During ISMB, thanks to Shirley Wu (FF announcement), there was an improvised BoF (Birds of a Feather) session on web tools for scientists. Given that the meeting was not really announced we were not really expecting a full room. I would say that we had around 20 to 30 people that sayed at least for a while. We talked in general about tools that are useful in science (things like online reference managers, pre-print archives, community wikis, FriendFeed, Second Life) and we also talked a bit about the culture of sharing and open science.
Curiosly, the most interesting discussion I had about open science was not at this BoF session but after it. In the following day the subject come up again in a conversation between me and tree other people (two PhD students and a PI from a different lab). I will not identify the people because I don't know if they would like that or not. The most striking thing for me about this conversation was the somewhat instinctive negative reaction against open science from the part of the two PhD students. After a long discussion they made a few interesting arguments that I will mention below but what was strange for me was that this is the first time I see someone react instinctively in a negative way against the concepts of open science.
One of the students in particular was arguing that the fact that scientists sharing their results online (prior to peer review) is not only silly on their part (the scooping argument) but it would be detrimental to science as a whole. The most concrete argument he offered was that seeing someone "stake claim" to a research problem might scare other people away from even trying to solve it. I would say that it would be better to have people collaborating on the same research problems instead of the current scenario where a lot of scientists waste years (of their time and resources) working in parallel without even knowing about it. He argues simply that some people might not want to collaborate at all and should be allowed to work in this way. I don't think scientists should be forced to put their work online before peer-review, I just happen to think that this would improve collaborations and decrease the current waste or resources.
The second argument against sharing of research ideas and results prior to peer review was more consensual. They all mention the problem of noise and how it is already difficult to find relevant results in the peer reviewed literature. They suggest that this problem would be further increased if more people were to share their ideas and results online. I fully agree that this is a problem but not related at all with open science. This is a sorting/filtering problem that is already important today with the large increase in journals and published articles. We do need better recommendation and filtering tools but sharing ideas and results in blogs/wikis/online project management tools is not going to seriously increase the noise since these are all very easily separated from peer-reviewed articles. No-one is forced to track shared projects, but if they are available it would make it that much easier to start a collaboration when and if it makes sense to do so. Are open source repositories detrimental to the software industry ?
It took around 3 years since people started discussing the idea of open science and open notebooks for these concepts to get some attention. It is inevitable (and healthy) that as more people are exposed to a meme that more counter-arguments emerge. I guess that a backlash only means that the meme is spreading.
Sunday, July 27, 2008
Thursday, July 17, 2008
ISMB 2008
I am leaving soon to Toronto to attend ISMB 2008. I usually stay way from big conferences since typically in small conferences is easier to really have time to talk to everyone. The nice thing about attending a big conference is that it looks like everyone is there. There is no shortage of science bloggers attending and it is going to be nice to get to know the people behind some of the blogs for the first time.
There is a room in FriendFeed were several people attending are gathered and for those not going it will probably be a good place to check for coverage of the conference. Alternatively here is a list of bloggers that are attending ISMB or some of the conferences before/after it:
Saturday, July 05, 2008
On the PLoS business model
Declan Butler wrote a news article about PLoS' business model that has generates a lot of discussion. A good summary of blog reactions is available from Bora's blog and there is a long thread of discussions at FriendFeed.
It is hard to read the piece as impartial reporting due to the general negative undertone. Describing PLoS ONE as a database and referring to PLoS ONE and other PLoS journals of lower impact as "bulk, cheap publishing of lower quality papers". I have nothing against the factual content in the news piece. From that perspective it is an interesting report on the PLoS business model. According to the news story PLoS is on track to become economically self-sustainable within two years. We learn that this is possible due to the expansion of PLoS as a publisher to cover a broader range of subjects and different degrees of perceived impact. This is hardly surprising. I wrote a year ago:
"On an author pays model, the most obvious way to limit the cost per paper and still provide a solid evaluation of perceived impact, is to have journals that cover the broad spectrum of perceived impact. In this way, for the publisher, the overall rejection rates decrease, the papers are evaluated and directed to the appropriate "level" of perceived impact."
Most people agree that in principle Open Access publishing would benefit science. Up until know publishers have been reluctant to admit that there is a viable business model with author fees. Some open access publishers (including BioMedCentral) were already showing that this was a viable business model but PLoS will be the first to have viable business model with high impact factor journals within the set of journals they publish.
Two of the most interesting comments on this discussion so far have come from Timo Hannay at Nascent and from Lars Juhljensen
Timo argues that PLoS has failed to show that it is possible to have a business model for a publisher that only has journals of high editorial input (high rejection rates and high perceived impact). Also, the existence of PLoS creates a barrier to entry to other science publishers interested in publishing with an open access (OA) model. There is no argument against the first statement, so far I have not seen any publisher that has managed to reduce the costs of maintaining such "high impact" journals to the point were authors fees would be sufficient. I think this is possible and the PLoS Community journals are the closest form of this but this is another discussion.
What I disagree with Timo is that PLoS somehow creates barriers to entry to other OA publishers. PLoS did require (still requires) philanthropic grants to establish themselves but pioneers have typically a harder time than creative followers. Anyone trying to follow PLoS has access to the records of success and failures, detailed financial reports and (I think) even the publishing infrastructure that they have developed.
Most people know that the strongest barrier to entry to scientific publishing is a perception of quality. NPG has used this fact to their advantage many times. Journals with Nature brand typically establish themselves quickly among the top of their topic. I am sure Nature invests a lot in excellent professional editors but without the Nature brand supporting these journals there would be nothing to choose from to start with. NPG also publishes many more journals than the Nature branded journals and as Lars has pointed out the majority of these have lower impact factors. I don't think there is financial information available so it is hard to know what is the fraction of NPG's income that comes from the high impact or lower impact journals.
Going back to one of Timo's main points, I don't agree that PLoS creates barriers to market entry to other OA publishers. At least certainly not because they used philanthropic grants until they reached break even point. If there are barriers in the market they are due to perception of quality and strong brand name. Here OA publishers have the added advantage that creating a strong brand is easier when most people perceive OA as something good. From the example of PLoS and to some extent BMC there are now clear paths for any publisher (specially one with a strong brand name) to set up a viable business OA model.
It is hard to read the piece as impartial reporting due to the general negative undertone. Describing PLoS ONE as a database and referring to PLoS ONE and other PLoS journals of lower impact as "bulk, cheap publishing of lower quality papers". I have nothing against the factual content in the news piece. From that perspective it is an interesting report on the PLoS business model. According to the news story PLoS is on track to become economically self-sustainable within two years. We learn that this is possible due to the expansion of PLoS as a publisher to cover a broader range of subjects and different degrees of perceived impact. This is hardly surprising. I wrote a year ago:
"On an author pays model, the most obvious way to limit the cost per paper and still provide a solid evaluation of perceived impact, is to have journals that cover the broad spectrum of perceived impact. In this way, for the publisher, the overall rejection rates decrease, the papers are evaluated and directed to the appropriate "level" of perceived impact."
Most people agree that in principle Open Access publishing would benefit science. Up until know publishers have been reluctant to admit that there is a viable business model with author fees. Some open access publishers (including BioMedCentral) were already showing that this was a viable business model but PLoS will be the first to have viable business model with high impact factor journals within the set of journals they publish.
Two of the most interesting comments on this discussion so far have come from Timo Hannay at Nascent and from Lars Juhljensen
Timo argues that PLoS has failed to show that it is possible to have a business model for a publisher that only has journals of high editorial input (high rejection rates and high perceived impact). Also, the existence of PLoS creates a barrier to entry to other science publishers interested in publishing with an open access (OA) model. There is no argument against the first statement, so far I have not seen any publisher that has managed to reduce the costs of maintaining such "high impact" journals to the point were authors fees would be sufficient. I think this is possible and the PLoS Community journals are the closest form of this but this is another discussion.
What I disagree with Timo is that PLoS somehow creates barriers to entry to other OA publishers. PLoS did require (still requires) philanthropic grants to establish themselves but pioneers have typically a harder time than creative followers. Anyone trying to follow PLoS has access to the records of success and failures, detailed financial reports and (I think) even the publishing infrastructure that they have developed.
Most people know that the strongest barrier to entry to scientific publishing is a perception of quality. NPG has used this fact to their advantage many times. Journals with Nature brand typically establish themselves quickly among the top of their topic. I am sure Nature invests a lot in excellent professional editors but without the Nature brand supporting these journals there would be nothing to choose from to start with. NPG also publishes many more journals than the Nature branded journals and as Lars has pointed out the majority of these have lower impact factors. I don't think there is financial information available so it is hard to know what is the fraction of NPG's income that comes from the high impact or lower impact journals.
Going back to one of Timo's main points, I don't agree that PLoS creates barriers to market entry to other OA publishers. At least certainly not because they used philanthropic grants until they reached break even point. If there are barriers in the market they are due to perception of quality and strong brand name. Here OA publishers have the added advantage that creating a strong brand is easier when most people perceive OA as something good. From the example of PLoS and to some extent BMC there are now clear paths for any publisher (specially one with a strong brand name) to set up a viable business OA model.
Tuesday, July 01, 2008
Bioinformatics around the globe
Did you ever wanted to have a global impression of the field of bioinformatics ? What types of tools they used, or how different is the work in academia versus industry ? Michael Barton from Bioinformatics Zen created a survey that will be running for the next month (until the 1st of August) that tries to address some of these questions. The more people complete the survey, the more informative the picture will be. The survey is anonymous and all information will be made available for those interested in analyzing it.
If you have a blog you can re-post it on your blog (see intructions here) or send a link to any of these blog pages that host the survey to other bioinformatic/computational biology researchers.
If you have a blog you can re-post it on your blog (see intructions here) or send a link to any of these blog pages that host the survey to other bioinformatic/computational biology researchers.
Subscribe to:
Posts (Atom)