Science 2.0


Web-enabled Biomedical Knowledge Discovery

Gene Information in Wolfram Alpha

I have been checking out Wolfram Alpha (a search engine that emphasizes number crunching and graphical representation of results). I really like the interface and the results it returns. Obviously very attractive to any science geek. I was trying different trivial search strings (like  “temperature in Dallas” or “Ugly Dolls”) and out of habit typed the name of one of my favorite genes without expecting any result (“Ugly Dolls” did not return any, which is somewhat reassuring). I was surprised to find that genes had been included as computable entities by Worlfram Alpha developers. Of course I can’t help thinking of the next step, which would consist in including actual genomic data. It’s only a matter of time obviously…

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Filed under: Information Dissemination

Treat Yourself with Mendeley

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Here is a fantastic tool for getting all those pdf files organized (who goes to the library to make copies anymore?). It doubles as a social network for scientists (yet another one). Keeping up with the literature has become a struggle, there is so little time left in any given day to indulge in reading (even less in socializing or blogging – which explain the length of this post). Mendeley should help dimish the guilt of having all those pdfs files scattered all over your hard drive (in vain attempts of organizing them, using various folder and file naming schemes which evolve over time). I would also like to keep track of articles for which I have not been able to obtain a pdf (but maybe will one day). The file parsing feature is truly amazing. Maybe you will even have some extra time on your hands to socialize with your peers!

Filed under: Knowledge Dissemination

If Nature Says So…

In a relatively recent editorial (I need to catch up), the journal Nature tells us that it is OK to blog. It might even be a good thing! This piece more specifically addresses “discussing” and even disclosing results that are slated for publication in their journal (and therefore are embargoed by the journal until publication).

Rationale for imposing embargoes on research to be published: “This embargo policy rests on the principle that scientists’ and the public’s best interests are served by press coverage of work that has been peer reviewed, and is available for others to see for themselves.” The peer review process is obviously critical but at the same time is fundamentally relying on trust and honesty. Also it cannot guaranteed that the results are indeed reliable,  especially when you realize how much a publication in a high impact journal can change the course of a scientific career. It is besides the point here but if you insist, read on: “Why Most Published Research Findings are False”.

The flip side: “At the same time, however, our cardinal rule has always been to promote scientific communication.”

The editorial then goes on to describe results communicated at conferences, on preprint servers or in blogs as fair game for journalistic coverage and this does not constitute a breach of embargo.

Some aspects of the embargo rule are to say the least confusing. What I find interesting is the notion that after all communicating data on the web, in a blog  is OK as far as a high impact journals as Nature is concerned. Now I wonder if this rule applies to data communicated and discussed in Knol.

One final comment: “The experience of journals such as Cell and PLoS ONE, which allow people to comment on papers online, suggests that researchers are very reluctant to engage in such forums. But the blogosphere tends to be less inhibited, and technical discussions there seem likely to increase.”

This editorial has been opened for discussion on the Nature Opinion Forum… which had to be closed promptly after being hit by spammers. That’s Web 2.0 for you!

You can also read an interesting post covering this topic from the evolving ideas blog.

More interesting reading material from Maxine Clarck the author is also available here.

Filed under: Knowledge Dissemination, Web Publishing


I received some interesting spam today. It invited the recipient to join a “scientific networking platform known as”, and it worked, I signed up!

Signing up was a painless, navigation is definitely on the slow side but that could easily be fixed. So I started looking around. In summary:

Science 2.0 concepts and vision are discussed in the about us page.
“Towards connected science – Science 2.0”. They have put clearly the emphasis on interaction and research collaboration.

The format is a combination between a forum (discuss various topics) and a social network (invite colleagues, friends), adding a platform for commenting on scientific publications.

An important aspect are the groups. There are dozens of them, covering some rather specific topics (FRET, Phytotron) and some very wide research areas (Cancer Biology, Immunobiology). The membership varies from 2 to several hundreds. Of course there is a group that immediately grabbed my attention: it is called “Science & Publication 2.0”. It did not seem terribly active but I will probably join the discussion one of these days!

Filed under: Experimenting

Posting Results in Real Time (almost)

We have published a discovery note in Knol about the potential role of Interleukin 27 in sepsis a couple of months ago. It was all based on gene expression microarray results. We just got the ELISA results back and levels of proteins are also elevated. The best part is that we were able to post the results almost immediately in knol!slide3-1

Filed under: Experimenting, Knol, Knowledge Dissemination, Web Publishing

RC1 Fever

Swamped with grant applications to plug in by the end of the month. They are those RC1 challenge grant funded through NIH recovery and reinvestment funds. Not much time to dedicate to anything except writing those applications and look foward to better days… (and so does this blog).

Filed under: Funding, Ramblings

Launching of “Blood Transcriptomics Research”

How hard can it be? Of course it depends on what your expectation of what a scientific journal is supposed to be. Creating a sustainable high-impact scientific journal takes a huge amount of resources, time and expertise. What I want to do is to create a journal as a spin out activity of our journal club, so let’s think about a slightly different format!

Information overload is not restricted to data. The rate of publication is rapidly increasing and it is becoming difficult to keep up with the literature. This fact lead to the development of text mining solutions (Omniviz) and other services that filter the must reads (Faculty of 1000). If on top of that people start publishing early finding on the web (e.g. discovery notes in Knol) it becomes impossible to keep up with the load of information (especially if someone needs to start sorting from the good, the bad and the ugly!). The later is actually an objection to the S2p0 approach that I get a lot and it is well founded so I have been thinking about this lately. Another objection that has been leveled at the model is that some good stuff may be published on the web but in the absence of proper peer review it would mostly be junk (this was not put as politely but you get the idea). Again point well taken. So how could these issues be addressed.

An idea would be to put a couple of people in charge of developing a “journal” around a very specific topic. It would of course be web based and focused on a rather narrow field of research, so not really high circulation.

This journal would serve a couple of purposes:

1) Aggregate the relevant literature about the topic of interest from all available traditional journals (of course full content may not always be available).

2) Aggregate relevant web content (e.g. Knols), that would be judged to be of sufficient quality to provide useful information.

This should help with information overload and at the same time operate a selection of the worthwhile web content (when ratings and peer feedback is not sufficient).

The field I work in (blood transcriptomics) does not have its own journal. So the idea would be to launch a web site focusing on this topic that would be the place to lookup new literature and web content relevant to this field. We don’t really have full time editors to dedicate to this task but I think doing this in the context of our jounal club should do just fine for now! We’ll actually most likely start this on a WordPress blog!  We just need to find a name. I guess “Blood Transcriptome Research” sounds OK.

Filed under: Challenges, Experimenting, Knowledge Dissemination

Funding for S2p0

Several request for proposal that recently came out of NIH are relevant to Science 2.0. That would be the case of the Eureka RFA (stands for Exceptional, Unconventional Research Enabling Knowledge Acceleration).nih_300

There are also two high priority topics that will be supported by ARRA funds (American recovery and reinvestment act) via the NIH challenge grant initiative:

  • 06-RR-101* Virtual environments for multidisciplinary and translational research. Virtual networking environments like Science Commons, Facebook, and Second Life, create platforms that can eliminate many barriers in scientific collaborations. These environments integrate fragmented information sources, enable “one-click” access to research resources, and assist in re-use of scientific workflows. Funded projects would develop and implement virtual collaborative environments to facilitate biomedical and translational research, e.g. addressing issues of privacy, technology transfers, and sharing resources. Contact: Dr. Olga Brazhnik, 301-435-0758,

Developing such environment can certainly be a challenge!

  • 06-RR-102* Infrastructure for biomedical knowledge discovery. Biomedical research depends on heterogeneous data of varying reliability that are increasingly multimedia and high-dimensional. Recent advances in web technologies enable discovery and aggregation of disparate data on specified topics, visualization and navigation of complex and abundant data, extraction of concepts from text, and detection of associations. Funded projects would coalesce the most effective information technologies with domain specific knowledge structures and data processing and to create computational infrastructures for integrated, customizable access to biomedical data.
    Contact: Dr. Olga Brazhnik, 301-435-0758,

Interestingly this sounds a lot like a tool we have been working on developing for a while: here is a sample profile out of more than half a billion available from our database! It brings together information from the microarray database itself, but also our LIMS system, NCBI annotations and literature database. It’s only a start!

The deadline for submitting an application is April 27!!

Filed under: Funding, Ramblings

Aloha from Waikoloa

I am participating to a conference on cancer biomarkers in Hawaii and feeling inspired. Not a bad time to start this blog. In fact this is the perfect opportunity to point out one of the benefits of Science 2.0; integrated data can be accessed and interpreted from anywhere in the world (yes, wifi connection near the pool is quite decent, thank you). Also as I write this sipping a Mai Tai (local drink) and gazing at the palm trees and Pacific Ocean beyond I cannot help but think that there is definitely a future for Science 2.0…


Filed under: Information Dissemination, Ramblings