Sunday, June 25, 2006

Quick links

I stumbled upon a new computational biology blog called Nature's Numbers, looks interesting.
From Science Blogs universe here is a list compiled by Coturnix of upcoming blog carnivals for the next few days. I also remind anyone reading that the deadline for submissions for bio::blogs is coming very soon so send in your links :).
Still in Science Blogs here is an introduction to information theory. I am getting interesting in this as a tool for computational biology but I have a lot to learn on the subject. Here are two papers I fished out that use information theory in biology.
Also, if you want to donate some money, go check out the donors choose challenge of several Science Bloggers. Seed will match the donations up to $10,000 making each donation potentially more useful.

Wednesday, June 21, 2006

Journal policies on preprint servers

I mentioned in a previous post that it would be interesting to separate the registration, which allows claims of precedence for a scholarly finding (the submission of a manuscript) from the certification, which establishes the validity of a registered scholarly claim (the peer review process).

This can only happen if journals accept that a manuscript submitted to a preprint server is different from a peer-review article and therefore it should not be considered as prior publication. So what do the journals currently say about preprint servers ? I looked around the different policies, sent some emails and compiled a this list:

Nature: yes but ...
Nature allows prior publication on recognised community preprint servers for review by other scientists in the field before formal submission to a journal. The details of the preprint server concerned and any accession numbers should be included in the cover letter accompanying submission of the manuscript to Nature. This policy does not extend to preprints available to the media or that are otherwise publicised before or during the submission and consideration process at Nature.

I enquired about this last part of their policy on the peer review forum and this was the response:
"We are aware that preprint servers such as ArXiv are available to the media, but as things stand we consider for publication, and publish, many papers that have been posted on it, and on other community preprint servers.As long as the authors have not actively sought out media coverage before submission and publication in Nature, we are happy to consider their work."

Nature Genetics/Nature Biotechnology: yes
(...)the presentation of results at scientific meetings (including the publication of abstracts) is acceptable, as is the deposition of unrefereed preprints in electronic archives.

PNAS: Yes!
"Preprints have a long and notable history in science, and it has been PNAS policy that they do not constitute prior publication. This is true whether an author hands copies of a manuscript to a few trusted colleagues or puts it on a publicly accessible web site for everyone to read, as is common now in parts of the physics community. The medium of distribution is not germane. A preprint is not considered a publication because it has not yet been formally reviewed and it is often not the final form of the paper. Indeed, a benefit of preprints is that feedback usually leads to an improved published paper or to no publication because of a revealed flaw. "

BMC Bioinformatics/BMC Biology/BMC Evolutionary Biology/BMC Genomics/BMC Genetics/Genome Biology: Yes
"Any manuscript or substantial parts of it submitted to the journal must not be under consideration by any other journal although it may have been deposited on a preprint server."

Molecular Systems Biology: Do you feel lucky ?
"Molecular Systems Biology reserves the right not to publish material that has already been pre-published (either in electronic or other media)."

Genome Research: No
"Submitted manuscripts must not be posted on any web site and are subject to press embargo."

Science: Do you feel lucky ?
"We will not consider any paper or component of a paper that has been published or is under consideration for publication elsewhere. Distribution on the Internet may be considered prior publication and may compromise the originality of the paper or submission. Please contact the editors with questions regarding allowable postings under this policy."

Cell: No ?
"Manuscripts are considered with the understanding that no part of the work has been published previously in print or electronic format and the paper is not under consideration by another publication or electronic medium."

PLoS - No clear policy information on the site about this but according to an email I got from PLoS they do consider for publication papers that have been submited in preprint servers. I hope they could make this clear in the policies they have available online.

Bioinformatics,Molecular Biology and Evolution - ??
"Authors wishing to deposit their paper in public or institutional repositories may deposit a link that provides free access to the paper, but must stipulate that public availability be delayed until 12 months after first online publication in the journal"

I sent emails to both journals but I only had an answer from MBE directing me to this policy common to the journals of the Oxford University Press.

In summary most journals I checked will consider papers that have been previously submited to preprint servers, so I might consider in the future to submit my own work to preprint servers before looking for a journal. Very few journals clearly refuse manuscripts that might be available in electronic form but a good number either have no clear policy or reserve the right to reject papers that are available online.

Monday, June 19, 2006

Mendel's Garden and Science Online Seminars

For those interested in evolution and genetics this is a good day. The first issue of Mendel's Garden is out with lots of interesting links. I particularly liked RPM's post on evolution of regulatory regions. I still think that evo-devo should focus a bit more on changes in protein interaction networks but more about that one of these days (hopefully :).

On a related note, Science started a series of online seminars with a primer on "Examining Natural Selection in Humans". This is a flash presentation with voice overs from the authors of a recent Science review on the same subject. I like this idea much more than the podcasts. I am not a big fan of podcasts because it is much faster to scan a text than it is to hear someone read it for you. At least with images there is more information and more appeal to spend some minutes listening to a presentation. The only thing I have against this Science Online Seminars initiative is that there is no RSS feed (I hope it is just a matter of time).

Friday, June 16, 2006

Bio::Blogs announcement

Bio::Blogs is a blog carnival covering all bioinformatics and computational biology subjects. Bio::Blogs is schedule to be a monthly edition to come out on the first day of every month. The deadline for submission is until the end of month. Submissions for the next release of Bio::Blogs and offers to host the next editions can be sent to:

I will be hosting the first issue of Bio::Blogs here and there will be a homepage to keep track of all of the editions.

For discussions relating Bio::Blogs visit the Nodalpoint forum entry.

Wednesday, June 14, 2006

SB2.0 webcast and other links

If you missed the Synthetic Biology 2.0 conference you can know watch the webcast here (via MainlyMartian).

Nature tech team over at Nascent continue with their productive stream of new products, including the release of Nature Network Boston and a new release of the Open Text Mining Interface. They even set up a webpage for us to keep up with all the activity here. They really look like a research group by know :) I wonder what will happen if they tried to publish some of this research... Open Text Mining Interface published by Nature in journal X.

Monday, June 12, 2006

PLoS blogs

Liz Allen and Chris Surridge just kicked off the new PLoS blogs. According to Liz the blogs will be used to discuss their "vision for scientific communication, with all of its potentials and obstacles". I thank both of them for the nice links to this blog :) and for engaging in conversation.

Chris Surridge details in his first post how news of PLoS One has been spreading through the blogs. I think this only happened because the ideas behind ONE do strike a chord with bloggers and I really hope their efforts are met with success and more people engage in scientific discussion and collaboration.
Science blog carnivals

What is a blog carnival ? In my opinion a blog carnival is just a meta-blog, a link aggregation supervised by an editor. They have been around for some time and there are already some rules to what usually is common to expect from a blog carnival. You can read this nice post on Science and Politics to get a better understanding of blog carnivals.

Here is a short summary I found on this FAQ:
Blog Carnivals typically collect together links pointing to blog articles on a particular topic. A Blog Carnival is like a magazine. It has a title, a topic, editors, contributors, and an audience. Editions of the carnival typically come out on a regular basis (e.g. every monday, or on the first of the month). Each edition is a special blog article that consists of links to all the contributions that have been submitted, often with the editors opinions or remarks.

There are of course science carnivals and I would say that their numbers are increasing with more people joining the science blogosphere. To my knowledge (please correct me :) the first scientific blog carnival was the Tangled Bank that I think started on the 21st of April 2004 and is still up and running.

These carnivals could also be seen as a path of certification (as discussed in the previous post). The rotating editor reviews submissions and bundles some of them together. This should guaranty that the carnival has the best of what has been posted on the subject in the recent past. The authors gain the attention of anyone interested in the carnival and the readers get supposably good quality posts on the subject. With time, and if there are more blog posts than carnivals we will likely see some carnivals gaining reputation.

Maybe one day having one of your discovery posts appear in one of the carnivals will be the equivalent of today having a paper published in a top journal.

With that said, why don't we start a computational biology/bioinformatics carnival ? :) There might not be enough people for it but we can make it monthly or something like this. Any suggestion for a name ?

Thursday, June 08, 2006

The peer review trial

The next day after finding about PLoS One I saw the announcement for the Nature peer review trial. For the next couple of months any author submitting to Nature can opt to go trough a parallel process of open peer review. Nature is also promoting the discussion on the issue online in a forum where anyone can comment. You can also track the discussion going on the web through Connotea under the tag of "peer review trial", or under the "peer review" tag in Postgenomic.

I really enjoyed reading this opinion on "Rethinking Scholarly Communication", summarized in one of the Nature articles. Briefly, the authors first describe (from Roosendaal and Geurts) the required functions any system of scholarly communication:
* Registration, which allows claims of precedence for a scholarly finding.
* Certification, which establishes the validity of a registered scholarly claim.
* Awareness, which allows actors in the scholarly system to remain aware of new claims and findings.
* Archiving, which preserves the scholarly record over time.
* Rewarding, which rewards actors for their performance in the communication system based on metrics derived from that system.

The authors then try to show that it is possible to build a science communication system where all these functions are not centered in the journal, but are separated in different entities.

This would speed up science communication. There is a significant delay between submitting a communication and having it accessible to others because all the functions are centered in the journals and only after the certification (peer reviewing) is the work made available.

Separating the registration from the certification also has the potential benefit of exploring parallel certifications. The manuscripts deposited in the pre-print servers can be evaluated by the traditional peer-review process in journals but on top of this there is also the possibility of exploring other ways of certifying the work presented. The authors give the example of Citabase but also blog aggregation sites like Postgenomic could provide independent measures of the interest of a communication.

More generally and maybe going a bit of-topic, this reminded me of the correlation between modularity and complexity in biology. By dividing a process into separate and independent modules you allow for exploration of novelty without compromising the system. The process is still free to go from start to end in the traditional way but new subsystems can be created to compete with some of modules.

For me this discussion, is relevant for the whole scientific process , not just communication. New web technologies lower the costs of establishing collaborations and should therefore ease the recruitment of resources required to tackle a problem. Because people are better at different task it does make some sense to increase the modularity in the scientific process.

Monday, June 05, 2006

PLoS One

There is an article in Wired about open access in scientific publishing. It focuses on the efforts of the Public library of Science (PLoS) to make content freely available by transferring the costs of publication to the authors. What actually caught my attention was this little paragraph:

The success of the top two PLoS journals has led to the birth of four more modest ones aimed at specific fields: clinical trials, computational biology, genetics, and pathogens. And this summer, Varmus and his colleagues will launch PLoS One, a paperless journal that will publish online any paper that evaluators deem “scientifically legitimate.” Each article will generate a thread for comment and review. Great papers will be recognized by the discussion they generate, and bad ones will fade away.

The emphasis is mine. I went snooping around for the upcoming PLoS One and I found a page to subscribe to a mailing list. It has curious banner with a subtitle of open access 2.0.

I found some links in the source code that got me to the prototype webpage. It sounds exactly like what a lot of people have been pushing for: rapid scientific communication, community peer reviewing, continuous revision of the paper (they call it interactive papers) and open access. This will be hard to implement but if successful it will do much to bring more transparency to the scientific process and increase the cooperation between scientist.

There is also something about the name PLoS ONE. They are really betting a lot on this launch if they are calling it ONE. It implicitly states that ONE will be the flagship of PLoS, where any paper (not just Biology) can be published.