30 November 2006

Social Network: Vidaeo

Vidaeo is the new name of the largest French social network previously known as Viaduc. The new site speaks English and is now open to everybody in the world. There are 623 members working in the sector of "Biotechnology".



Proteins@Home, a large-scale protein structure prediction project , is now open for beta-testing. Proteins@Home is based on BOINC, a program that lets you donate your idle computer time to science projects like SETI@home, Climateprediction.net, Rosetta@home, World Community Grid, and many others.

23 November 2006


Via : GO friends
OBO-Edit, the open source ontology editor written in Java. OBO-Edit is optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. It now has its own website! Visit http://www.oboedit.org for the central online resource for all things OBO-Edit.

21 November 2006

JAVA, multithread, k-means, clustering, OTMI.

K-means: A tutorial about the Java concurrency API posted on javaworld contains a java code about the k-means clustering algorithm which is an algorithm to cluster objects based on attributes into k partitions used in commonly used in bioinformatics.

OTMI: The Open Text Mining Interface (OTMI) was introduced on nascent a few monthes ago. OTMI aims to enable scientific, technical and medical (STM) publishers, among others, to disclose their full text for indexing and text-mining purposes but without giving it away in a form that is readily human-readable. There is now a wiki dedicated to OTMI at http://www.opentextmining.org/.

14 November 2006

UCSC Genome Browser wiki site launched

Via: Genome-announce.

The UCSC Genome Bioinformatics group has launched a wiki site for sharing
information about the UCSC Genome Browser and its data. The wiki -- at
http://genomewiki.ucsc.edu -- provides an informal forum for the browser users,
mirror sites, and staff to discuss topics of interest in the genome biology
field and exchange usage tips, scripts, programs, and notes about mirroring the
Genome Browser and working with the Genome Browser source.

09 November 2006

Photo tourism

Photo tourism is a system for browsing large collections of photographs in 3D. Amazing.

Noah Snavely, Steven M. Seitz, Richard Szeliski, "Photo tourism:Exploring photo collections in 3D," ACM Transactions on Graphics (SIGGRAPH Proceedings), 25(3), 2006, 835-846.

06 November 2006

State of the Blogosphere

Via Technorati.

On July 31, 2006, Technorati tracked its 50 millionth blog. The blogosphere that Technorati tracks continues to show significant growth. The blogosphere has been doubling in size every 6 months or so. It is over 100 times bigger than it was just 3 years ago....

03 November 2006

Soylent Green

Via : Science Mag:
Impacts of Biodiversity Loss on Ocean Ecosystem Services: Boris Worm & al.
(...).We analyzed local experiments, long-term regional time series, and global fisheries data to test how biodiversity loss affects marine ecosystem services across temporal and spatial scales. Overall, rates of resource collapse increased and recovery potential, stability, and water quality decreased exponentially with declining diversity. Restoration of biodiversity, in contrast, increased productivity fourfold and decreased variability by 21%, on average. We conclude that marine biodiversity loss is increasingly impairing the ocean's capacity to provide food, maintain water quality, and recover from perturbations. (...)

Conclusions. Positive relationships between diversity and ecosystem functions and services were found using experimental and correlative approaches along trajectories of diversity loss and recovery. Our data highlight the societal consequences of an ongoing erosion of diversity that appears to be accelerating on a global scale. This trend is of serious concern because it projects the global collapse of all taxa currently fished by the mid–21st century (based on the extrapolation of regression to 100% in the year 2048)(...).

02 November 2006


Via public-semweb-lifesci.
The Bio2RDF project is a tool to convert bioinformatics data and knowledge bases to RDF format. It is a kind of generalized rdfizer for bioinformatic application, and it is a place for the semantic web life science community to develope and grow. It is said to be optimized with a Firefox Search plugin and Simile Piggy Bank.


"XML, SQL, and C" by Jim Kent

Jim Kent the author of the BLAT algorithm has published an article in "Dr Dobb's Journal" (I guess you cannot find this via pubmed :-) ! ): XML, SQL, and C Tools for mapping between C and XML data structures, among other tasks. XML is an increasingly popular format for exchanging data. It handles optional fields and hierarchical data structures well, is readable by humans as well as computers, is portable across a wide variety of platforms, and it can even handle recursive data structures. In my own field of bioinformatics, XML has become almost as common as the venerable tab-separated file for exchanging information between databases. Still, integrating data from XML sources into our relational databases and our largely C code base sometimes seemed to involve more work than it should. Consequently, I was motivated to write the four tools—autoXml, AutoDtd, sqlToXml, and xmlToSql—presented in this article.


01 November 2006

Honey Bee Genome

Genomic Research has published a special issue about the honey bee genome.
There's also a Honey Bee Genome Focus in Nature.


PubMed as a Search Engine

Via PubMedNews.
PubMed is now available as a search engine add-on on the search bar in the upper-right corner of Firefox 2.0 and Internet Explorer 7.0. From a PubMed Web page, click the search box drop down arrow next to the default search engine Google, and then select Add PubMed search.