Seven Major Trend Changes of 2013 - (iv) Publishing and Social Media

Seven Major Trend Changes of 2013 - (iv) Publishing and Social Media

4. In Scientific Communication, Social Media Took over Cell/Nature/Science

In August 2012, we wrote a commentary titled -

Nature Journal Recognizes (or its own Wile E. Coyote Moment)

At that time, both concepts promoted in the commentary were ridiculous. Everyone told us that ‘biologists would not post preprints in’ and ‘dominance of Nature/Science/Cell would never go away’. Fast forward by sixteen months and you find - (i) NIH and CSHL establish bioarxiv, (ii) a Nobel laureate utilize the publicity of award-ceremony to talk against Cell/Nature/Science culture.

Here is the real evidence that the so-called ‘high-visibility’ journals are losing their dominance. During early 2013, K. R. Bradnam and collaborators submitted their Assemblathon 2 paper to arxiv and GigaScience. Assemblathon 2 paper had been a colossal failure by accepted standards of biology, because it was not published in a ‘high-visibility journal’. GigaScience, being an upstart journal, is fairly low in the pecking order.

On the other hand, based on the measure of actual high-visibility, the Assemblathon 2 paper was immensely successful. The paper was widely discussed in the community, and its author used social media (twitter - @assemblathon and blog) to generate and maintain interest in the work. Moreover, the open review model of GigaScience made the process transparent, constructive and beneficial for the scientists involved. We are definitely seeing a major change in trend in the overall publication and scientific communication process.

The last point is best understood by comparing open review model of GigaScience with the closed review process experienced by Heng Li for his BWA- MEM paper. An anonymous reviewer called the author ‘scientifically dishonest’ for no good reason. As a result, frustrated Heng Li posted his preprint in arxiv and got done with it. More details are available in the following commentary.

Mapping God Found Scientifically Dishonest by Anonymous Peer Reviewers

Overall, 2013 saw an explosion in the use of social media (e.g. blog, github, twitter, slideshare, biostar, etc.), through which scientists from all over the globe started to communicate directly with each other (for example, here is a cuban blog on bioinformatics and proteomics). In earlier years, publishing a paper in a high- profile journal or presenting in a high-visibility conference were two only modes of communications, but now publish or perish is being replaced by Tweet or Perish.

The biggest benefit of internet communication is the creation of new services and ways of sharing, whose equivalents did not exist in the earlier era. Three examples are shown below.

Rosalind and Stepic

Rosalind has been very popular bioinformatics teaching tool and its creators went on to build another useful service called Stepic. The relevant commentaries are shown below.

Rosalind Project at Algorithmic Biology Laboratory, St. Petersburg

Rosalind Will Get Even More Marvelous

New Announcement from the Rosalind Team


In a series of commentaries, we discussed about various aspects of Biostar - an online question-answer forum for bioinformaticians.

Biostar I Discussions with Biostars Istvan

Biostar II the Code

Biostars III The Community

Biostar: Comments from Khader Shameer

Biostar the Final Verdict

SOAPdenovo Demystified

In mid-2012, we received an early access of SOAPdenovo2 executable code and found it useful.

Testing SOAPdenovo2 Pre-release Version

When the SOAPdenovo2 paper was published six months later, we decided to understand the 40,000 line C-code, and shared the insights with our readers. We used blog and wiki for this effort.

Our First Look at SOAPdenovo2 Source Code

SOAPdenovo2 Demystified part (a)

SOAPdenovo2 Demystified part (b) [multi-thread implementations]

SOAPdenovo2 Demystified A Rough Guideline of Functionality


Coming up next -

Seven Major Trend Changes of 2013 (v) Era of Contention Begins

Written by M. //