nodalpoint.org

Scientists usually share information with collaborators from all around the world. For that purpose, eyeOS (www.eyeos.org) provides an invaluable system to access and share documents, create and save data files or store crucial personal and professional information.

To see eyeOS widely used by scientists all around the world, we initiated the eyeLIMS project ! eyeLIMS is a community-driven project which aims at providing a Free, web-based, Open Source Laboratory Information Management System (LIMS) powered by eyeOS.

I've just got around to trying out Slideshare and I noticed a small collection of presentations under the bioinformatics tag - including several from the "usual suspects".

A suggestion: how about when Nodalpoint users upload to Slideshare, they include "nodalpoint" as a tag? That way we get to learn more about what everyone is working on. If you have pre-made presentations that you're willing to share, it's a quick and easy way for us all to get an idea of the collective expertise here.

I've put together a web site called http://bioguid.info which, rather grandly, is an attempt to bootstrap the biodiversity Semantic Web by providing resolvable URIs for biological objects, such as publications, taxonomic names, nucleotide sequences, and specimens. These URIs (or "GUIDs") can be resolved by a web browser to display HTML, but under the hood are resolved to RDF (which you can see by viewing the source of the web page you get for a URI).

I have been using the "user powered content" site Digg (any excuse at the moment to distract me from thesis writing) and I am enjoying the fact that the stories are coming to me with little effort, in other words I don't have to find the blog or site first and then subscribe. One of the "stories" that I found on Digg was an interview with Matthew Sparkes, Web Executive at New Scientist, about the effects of social media on online publications (i.e Digg). It highlights the increase in social media sites such as blogging and user driven content, on the traditional media and even the traditional content providers. It stops short of saying how New Scientist are going to deal with this phenomenon but they obviously recognise the importance and impact.

We just posted an overview document of our idea for a Gene Wiki at The Synaptic Leap

We encourage all folks at Nodal Point to come and add their comments. To maximize our feedback (the more the better), I have removed the login restrictions for comments for a brief period.

Thanks in advance for helping us out.
-Ginger

Tom Oinn, lead developer of the Open Source Taverna toolkit, has posted some (quite bad) pictures from SciFoo (Science Friends Of O'Reilly), which might be of interest. Some (much better) pictures of this Scifoo at the Googleplex can be found on Flickr.

I am back in Heidelberg after the weekend in the Googleplex in the Science Foo Camp. I missed the introduction to the meeting due to flight delays but you can read about it here and here. The schedule was set up on a board where anyone could write in a talk on one of the slots. There where up to 14 small and big rooms available at any time for anyone to set up a discussion.

I found the prototype page of the upcoming PLoS One. It goes by the subtitle of Open Access 2.0 and according to the webpage it will try to change a lot of things about science communication.

Later this year, PLoS will launch PLoS ONE.
* A peer-reviewed publication that publishes all rigorously performed science
* A vibrant online forum that encourages scientific dialogue and debate
* A "hassle-free" process that gets your work online within weeks

This is an announcement of a bioinformatics tool, published as freeware for the community.

Geneious is an easy-to-use, cross-platform (Windows, OS X, Unix) bioinformatics data analysis and visualization tool. It has an open API for writing plugins. You can use Geneious to compare genes from different species, to build an evolutionary tree to see how closely related they are, or to search for literature on any topic in medicine or biology. You can view and extract gene annotations from whole genomes, and interactive 3D graphics allow you to move around protein structures.

Version 1.0 of Geneious has just been published as freeware. Biomatters hopes that you will put the program to good use in your research, and we are eager to hear your comments and feedback.

Biomedcentral is arguably one of the more progressive online publishers, they have allowed reader comments on each published article for some time now. Recently I tried to track down a comment I made a while back and couldn't actually find a central comments page, so I emailed the support people and asked if they had or planed to implement an RSS feed for comments. At the time no, but now they have a comments page (amazingly Matt Cockerill, who is in charge of Biomedcentral, responded to the support request). Based on Biomedcentral's RSS page you should be able to access the RSS feed of the page by adding rss to the end of the link. This doesn't work at the moment, but I'm sure it will.