An interview with the creator of BioTorrents

Who better to interview the creator of BioTorrents than the creator himself? :)

Interviewer: So Morgan, your article entitled “BioTorrents: A File Sharing Service for Scientific Data” was published today in PLoS One. BioTorrents uses the popular peer-to-peer file sharing protocol, BitTorrent, to allow scientists to rapidly share their results, datasets, and software. Where did this idea come from?

Morgan: Well about 6 months ago I was downloading some genome files from NCBI's FTP site and was watching the download speed hover between 50-100Kb/s and I said to myself (much like this interview) I wish could download these with BitTorrent. I have used BitTorrent for downloading other non-scientific data (lets not discuss what they may be) and I know it is a much faster and more reliable way for getting large files. A few minutes later I posted to Twitter asking if anyone had thought about setting up a BitTorrent tracker for scientific data and the response was over-whelming (well only 1 response, but I could feel it had a larger impact). About a week later, I brought up the idea again over coffee with some members of my lab and more importantly my post-doc supervisor Dr. Jonathan Eisen. He thought it was a good idea and well worth pursuing, which was all I needed to push aside all my other "real" research and focus on this much more "fun" project.

Interviewer: Thanks for that long-winded response. Maybe you could comment more briefly on the benefits of using BioTorrents/BitTorrent for sharing scientific data.

Morgan: I think it is explained fairly well in the manuscript and in my previous blog post, but to reiterate the major benefits are:
1) Faster, more reliable, and better controlled downloading of data that scales well for very large files.
2) Instant "publishing" of data, results, and software.
3) Very easy for anyone to share their data. No dedicated web server needed.

Interviewer: Who should consider sharing data on BioTorrents?

Morgan: Everyone that has something to share. Large institutions can benefit from reduced bandwidth requirements, while individual users can benefit from the simplicity of sharing with BitTorrent technology. Personally, I really like the idea of open data and the idea of sharing results before publication. How many times has someone done an all vs all blast of microbial genomes? In theory this can be done once, and that person can be recognized (referenced, co-authored, etc.) when other researchers use that data.

Interviewer: Are there any challenges/limitations to using BitTorrent with scientific data?

Morgan: BitTorrent excels at transferring very large popular datasets. Therefore, if only one person is "seeding" a file and only one person is downloading the file most of the advantage to using BitTorrent is lost. However, even in this worst case scenario, the transfer speed would be roughly equivalent to using traditional file transfer methods such as FTP/HTTP and BitTorrent still provides the benefit of error checking and ease of data transfer control (pause, resume, etc.). Another possible problem is that some institutions often try to limit BitTorrent traffic since it is often considered illegal non-work related network traffic. However, I would encourage users at these institutions to explain to their network administrator that many times BitTorrent traffic is legitimate and shouldn't be blocked.

Interviewer: Why publish in PLoS One?

Morgan: I have been a big fan of the PLoS One journal and ever since I blogged about it last year "Is PLOS One the future of scientific publishing?", I have been wanting to submit a paper there. Also, considering that BioTorrents is aimed at improving open access to data in all fields of science, PLoS One seemed like the most obvious journal choice for our manuscript.


Langille, M., & Eisen, J. (2010). BioTorrents: A File Sharing Service for Scientific Data PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010071

Is PLOS One the future of scientific publishing?

I just read about PLOS One's new features through their relatively new blog, EveryOne. Although the new features are not really ground breaking they do provide a much improved layout and a new "Related Content" page. These changes show that One is dedicated to improving connectivity between peer-reviewed papers and commentary from comments, blogs, etc., giving me some hope that publishing may be changing (yet still at a snails pace).

So back to the question that is asked in the title of this post, "Is PLOS One the future of scientific publishing?", I am going to have to say a tentative "Yes". I think their basis of publishing papers not on novelty, but focusing peer-review on ensuring that the methods, and conclusions drawn from the results are scientifically sound, opens many doors for how scientists publish their findings. Currently, scientists compete for a limited space in a "high-impact" journal. In the majority of cases papers are not rejected because of their methods, results, and conclusions are not valid, but due to a better paper being submitted at the same time. This competition is justified, but in this current format has various drawbacks including:

1. Importance of research is determined by a very small number of reviewers and usually a single editor has the final decision
   
2. Significance or novelty of research is very subjective and can vary widely between reviewers
3. Significance can change over time as future experiments confirm or depend on the results of the current research (including negative results)
   
4. Not making the cut (i.e. rejection) results in a large waste of time as authors have to reformat, resubmit, and respond to new reviewers comments

The separation of the evaluation for competitiveness, novelty, significance, etc. versus scientific robustness helps reduce many of these problems. The largest hurdle to overcome using this model is to move from a journal impact factor to a paper impact factor measurement. Therefore, "signficant" papers are still valued and reconizable in PLOS One and other journals that will likely follow their publishing methods.

Personally, I have never published in PLOS One and by no means do I think PLOS One in its current form is the pinnacle of publishing. However, I do appreciate that they are trying to change the way science publishing is currently conducted.