Monthly Archives: June 2012

Announcement: From genomes to cells and systems

Later this year Peer Bork, Jeroen Raes, Roland Krause, David Torrents, and I will be organizing the EMBO practical course “Computational biology: From genomes to cells and systems”. It will take place October 14-20 in L’Escala Girona, Catalonia.

In times when high-throughput data are the norm rather than the exception, computational skills to turn masses of data into tangible biological insights have become crucial. This course will teach advanced computational methods for analysis of high-throughput data in molecular biology, covering both inter-individual and inter-species variation in (meta-)genomes and linking it to clinical applications. The course will span protein and pathway level variation from single genomes to entire microbial communities.

To participate in this course, fill in the online application form at the latest July 31, 2012. The registration fee is 250 euros for participants from academia, and 600 euros for industry.

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Analysis: Is PeerJ cheaper than other Open Access journals?

The newly announced Open Access journal PeerJ has caused quite a fuzz, not least because of their catch phrase: “If we can set a goal to sequence the human genome for $99, then why not $99 for scholarly publishing?”

This at first sounds very cheap; however, the $99 is not what you pay per accepted paper. PeerJ operates under a different scheme than traditional Open Access journals: instead of paying per publication, you pay a one-time fee that you pay to be able to publish in PeerJ for life. This sounds almost too good to be true.

There are a few catches, however. Firstly, $99 only entitles you to submit one manuscript per year to PeerJ. If you want to be able to submit two manuscripts per year or unlimited manuscripts, the price rises to $169 and $259 respectively.
Secondly, all authors on a manuscript must be paying PeerJ members at the time of submission (except if there are more than twelve authors, in which case it is enough that 12 of them are members). This suddenly makes the comparison to other Open Access journals much more complex, as the actual average price per manuscript depends on the number of authors, the number of other PeerJ manuscripts submitted by the same authors in their lifetime, and the acceptance rate of PeerJ. In this post I try to do the math and compare PeerJ to traditional Open Access journals, where you pay per accepted publication.

PeerJ compares itself to PLoS ONE, so I base all comparisons on that. From 2006 when PLoS ONE was launched up to and including 2011, a total of 29,042 publications have appeared with a total of 150,020 authorships. This amounts to an average of 5.1 authors per publication. When PeerJ is initially launched, no authors will have the benefit of already being members, so at first this implies that all authors will have to pay an average cost of $99*5.1 = $511 per submitted manuscript (ignoring the discount on manuscripts with 12+ authors). According to the PeerJ FAQ, this is expected to be approximately 70%. Assuming that this holds true, the average cost incurred by the authors per accepted paper will be $511/0.7 = $730. This is already considerably less than PLoS ONE, which has a publication fee of $1350 per accepted paper. From a pure cost point-of-view, PeerJ thus looks to be about half the price of PLoS ONE.

I do have some concerns related to the model of charging per author. First, I find it to be illogical, since the actual costs related to handing a manuscript are independent of the number of authors. Second, the average number of authors per paper varies between research fields, which implies that the average fee per manuscript will in some fields be higher than $730. For a manuscript with 12 authors, neither of whom are already PeerJ members, the fee per accepted manuscript is $99*12/0.7 = $1697, which is more expensive than PLoS ONE. Third, the new model gives a direct financial incentive to not include authors who made minor contributions.

In summary, I think PeerJ is a refreshing new idea – I can only applaud efforts to lower the price of scientific publishing. However, although $99 for scientific publishing sounds revolutionarily cheap, PeerJ will at first only be ~2x cheaper then PLoS ONE. Also, the new payment model, which effectively boils down to a per-author charge, is in my opinion not without its own problems.

Full disclosure: I am an associate editor of PLoS Computational Biology.

Announcement: Computational analysis of protein-protein interactions for bench biologists

Once again I will be one of the teachers on an EMBO Practical Course. This time we will be teaching wet-lab biologists about how to do computational analysis of protein-protein interactions. The course will take place September 2-8 at the Max Delbrück Center for Molecular Medicine in Berlin, Germany.

The course aims to help bench scientists become more effective at exploiting the wide range of commonly-used databases and bioinformatics tools that can be used to identify, understand, and predict protein interactions by analyzing their structure, sequences, and other features.

The target group for the course are experimental scientists needing to analyse interaction data in their work, and who have limited experience using bioinformatics tools and resources. The course covers analyses and tools that are applied after potential interactions have been identified. It does not cover analysis of the raw data from, for example, mass spectrometry.

To apply for the course, fill in the online application form. The registration deadline is Friday June 15th 2012. The course fee is 200 euros for academics and 1000 euros for scientists from industry.