(via Notes from the biomass) EMBL is organizing the 1st PhD online symposium (4-8 December). It will be fully online, available for free to anyone. Participants can register to participate in the discussions and watch the presentations when they are made available. The users can create pages to share posters, talks or anything that might be relevant to the conference. In all, it could be a good playground to try out new ideas for online conferences. We could ask Nature to broadcast it in Nature island inside second life ? :)
Register, create your pages, share some thoughts. The topics are: Career Development Omics Session / Systems Biology Scientific Communication 2.0
What is a scientific journal ? One possible definition could be - a content provider that filters and selects scientific content appropriate (of interest) to a particular group of people. Currently, journals select papers based on the decisions of a small group of people, maybe one or two editors supported by a few referees. The internet allows for alternative methods to select and filter content based potentially on the knowledge of a larger group of people. Eventually, these methods might one day replace the expansive editorial procedures now in place in most journals, but before that happens these approaches have to be evaluated. Also, even if we don't use these methods to replace current editorial procedures, they can be used to help us highlight the most interesting works published in certain fields.
So, why not consider tags in social bookmarking services like Connotea as scientific journals ? Here is the journal Connotea tag:evolution. I took from Connotea yesterday (21/11/2006) all papers tagged with the tag "evolution" , that were published in 2003 or 2004 (85 papers). I used the web of science to get the number of citations of each of these papers (see figure below). This was unfortunately done one by one. I am thinking of scripting some tool to do it automatically but if someone knows a better way please let me know.
As expected the most represented journals are some of the journals with higher visibility but still more than 50% of the manuscripts were tagged from more specialized journals.
So how does the average number of citations per paper of this "new journal" compare with well established journals ?
Although Connotea Evolution is low volume compared to other journals it does have a higher average citation per paper than journals such as Nature and Science. I did not separate potential non citable items from any of the groups so it should be a reasonable fair comparison.
I think this suggests that we should evaluate potential mechanism to guide us to interesting scientific content. By itself, these evaluations might establish a form of reward for the community to come up with more sophisticated tools. It is important therefore to carefully pick the measurements. I used the citations per paper but others might be more adequate.
Any group of people can use the internet to re-group scientific content (specially if it is open access) into "journals" of potentially more value than those currently available.
I only noticed today BMC also had a Systems Biology journal. There are no papers yet but the editorial board looks interesting enough. From the types of articles they expect I think they will take a lot of bioinformatics related manuscripts. This adds to two other Systems Biology journals that I am aware of: Molecular Systems Biology (also open access) and IET Systems Biology.
(via BioHacking) On a more creative note, here is the Journal of Visualized Experiments. It is a "journal" of recorded experiments that should help others learn protocols with the aid of videos. Currently the submissions are subjected only to editorial evaluation and are expected to get published in about 14 days. They plan to apply for listing in PubMed and other databases. The videos are accompanied by a very short written explanation and are tagged for searching. There are no comments or RSS features that I could see.
With this continuing expansion of journals in all publishing houses aren't we quickly reaching a point when manuscripts will be the scarce resource ? I really hope someone develops nicer tools to suggest communications to read based on my interests. Is there a place for researchers whose job is just to associate and shuttle communications around ? Tagging communications as FOR_SMITH_J to show up in some reader with a comment: "solves your problem X".
As part of the OpenWetWare's Seminar Series on Open Science, here is Chris Surridge explaining PLoS ONE. Some random things I remember: - No-one reads full table of contents anymore so why not create a journal with broad scope ? (I do read full table of contents of many journals, it's the first thing I do in the morning) - They are aiming at a very high volume (hundreds of manuscripts) - The journal will probably have portals for subject areas - Anyone is free to reuse the open access content, so anyone could in theory be an editor by reusing open access content and focusing it for a particular target audience. - They might also pool in papers from other open access journals - There will be probably a karma system to rate the contributions - The system of having different versions of the same manuscript will not be on the first version of the journal. - The journal might be up on the 29th of this month (not sure yet) - Chris Surridge moves around too much :)
The Bork group published recently a revised tree of life in Science. You can have a better look at the tree using this nice interactive tree viewer that they put up on the web (publication).
You can zoom in and out, re-root, swap branches, and export the trees. You can also upload your own trees and annotations to have them drawn by the viewer. Hovering over the species brings up a box with some information. Did you ever wonder who donated DNA for the human sequencing project ? The Bork group has found out for us:
Go have a look at the PLoS websites, they have been redesigned. I like the look but the only notable changes are a box "From the Blogosphere" that currently links to the Open Access News blog (I wonder why:) and a link to "Readers Respond" on the left, that should put more emphasis on user participation. The PLoS Medicine site has some notable differences. First they include the PLoS Medicine blog on the home page and the "From the Blogosphere" links to a Guardian article. I guess that these are customizable and left to the editors to use to point out interesting things related to the journal or field. Now ... when will PLoS Comp Bio start a blog ? Still no journal is taking in blog comments. It would be easy to use Postgenomic's index or trackbacks to let readers comments papers trough their blogs.
There is also an editorial in PLoS Biology about PLoS ONE: "ONE for All: The Next Step for PLoS" The only new thing I got from the editorial was the concept of portals withing PLoS ONE. I would say it sounds a bit like the Nature Gateways, an area for the aggregation of papers and other resources related to a particular field or project. Sounds like a good idea. Again, they mention that at the start it will look like any other journal and that they will build on it in time, so I don't expect much in the launch day.
Greg has volunteered to host the 6th edition of Bio:Blogs at Nodalpoint (half a year already). It should take place on the 1st of December. Anyone that wants to participate just has to point out an interesting bioinformatics related blog post by email to the usual bioblogs _at_ gmail _dot_ com.
Some links: (via postgenomic and Clinical Cases and Images) The Lancet started a blog (creatively called The Lancet blog) . If it funny that some of the oldest journals are testing new ideas in publishing leaving some of the more recent ones lagging behind.
Here is another bioinformatics related blog. From a research associate at Newcastle University, interested in neuroscience.
Fallowing the tip from Deepak I decided to give MeeboMe a try here in the blog. Fell free to interrupt my thesis writing :) by writing something there on the box.
Several years ago I read a book by Nicholas Negroponte entitled "Being Digital". It was a really great introduction to the digital revolution and provided with a glimpse to some of the changes that are still ongoing in our society. I find fascinating the ability that some technologies have to change so much our ways of living, opening up with a simple stroke so many new possibilities. The digital revolution was one of these events. An apparently simple concept of having information coded in a digital format that can be transported anywhere at near instantaneous speeds. Now we have the internet that as provided with so many wonderful advantages. I can learn anything I want, provided I have time. I can collaborate with people I have never even met before to build new things. It is difficult even for me to imagine living in an unwired world (but that might be a bit geeky thing to say :).
I read today this profile on Neil Gershenfeld and his work on home manufacturing at MIT and I though that this would also be a very empowering technology. He is pushing the concept of personal fabrication, enabling anyone to easily create any physical thing. He wants to bring the same speed to making atoms that we have today for bits. You could grab a funny chair design that you made in your computer, send it to your friends by email and they would open it .. very literally by "printing" it and sitting on it to try it out. I guess there are lots of details to think about, but generally the idea sounds fun.
I was thinking that some companies should have a go at this already. I am not really into design but I guess that several companies today focus on constantly renewing their stock with new designs and trend setting ideas. Why not have an Ikea section of "do your own" furniture. Something like social web manufacturing of clothes, accessories, furniture, etc.
Also, why not have collection of the most used objects in Second Life, built every quarter or half a year. Second Life authors would have to agree and probably negotiate a cut of the profit. Here is someone building a guitar :)
Where is the print button to get one of those right now?
A blog post by Ian Hughes on home fabrication. A wiki page fab@home with instructions to make "fabbers", machines that can make almost anything, right on your desktop.
A paper published online in PNAS described a possible new form of regulation of gene expression by small RNAs. The authors found that small dsRNAs can also serve as transcriptional activators. They showed that the mechanism for gene expression activation also prefers dsRNAs of ~21 nt in size and requires the Argonaute 2 protein.
The story was covered by a news article in Science. From the news article it looks like there is some fear that the result might be due to indirect effects (inactivation of other genes leading to gene expression activation). Also, some wonder why this as not been picked up before by other studies.
I am very tempted right now to get some of the high-throughput screens of RNAi to try dig out some more examples that might have gone unnoticed (if I actually had any time to do it :).
The November edition of our bioinformatics blog journal is up at Chris' blog. This edition is mostly focused on potencially interesting tools to use, including Zotero, a bibliography manager Firefox extension and Bioclipse, an open-source workbench for bio/chemi-informatics.
I forgot to ask Chris to link to the bio::blogs icon challenge. I guess we can run it for another month. If you don't like thesetwo icons and you think you can do better give it a try :) until next month.
We are in need of a volunteer to host the December edition. If you run a bioinformatics related blog and are interested send in a link to your blog to bioblogs at gmail.com or leave a comment below.
