. Most of us have come across with certain comic strips that reflect exactly what we experience on a daily basis and, as someone else has said "It makes you feel you're not the only one out there".

Some are just plain funny.

This week's issue of Science has an extensive profile on the man behind PHD, on the News Focus section [PROFILE: JORGE CHAM: Piled Higher and Deeper: The Everyday Life of a Grad Student]

I leave you with some of my favorite strips so you know what I'm talking about:

[Hat Tip:Andre at Biocurious]


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Wednesday, March 25, 2009

Snapshots: Auxin

The plant hormone Auxin is a key player during pattern formation and organogenesis and is involved in virtually every aspect of plant growth and development.

Growing evidence suggests that its signaling pathway may be more complex than previously anticipated. During the past 15-20 years we have been able to identify important components of its signaling pathway and generate models to explain how auxin regulates different developmental processes 1,2.

The latest "Snapshot" from Cell, depicts "Auxin Signaling and Transport".
For a full list of SnapShots, click here. I'm sure you'll find something interesting.

1 Lau S, Jürgens G, De Smet I (2008) The evolving complexity of the auxin pathway. Plant Cell. 2008 Jul;20(7):1738-46.
2 Mockaitis K, Estelle M (2008) Auxin receptors and plant development: a new signaling paradigm. Annu Rev Cell Dev Biol. 2008;24:55-80.


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Saturday, March 21, 2009

Are we training pit bulls to review our manuscripts?

Virgina Walbot has recently published an article in the Journal of Biology discussing the idea that grad students and postdocs can turn out to be excessively (and in some cases unjustifiably) critical and even ‘savage’ in their review of articles (when asked to referee), and that this issue is a result of their training. She argues that this "problem" may be addressed by some exercises during their tutelage. She suggests a way to prevent them turning into “future generations of manuscript-savaging reviewers” ultimately by understanding what a ‘publishable unit’ is and also that a single paper is not supposed to provide complete proof of a major concept.

She opens her article by commenting on a rather common scenario: getting a bad review from one referee, while the others may have favorable comments about the manuscript.

(…the bad review, while) detailed in its critique, it relentlessly measures the work against a 'gold standard of excellence' using the latest and best techniques, before dismissing the years of labor (...)
This doesn’t normally happen. Reviewers like that are rapidly dismissed by editorial offices (ideally). If you submit a manuscript using a cDNA microarray, nobody will reject it on the basis that an Affymetrix chip should have been used or that high-throughput sequencing may have been the way to go. If you have the proper controls, the manuscript is sound in its conception and the results are well discussed, you are good to go (I know, this may sound like “too much” but it’s what is expected from an article). It is common (and even understandable), however, that if you make some claims regarding, for example, the generalized importance of a single transcriptional regulator by exemplifying with only a few supposedly target genes, that this “particular” referee may be interested in the whole transcriptional profile of a mutant defective in this regulator to be convinced of its widespread role and general importance, or some other experiments (wouldn’t we all?). As a referee you are free (and even encouraged) to ask for whatever you feel is needed to support the claims being made. Of course, this doesn’t mean the authors must perform the experiments. The editor (if a good one) will know that asking for certain experiments is just unrealistic or that these experiments may not be crucially needed to support the claims being made by the authors. The manuscript, then, will not be rejected just because the authors can’t fulfill the reviewer’s particular request. Authors are also given the chance to communicate directly to the editor their position regarding certain revisions.

The reviews from the other referees are also of extreme importance to the Editor for him/her to make a decision. But what if the editor is not that good, experienced or knowledgeable? How can he/she just ignore a devastating review from someone who is supposed to be an expert on the matter?

This is where the importance of Walbot’s article lays. She argues that with proper training, our grad students and postdocs can learn to assess the importance of each paper and to make reasonable requests in order to improve the article, and not to demand that a single manuscript provides complete proof of an idea.

She introduces the concept of “timely publishable unit” which I think is very useful. This is an article that with the available knowledge and tools constitutes a contribution of new ideas and partial proofs towards the understating of a particular biological process.

So what does Walbot suggest we do? How can we better train our students to appreciate and properly judge the contribution of a single paper, understand what a publishable unit is and to become better reviewers?

She first suggests that we make our students 
Read a short review and all of the constituent papers to understand how solid, but as yet incomplete, papers add up to a new paradigm.
This is a great idea. This will be of great help in illustrating the concept of publishable unit and students will be able to appreciate that is not a single paper that solves a particular problem, but rather a series of papers each making a partial contribution. She suggests that several points should be discussed with the students. For example:

What were the claims and evidence in the papers cited in the review? What constituted a publishable unit in this field, at that time? Is there a substantial difference in quality between papers in the most prestigious journals, in specialty journals in the field, and in obscure journals? In retrospect, given the emphasis in the review article, are the key conclusions primarily from the papers in the best journals? That is, did reviewing at the time identify the papers that best established new points or clarified existing concepts?
This will also teach them (if you haven’t told your students already) two things: 1) not everything you find in CNS journals (Cell, Nature, Science and in other one-word-title journals) is true and 2) just because a journal has low impact factor it does not mean that articles published there are weak and should not be considered in your research.
While I’m on the matter, make your students learn what impact factor measures and what it definitely does not: don’t let your students think that “the better the impact factor of a journal, the better –and true– an article in there is”.

Walbot also suggests students should
Listen to short presentations from several graduate students and postdoctoral fellows from one lab (equivalent to a faculty research seminar in depth and breath) and then discuss what's ready for publication
After attending these seminars a few questions could be discussed: “Should this 'story' be just one publication or can the work be broken into distinct publications? Should it be broken up?”
She argues this may help in making students understand
what constitutes a timely publishable unit of information in a particular field and how the ongoing contribution of new ideas and partial proofs stimulates work in the field.
For this, of course, students should be able to follow the “story” for a considerable amount of time (1-2 years for example). This is why I’ve always argued that graduate student seminars are extremely important and I completely agree with Walbot on this point.

While I agree that teaching students the importance of each paper and that each one is supposed to be understood as a contribution towards understanding a particular phenomenon, I don’t agree that reviewers turn out to be “savages” (as Walbot describes) due to a particular training method in grad school (which is the same most schools use, that is, analyzing classic great papers and also flawed ones, to make a point).

Every reviewer was first an author. As authors, they have faced the inherent problems of research, how slow it moves and how much “sweat and blood” each submission represents (particularly early in their careers). Many reviewers are sympathetic and make suggestions with the idea of improving the manuscript and helping the authors.
It is also true, however, that many reviewers are not like this. They may ask for experiments that are not within the reach of the authors, either in terms of resources or just time and in many cases, that will not be that great of a contribution to the point being made in the manuscript.

This is why Walbot’s article deserves to be read and discussed: it makes as consider the fact that we can train our students not to be like that. This does not mean that our students (and future reviewers) should look the other way when a control is missing, or that they shouldn’t judge to the best of their capabilities the quality of the evidence for each claim, or look for even the tiniest faults in the manuscripts they review. In fact, I’m a strong supporter of such reviewing attitude. In what I do agree, and is the main point being made in this article, is that besides their own experience as authors, they can be taught to evaluate the importance of each paper and what a particular paper represents in the efforts towards understanding a particular process, through some small practices during their training. This results in them being better reviewers (critical, yet realistic and helpful) and better scientists. I share the idea that such exercises can be of great help. This will ultimately be in science’s best interest.

And who knows? Your former grad student may be chosen as a reviewer for your next submission!

Walbot, V. (2009). Are we training pit bulls to review our manuscripts? Journal of Biology, 8 (3) DOI: 10.1186/jbiol125


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Monday, March 16, 2009

Young women in science

There are several initiatives throughout the life sciences celebrating women in science. For example, the RNA Society celebrates a "Women in Science" dinner at every meeting. For obvious reasons I've never attended, but in those dinners, successful female scientists talk about their experience in the scientific world in a way to inspire young female researchers.

Also, the L'Oréal-UNESCO For Women in Science Awards are awarded annually to five outstanding female scientists worldwide.
One Award Laureate is named from each of five continents: Africa, Asia-Pacific, Europe, Latin America and North America. Notably, the Laureates receive individual awards of US$100,000.
Commemorating the International Women’s Day (March 6th), five of the world’s women leaders in science each received the award at a ceremony in Paris.

In a way to highlight this event, Science/AAAS, in collaboration with the L'Oréal Corporate Foundation, have put together the "Young Women in Science booklet". It's full of exciting and inspirational stories about young women beginning their scientific careers.

These new profiles, from interviews with young women at the start of their science careers, tell their stories of passion and persistence —what drives and excites them about their work in the sciences. We hope that young girls (and boys)—as well as their educators—will find fun and inspiration in these pages and learn a little about what life as a scientist is all about.
The booklet includes:


* Common Passion for Common Good
* Encouraging Talent
* Changing the Face of Science - A Word from The L'Oréal Foundation
* A Word from UNESCO


* Spreading the Seeds of Knowledge
* Many Ways to Make a Difference
* A Big Problem in a Small World
* Unlocking Nutrition's Cancer-Prevention Potential
* Personal Challenge, Shared Triumph
* From Math Geek to Malaria Genetics
* Continuing the Family Business
* Revealing Nature's Pharmacopeia
* Believing in the Environment
* Ministering to the Needs of a Nation
* The Romance of Biodiversity
* Tackling a Pesty Problem from Different Angles
* Finding the Right Balance
* Virus Crime Scene Investigator
* Resilience in the Face of Stress
* Flourishing to the Extreme
* Folk Medicine for the 21st Century

Check it out!


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Friday, March 13, 2009

John Mattick is coming to Chile

I've always been interested in the RNA field, particularly RNA splicing. In fact, I'm currently working on RNA metabolism and gene expression regulation in plant organelles.
During my stay at Jon Staley's Lab in the University of Chicago in 2007, I worked on a project aimed at evaluating the functional relevance of introns in the genome of Saccharomyces cerevisae.
It's then no surprise that since I've been here at P. Universidad Católica de Chile I've been pushing to invite a prominent scientist working in the RNA field for him/her to give a talk and maybe some lectures for graduate students in the Molecular Genetics graduate program.
My candidates list was a long one and included people like David Bartel, Joan Steitz, Victor Ambros and Phil Sharp just to name a few. Considering how exciting their work is, you can imagine how difficult it was going to be to choose just one.

Finally, in late 2008, together with the Dean at my school, we decided on Professor John S. Mattick. Mattick has put forward to idea that most genetic information in mammals is conveyed by RNAs that control differentiation and development and that a regulatory mechanism (signaling network), based on RNA, could partly explain the increases in eukaryote complexity1.

I'm extremely please John accepted our invitation to visit Chile, which will undoubtedly be an exciting and enriching experience for both grad students and faculty members at our school.

He will give a faculty seminar on April 14th and lectures on the 15th and 17th. If you are in the area (Santiago, Chile) just sent me an email for more info.

1 Mattick JS. RNA regulation: a new genetics? Nature Rev. Genet. 5, 316–323 (2004).


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Thursday, March 12, 2009

New feature in MolBio Research Highlights

As you have probably noticed, we have recently decided not just to post articles on the blog, but also to discuss them in order to provide a better service for our readers. These articles are generally submitted to Researchblogging [MolBio Research Highlights joins] as we consider them to be an interesting contribution to the field of molecular biology; few blogs write about molecular biology in a way directed to scientists, rather than writing for the general public.
Unavoidably, however, this has resulted on fewer articles being posted on the blog, as reviewing and analyzing them requires a fair share of time (and we are all grad students).
To overcame this and continue with our goal of being the best site for highlighting selected articles in molecular biology, we have added a tool called "Around the journals" which you can access from the left sidebar. Through that tool, we will post selected articles from a hand-picked list of journals directly from our Google Reader, for them to be displayed on the blog as soon as we receive them. This will be an important addition as we will be able to bring to your attention more articles, from which we are sure some will pique your interest. This, however, does not mean that we won't sometimes display some of these articles as posts (which has the advantage of being part of the RSS feed) when we see fit. Also, we will continue discussing selected articles at length.

We hope you will find this tool useful and continue visiting MolBio Research Highlights.


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Wednesday, March 11, 2009

More on Science 2.0: Cell Press

I've just learned that Cell Press, the publisher of journals like Cell, Neuron, Developmental Cell, the Trends Series and the great (IMHO) Molecular Cell, has recently announced the launching of a Cell Press channel on YouTube where you can
"Watch videos of scientific discoveries published in Cell Press journals, experience the observations behind the papers and explore our showcase of exciting biology—from the molecule to the population"

Although I haven't checked the quality (scientific quality that is, in terms of the depth of the analyses) of the videos or the target group they are supposed to be made for, I think this is a great idea, as I have argued before that web videos are great tools for advertising [Commecials in life science research: Roche] be it new technologies or, as in the case of the Cell press channel, recent papers.

So check it out!


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Tuesday, March 10, 2009

The Nano Song

Nanotechnology is “the ability to work at the atomic, molecular and supramolecular levels (on a scale of ~1–100 nm) in order to understand, create and use material structures, devices and systems with fundamentally new properties and functions resulting from their small structure”1.

Nanotechnology has been successfully applied to the study of biological systems, aiding in the more in-depth comprehension of diverse fundamental biological processes. Nanobiotechnology emerges from a collaborative effort between biological, physical, chemical, and engineering sciences, being a hallmark of the power of integrating different disciplines to help in the understanding of diverse systems, including biological ones.
One example of its utility comes from single molecule measurements which allow us to further our understanding on the dynamics and mechanistic properties of biological molecular motors.
A recent paper also highlights the importance of nanotechnology in biomedical research [Twin nanoparticle shown effective at targeting, killing breast cancer cells].

The reason why I'm talking about this is solely to have an excuse to post the following video entitled “The Nano Song” which I think is just awesome.

The Nano Song from nanomonster on Vimeo.

[H/T]:Andre at

1 Roco MC. Nanotechnology: convergence with modern biology and medicine (2003).Current Opinion in Biotechnology 2003, 14:337–346.


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Sunday, March 8, 2009

Commercials in life science research: Roche

A few months ago I commented on a ad by the people at Eppendorf [Are you tired of pipetting?]. They even created a whole website and a music video featuring a boy band to promote a new system called epMotion. Before that, BioRad made a whole bunch of scientists around the world laugh with their "PCR song". Several other companies are now making use of the Web 2.0 to promote their lab equipment and new technologies. Instead of (or mainly in addition to) distributing boring serious flyers (although I know they have to), companies like the ones mentioned and others are composing funny and attractive videos or setting up whole websites to promote their technologies. These videos, as opposed to the aforementioned flyers, are indeed watched from beginning to end by users and are continuously forwarded to their friends, when attractive, provocative or just plain hilarious (In my case and of those close to me, we never read flyers completely, except when you are REALLY interested in the product being sold, but we always thank a funny video on any new technology. Let's face it, we have a lot of downtime in research). These videos will normally take about 2-3 mins. of your life and can really get you thinking on what they are selling, even if you will never ever buy it. At least it will keep circling in your mind, and that's what a good commercial is supposed to do.

After this short commentary, let me introduce an ad by Roche on the LightCyler 480:

[Thanks to Greg Laden]


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Thursday, March 5, 2009

OA week will take place in October

I've just received an email from Jennifer McLennan, the Director of Communications at SPARC, who coordinated last year's Open Access day .
Last year, the first ever Open Access Day took place, and due to its success, this year events will be schedule for a whole week on October (19-23).

Here's her email:

Open Access Week declared for 2009
Popular global event extended over one week, October 19 – 23

Washington, DC – March 5, 2009 – To accommodate widespread global interest in the movement toward Open Access to scholarly research results, October 19 – 23, 2009 will mark the first international Open Access Week. The now-annual event, expanded from one day to a full week, presents an opportunity to broaden awareness and understanding of Open Access to research, including access policies from all types of research funders, within the international higher education community and the general public.

Open Access Week builds on the momentum generated by the 120 campuses in 27 countries that celebrated Open Access Day in 2008. Event organizers SPARC (the Scholarly Publishing & Academic Resources Coalition), the Public Library of Science (PLoS), and Students for FreeCulture welcome key new contributors, who will help to enhance and expand the global reach of this popular event in 2009: (Electronic Information for Libraries), OASIS (the Open Access Scholarly Information Sourcebook); and the Open Access Directory (OAD).

“I’m participating in Open Access Week again this year because I want to shed light on the tremendous potential of Open Access,” said Allyson Mower, Scholarly Communications & Copyright Librarian for the University of Utah’s Marriott Library. “People searching for information usually consume whatever is readily available. Open Access ensures that quality information is at people’s fingertips.”

“ works to make intellectual outputs of developing and transitional countries more visible and more easily accessible,” added Rima Kupryte, Director of “We believe that Open Access contributes to improved education, teaching, and research, and accelerates innovations and economical developments in these countries. Open Access Week is a great opportunity to promote Open Access globally.”

This year’s program will highlight educational resources on Open Access that local hosts can use to customize their own programs to suit local audiences and time zones. OASIS will serve as the centerpiece of the 2009 program, delivering resources for every constituency and every awareness level. The Open Access Directory will again provide an index of participants on five continents, as well as their growing clearinghouse for all OA resources. Through the collaborative functionality of the two initiatives, OA videos, briefing papers, podcasts, slideshows, posters and other informative tools will be drawn from all over the Web to be highlighted during Open Access Week.

The organizers will also work with registrants to develop a variety of sample program tracks, such as “Administrators’ introduction to campus open-access policies and funds,” “OA 101,” and “Complying with the NIH public access policy” that take full advantage of available tools. Participants are invited to adapt these resources for local use, and to mark Open Access Week by hosting an event, distributing literature, blogging -- or even just wearing an Open Access t-shirt.

“After the success of last year’s Open Access Day, we’re delighted to be co-organizing the first ever Open Access Week with our fellow collaborators, again in conjunction with the anniversary of one of our flagship journals,” said Peter Jerram, CEO for the Public Library of Science. “We ask our supporters to celebrate the fifth anniversary of PLoS Medicine by spreading the word about Open Access and getting involved in the week.”

“There’s no more certain sign of the momentum behind Open Access to research than an annual, global celebration of this scale,” added Heather Joseph, Executive Director of SPARC. “Occasions like this are the best possible way to attract attention from busy faculty members and administrators, and to demonstrate the widespread appeal of Open Access. It’s SPARC’s pleasure to be working with our partners to realize the event once again this year.”

For more information about Open Access Week and to register, visit

I'll keep you posted.


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Web (and science) 2.0

An article by David Larousserie discussing how the Web 2.0 can help in science communication has recently by posted in Sciences et Avenir (issue February 2009). It comments on blogs, wikis, online journals and online networks (such as Facebook).
Take a look at it, but please note that it's in French.

(Thanks to Gavin Baker)


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