Profilactic Mashup - neilfws

Last.fm: The Damned – Lively Arts

Fri, 04 Jul 2008 14:51:02 GMT

http://www.last.fm/music/The+Damned

twitter: having weird flashbacks to 1980

Fri, 04 Jul 2008 13:26:49 GMT

neilfws: having weird flashbacks to 1980

Google Reader: Collaborating for breakthroughs

Fri, 04 Jul 2008 11:33:52 GMT

Over at the FasterCures blog, Margaret Anderson, the organization’s Chief Operating Officer, has a post on the recent Institute of Medicine forum: Breakthrough Business Models: Drug Development for Rare and Neglected Diseases and Individualized Therapies. Anderson, who moderated a panel at the forum, observes that while the Michael J. Fox Foundation is often cited as an example of what’s working well, surprisingly few research foundations embrace its innovative approaches. Key among them: pursuing collaborations with for-profit companies.

The focus of the forum was on finding new models for drug development, and many speakers echoed Anderson in emphasizing the need for more public-private collaboration. Our own Kaitlin Thaney was there, and spoke with fellow participants about our newest project, the Health Commons. The project, launched in collaboration with CommerceNet, CollabRx and the Public Library of Science (PLoS), is designed specifically to lift barriers to collaborations among non-profit and for-profit entities.

“In the Health Commons, participants agree to share data, knowledge, materials and services under standard, pre-negotiated terms and conditions,” explains Thaney. “That way, resources can move smoothly among participants, without the legal wrangling and delays that can derail collaboration.”

One of the most troublesome areas, for foundations and companies alike, is materials transfer. On the panel that Anderson moderated, Michael Mowatt, who directs the Office of Technology Development at the National Institute of Allergy and Infectious Diseases, NIH, described how using standardized agreements and repositories can facilitate collaboration, and explained how our Biological Materials Transfer Agreement (MTA) project lays the groundwork for “virtual repositories” of biological materials.

You can find more information about the MTA project here. If you’d like to learn more about the Health Commons, you can check out the white paper or video introduction at the project site. And if you’d like more details on the IOM forum, you can find the agenda and a collection of audio recordings and slides at the IOM forum website.

Technorati Reactions: Collaborative Intelligence for Biomed

Fri, 04 Jul 2008 08:26:34 GMT

and will/should be developed in the next few months. By the way, I seize the opportunity to give a link to my personal page. Pubmed API This little known API is open, free, and very useful. It is well explained in the NCBI Handbook. I read on another blog post a nice script to get all the chapters of the NCBI Handbook and make just one nice pdf book of them. Read my comments on that post to update the proposed script. Keep on reading, have fun!

twitter: just noticed you can drag tracks in latest gbrowse - cool!

Fri, 04 Jul 2008 05:54:56 GMT

neilfws: just noticed you can drag tracks in latest gbrowse - cool!

Google Reader: Badger cull proposals rejected

Fri, 04 Jul 2008 05:31:32 GMT

Shared by neilfws
I should think so, too.

The government has decided against a cull of badgers to control TB in English cattle, the BBC understands.

twitter: is it wrong that the phrase "independence day" just makes me think of the whitehouse exploding in the movie of same name?

Fri, 04 Jul 2008 04:30:10 GMT

neilfws: is it wrong that the phrase "independence day" just makes me think of the whitehouse exploding in the movie of same name?

twitter: complete algorithmic brain freeze

Fri, 04 Jul 2008 03:12:36 GMT

neilfws: complete algorithmic brain freeze

twitter: hey look, twitter came back up; thought friendfeed was oddly quiet

Fri, 04 Jul 2008 02:33:52 GMT

neilfws: hey look, twitter came back up; thought friendfeed was oddly quiet

del.icio.us: Bertrand Russell - Wikiquote

Fri, 04 Jul 2008 01:08:35 GMT

CiteULike: Taxonomic distribution of large DNA viruses in the sea

Thu, 03 Jul 2008 23:30:16 GMT

Genome Biology, Vol. 9, No. 7. (2008)

BACKGROUND:Viruses are ubiquitous and the most abundant biological entities in marine environments. Metagenomics studies are increasingly revealing the huge genetic diversity of marine viruses. In this study, we used a new approach - "phylogenetic mapping" - to obtain a comprehensive picture of the taxonomic distribution of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition metagenomic data set.RESULTS:Using DNA polymerase genes as a taxonomic marker, we identified 811 homologous sequences of likely viral origins. As expected, most of these sequences corresponded to phages. Interestingly, the second largest viral group corresponded to the one containing mimivirus and three related algal viruses. We also identified several DNA polymerase homologs closely related to Asfarviridae, a viral family poorly represented among isolated viruses and until now limited to terrestrial animal hosts. Finally, our approach allowed the identification of a new combination of genes in "viral-like" sequences.CONCLUSIONS:Albeit only recently discovered, giant viruses of the Mimiviridae family appear to constitute a diverse, quantitatively important and ubiquitous component of the population of large eukaryotic DNA viruses in the sea.

CiteULike: Deducing topology of protein-protein interaction networks from experimentally measured sub-networks

Thu, 03 Jul 2008 23:29:09 GMT

BMC Bioinformatics, Vol. 9, No. 1. (2008)

BACKGROUND:Protein-protein interaction networks are commonly sampled using yeast two hybrid approaches. However, whether topological information reaped from these experimentally-measured sub-networks can be extrapolated to complete protein-protein interaction networks is unclear.RESULTS:By analyzing various experimental protein-protein interaction datasets, we found that they are not random samples of the parent networks. Based on the experimental bait-prey behaviors, our computer simulations show that these non-random sampling features may affect the topological information. We tested the hypothesis that a core sub-network exists within the experimentally sampled network that better maintains the topological characteristics of the parent protein-protein interaction network. We developed a method to filter the experimentally sampled network to result in a core sub-network that more accurately reflects the topology of the parent network. These findings have fundamental implications for large-scale protein interaction studies and for our understanding of the behavior of cellular networks.CONCLUSIONS:The topological information from experimental measured networks network as is may not be the correct source for topological information about the parent protein-protein interaction network. We define a core sub-network that more accurately reflects the topology of the parent network.

Google Reader: [REPORTS] Phylogenetic Signal in the Eukaryotic Tree of Life

Thu, 03 Jul 2008 23:26:24 GMT

Shared by neilfws
One for Jonathan :)

A survey of sequences in GenBank, which represent about 10 percent of described species, shows that the patchy distribution of data is insufficient to build a eukaryotic tree of life.

Author: Michael J. Sanderson

twitter: buggered; and again, failed to make ISMB plans; tomorrow

Thu, 03 Jul 2008 13:44:25 GMT

neilfws: buggered; and again, failed to make ISMB plans; tomorrow

twitter: wondering if presence of gbrowse track keys can be made conditional on presence of feature in GFF

Thu, 03 Jul 2008 13:39:22 GMT

neilfws: wondering if presence of gbrowse track keys can be made conditional on presence of feature in GFF

del.icio.us: Australian Art - Home

Thu, 03 Jul 2008 13:12:53 GMT

twitter: @Berci And you got wiki and web2.0 in the title - nice work

Thu, 03 Jul 2008 13:08:51 GMT

neilfws: @Berci And you got wiki and web2.0 in the title - nice work

del.icio.us: Picture Australia

Thu, 03 Jul 2008 13:03:03 GMT

twitter: love how our local building site park their cranes in formation

Thu, 03 Jul 2008 12:46:47 GMT

neilfws: love how our local building site park their cranes in formation

twitter: @mza What I'm doing right now

Thu, 03 Jul 2008 12:39:52 GMT

neilfws: @mza What I'm doing right now