Scifoo Lives On: Definitions in Open Science

I am having a quick look at the session Definition in Open Science, going on in Second Nature (I'm Duriel Akula in Second Life). The place looks very different from the first time I had a look around the island. It is full of posters and other interesting material. Here is a picture as some of the first people started gathering:


Live coverage of the event by Berci (also in the picture).

Bio::Blogs #14 - Update

The 14th edition of Bio::Blogs will be hosted by Ricardo at My Biotech Life. It will be made available on the 1st of September and submissions can be sent by email as mentioned in his blog post.

Update: The 14th edition is now posted at My Biotech Life. With all the deadlines I had this past month I left it almost until the end to organize a host. Thanks again to everyone that contributed on such short notice.

Is anyone interested in serving as host for the October edition ?

SciVee.tv background info

A while ago SciVee was announced via several blog posts. Here is a link to the first one I read by Deepak and a link to the cluster in Postgenomic.

I thought at first glance that this was a partnership between some small start-up and a content provider (PLoS). After browsing a couple of the videos I noticed that most are from papers authored by Philip E. Bourne. Given the connections to both PLoS and SDSC (two of the site's partners) I thought that this might be an academic effort after all.
A couple of searches tells us that abailey was responsible for a Scivee mailing list at SDCS that no longer exists. abailey apparently stands for Apryl Bailey, someone involved in the SDSC CI Channel, a "webcast video service and resource for the scientific communities" (from their about page).

Apryl Bailey also appears listed in the Scivee Team in one of the slides of a talk (PDF) that Philip Bourne gave in June this year. According to this recent news story it looks like the launch was actually premature and triggered by this talk:
"According to one founder, Philip Bourne of the University of California–San Diego (UCSD) and founding editor in chief of PLoS Computational Biology, he talked about the project at a scientific meeting and the buzz began prematurely."

It is an academic effort, probably related to this CI Channel mentioned above:
"The project began with some pilot pubcasts done at UCSD to test video formats and has involved the other PLoS editors. There are currently eight people on the SciVee team. The SDSC is providing the site hosting."

From one of the slides of the talk:
Developmental Phases
• Phase I (One Year) – Invite authors of papers published in PLoS journals to upload a video or podcast to SciVee.tv describing the motivation, key results and major conclusions of the published study. Establish linkage between literature and video – source of metadata etc. – September 2007

• Phase II (Years 2- 3) - Scrape PubMed on a daily basis and extend the invitation to authors of all papers in the life sciences; develop video authoring server; provide
ratings and virtual community comment

• Phase III (Year 4- ) - Extend to other scientific disciplines

The ephemeral journal

Recently I mentioned the start of yet another journal covering one of the topics I would place on the top of a hype cycle curve. This together with the apparent ever increasing number of journals everywhere got me thinking of birth/death of science journals. The cost of starting up a new journal is so low that the turn-over can only be higher. Still, we don't typically see a lot of "journal death". They are meant to be respected and built up reputation among the public audience they serve.
It looks however inevitable that with a limited attention capacity and ever increasing number of journals that science hype cycles might have a strong influence on a journals activities. If hyped up subjects sprout out new journals quickly (i.e stem cells, systems biology, synthetic biology), underperforming science memes will suffer from lack of attention. If I had a biomedical related science publishing house I would probably be thinking of launching a journal to cover metagenomics and another to cover personalized medicine.

Creating and destroying journals based on hype cycles sounds a bit exaggerated but at least there is no reason to think that a journal is here to stay. This can also happen via in a more subtle way, trough re-grouping of content after publication. Call it a gateway, a report, a topics page,a portal (harder to find), the idea is there are several ways one can group published papers to serve a target audience. Digital works are not things, they can be in several places and we can slice and dice the views as we wish. One great thing about these views is that they are more likely to attract discussion since there is more likely a group of people around with similar interests. This would be even more so if the users had some power to control the content. Nature Reports allow users to submit papers and to vote on them but it is still too soon to tell if discussions in topic pages are more frequent than on a site like PLoS ONE.

Instead of subscribing to the high impact journals, and lower impact journals of our topics of interest, we would state our interests in the views/portals/gateways we select to participate in and hopefully the works would be distributed to target audiences as fitting. Things that are of very high perceived impact would be cross-posted to many more views than more specific works. The value could still be perceived either pre or post publication.

The main advantage for the publisher is many more pages with well targeted audiences. Some of these views could even be of interest to a very wide non scientific audience. All of these should improve advertisement revenue.

Quotes

Another interesting SciView interview is available at Blind.Scientist. Here is one quote from Alexei Drummond (Chief Scientist of Biomatters) that I liked:

"I think that bioinformatics has to become a field where people without programming skills can contribute substantially. I would argue that all of the programmers in bioinformatics should be working very hard to program themselves out of their jobs (and into more satisfying jobs)."

Science advances quickly and so do the computational needs. Can we ever do away with these one off scripts if there are always new data types and innovative ways of analyzing them ? I guess the ideas around workflows and such could lead to very visual oriented programing that anyone can do.

First issue of IET Synthetic Biology

The first issue of (yet) another journal related to systems&synthetic biology is now online. IET Synthetic Biology will be freely available during this year. This issue covers several works from iGEM and the editorial is worth a read to have a look at the future direction of the journal.

In addition to conventional research and review articles, we see an important need for practical articles describing technical advances and innovative methods useful in synthetic biology. We will encourage submission of technical articles that might describe novel BioBrick components, construction techniques, characterisation of a new biological circuit, new software or a practical ‘hands-on’ guide to the construction of new instrumentation or a biological device.

In addition to the print journal, we are developing associated web resources. These will include a repository of online video resources, specialised review material and research tools for synthetic biology.

Some journals tracking similar fields:
Molecular Systems Biology
BMC Systems Biology
Systems and Synthetic Biology
HSFP Journal
IET Systems Biology

TwoThree new bioinformatic related blogs

A quick post to link out to two new bioinformatic related blogs:

Freelancing science (by Paweł Szczęsny)
Open.nfo (by Keith)

I will be happy the day there are too many to track :).

Updated: It could the official month of "start your own bioinformatics blog". The bio.struct blog is the third one so far.

SciFoo starts ...

and I am not there :). No fun ! The Science Foo Camp 2007 has started at Googleplex and there is already some blog coverage. To have a look at what is going on at camp here is a tip from Andrew Walkingshaw:

* http://www.lexical.org.uk/planetscifoo/ - participants’ blogs
* http://flickr.com/photos/tags/scifoo/ - photos
* http://www.technorati.com/tags/scifoo/ - general blogosphere commentary

There is also some live Twitter feeds from Deepak and Nat Torkington.

To start off go have a look at pictures posted by Bora, you might recognize one or two of these bloggers.

Maybe next year we can try to organize a Science Barcamp :) Why should they have all the fun.

Bio::Blogs#13

A great edition of the monthly Bio::Blogs is up at Neil's blog. This month there are plenty of tutorials and a round up of blog coverage about the ISMB/ECCB 2007 conference.

PDF version for offline reading of the editorial and highlighted posts is here and here (Box.net copy).

If someone wants to give it a try at editing future editions of Bio::Blogs let me know.

Speaking of community projects, the list of webservers published in that last NAR webserver edition are in this Nodalpoint wiki webpage. If you try one of these services spend a minute noting down if it was even available, if it worked well, etc.

Microattribution

(via Peter Suber) An editorial in Nature Genetics discusses the need to establish microatribution systems:
"When requiring authors to deposit data in public databases, journals, databases and funders should ensure that quantitative credit for the use of every data entry will accrue to the relevant members of the data-producing and annotating teams. In an era in which consortia are producing more (and more useful) papers than individuals and small groups, the careers of individuals are as much in need of specific credit as those of the scientific visionaries and wranglers who hold the consortia together."

This sounds great. From the journals point of view this would mean "encouraging" the authors to link to all resources used. This information would then need to be aggregated and made available to everyone. This and other measures would help to change the current credit system that tends to reward researchers for producing papers in high impact factor journals (that does not correlate with individual paper citations) instead of rewarding scientists for the usefulness of their research.

Bio::Blogs #13 call for submissions

Neil has kindly agreed to host the next edition of Bio::Blogs, due out on the first of August. Send in links to blog posts of bioinformatics/chemioinformatics/omics/open science related content to bioblogs at gmail and they will be re-directed to him.

Trade books vs Nature publishing

(via Richard Charkin blog) Richard Charkin is the Chief Executive of Macmillan (Nature Publishing is a subsidiary of Macmillan). He posted his thoughts on digital books are not as successful as the digital publishing going on at Nature.

I can't help noticing the second reason (my emphasis):

2. Scientific publishing has been intrinsically more profitable than trade book publishing. This allowed the major publishers and societies to invest the significant sums needed to create electronic delivery and storage platforms for scientific information. These platforms are a cornerstone for the creation of a new business and communication model.

and read it as "higher profit margins".

Google code for educators

(via the Google Blog) Google started a website to gather teaching materials for CS educators, covering some of the most recent technologies. Right now it has some material for AJAX Programming, Distributed Systems and Web Security. There are some video lectures and presentations. There is already some material on parallel programming (mostly related to their MapReduce) that should be of use to bioinformatics.

One a related topic Tiago has on his blog started a multipart series about "Bioinformatics, multi-core CPUs and grid computing". The first and second part are already available.

Slideshare adds voice

(via TechCrunch) Slideshare, a site to share presentations online has added voice synchronization. We can now provide a link to an mp3 file and Slideshare provides with some tools to sync the audio to the slides, such that each slide is linked to part of the audio track. More information and examples can be found in this FAQ page.

In related news, Bioscreencast has now a group in Facebook.

Another Open lab book

(Via Open Reading Frame) Jeremiah Faith is given open notebook science a try and compiling some tips. He joins Rosie Redfield (microbiology) and Jean-Claude Bradley (chemistry) in exposing most of their research online and leading the way to changing the mindset towards open science.

Jeremiah Faith also has an interesting idea about using conference money to pay for advertisement. He figures that well targeted ads can get you more attention than a talk. He like the idea because it is thinking out of box but I think that the type of connection that one can create on a conference with other people is not so easy to recreate online. Also, there might not be any need to spend money on advertisement if the blogs keeps on topic and is interesting enough to get incoming links. The blog can be a good personal marketing tool.

Early response to PLoS ratings

PLoS ONE pushed out a rating systems in the latest update of their website. I though it was another quiet update but several announcements are now up.

The technical details were described by Richard Cave and Chris Surridge invites everyone to "Rate Early, Rate Often". Bora (that now works for PLoS) summed it up in a blog post as well.

And just because they make it so easy to query the data, here goes the stats 3 days after the announcement:
Number of papers queried: 611
Number of papers rated: 47
Number of ratings: 50
Ratings: Average - 75%; Max - 100%; Min - 40%

Top rated papers (all with 100%)
10.1371/journal.pone.0000288 (rated by: brembs)
10.1371/journal.pone.0000354 (rated by: brembs)
10.1371/journal.pone.0000439 (rated by: brembs)
10.1371/journal.pone.0000349 (rated by: Complexity_Group)
10.1371/journal.pone.0000351 (rated by: crusio)
10.1371/journal.pone.0000455 (rated by: crusio)
10.1371/journal.pone.0000123 (rated by: Damien)
10.1371/journal.pone.0000224 (rated by: Damien)

Maybe in the long run it would be nice to know if the user that rated is also an author in the paper :), or put a comment in the ratings suggesting that authors are not very good at evaluating their own work.

Number of users that have rated: 24
Top 3 users:
Chris_Surridge
Complexity_Group
jstajich

The lowest rating so far:
10.1371/journal.pone.0000257 (rated by:godzikc)

There is no point in trying to conclude anything from this. It was just for the fun of it. If I could make a small wish it would be have a similar way to query for the accumulated number of page views or visitors for a given DOI.

Open-source architecture to house the world

Here is a very energetic talk (filmed in February 2006) by Cameron Sinclair hosted at TED talks. He is part of the Architecture for Humanity organization that promotes architectural and design solutions to global, social and humanitarian crises. A very inspiring example of how internet really makes the world small and how ideas like crowdsourcing and the open access to innovation can make a difference. The first time I heard about a creative commons house design.

They have started a project called Open Architecture Network to serve as hub for collaborative efforts.

What is the $value$ of an editorial decision ?

(warning: random thoughts ahead)

From my viewpoint open access is doing great. PLoS has demonstrated that authors want to publish in open access journals and that these journals can quickly establish themselves as high impact forums for their respective audiences. BMC is set to show that open access can be profitable and within BMC some journals are are also trying to position themselves in the top tier of perceived impact.

How will BMC manage this and will PLoS and others find a way to serve the authors interest while keeping the direct costs to the authors within reasonable ranges (even if they are paid by the funding bodies) ? I can't really answer this :) but I do note a trend. Open access publishers like PLoS and BMC are increasingly publishing more and decreasing the rejection rates (when considering all that is published within the brand).

BMC has primarily focused on publishing high volume (peer-reviewed) articles without regarding to much on perceived impact in the field. I might be incorrect but more recently they have been trying to highlight a group of flagship journals (BMC Biology, Genome Biology and Journal of Biology) where they filter on perceived impact. They have even said that papers submitted to other BMC journals can even be suggested "up" if they are found to be of high impact.

PLoS on the other hand had the the exact opposite direction. PLoS started with their flagship journals (PLoS Biology and later PLoS Medicine), then created the community journals (PLoS Genetics, Computational Biology and Pathogens) and now opened PLoS ONE that will not filter on perceived impact.

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.

Also, on closed publishers it is custom to be able to transition a manuscript with the peer-review comments from one journal to another of the same publisher. This practice is can be advantageous to everyone. saving the time of the another peer-review process.

Taking away the costs of editing and printing (online this can be very small) most of the costs of sustaining a science journal should mainly come from the editorial staff. So, what is the value of an editorial decision ? In other words, could there be freelance editors ? Could the editors be separated from the publisher ? Imagine I read a paper from a pre-print server, ask some people to peer-review (why would they?) and sell our evaluation to a journal.

Also, can a publisher sell the editorial decision to another publisher ? Lets imagine a journal that has a very high rejection rate, the editor asks referees for comments but ultimately the manuscript is rejected. The editor could then ask the authors where they want to send it next and offer to provide the referee report and editorial comments directly to the next journal to expedite the process. Could this journal get paid for this ?

User ratings in PLoS ONE

Another quiet update on the PLoS ONE interface. They have introduced an interface for user ratings. The overall rating can be seen in the right bar (when reading a paper on the site) and expanded to show a dissection into 3 categories: insight, reliability and style.

A click pops up a voting screen:



The nice detail is that we can query rating data by DOI. (example). It is not really an API, but the info is there and it is easily parsable. The PLoS ONE managing director, Chris Surridge, mentioned in the PLoS Facebook page, a couple of days ago that this change would be up soon.

Filtering papers on number of downloads

I was having a look at highly accessed papers for BMC Bioinformatics. In BMC, all journals have a page with the statistics of the most highly accessed papers of the last month. Several other journals now provide a similar service. The cool think about BMC is that they even tell you how many views per paper (sum of abstract, full text and PDF accesses on BioMed Central in the last 30 days). Not only that, the information in on the RSS feed they provide. That makes it very easy to feed into a pipe and have a threshold for number of views above which it will show up on the filtered feed.

Here is pipe example to filter out BMC Bioinformatic papers below 1000 views. The only problem is that the information is not stored as a number (example :"Number of accesses: 1226"). That is why I used a regular expression [1-9][0-9][0-9][0-9]$ instead of number filtering. I also don't know if the numbers are updated everyday .. but I hope so.

Even better would be to have some kind of service that given a DOI BMC would provide exactly this information structure. If other repositories provide a similar service then there is no point in worrying about the dilution in the number of page views because of open access because we could just sum views in the publishers site with Pubmed Central, etc.