Tranche in the news: More wins for Open Data
May 2, 2008
Proteome Commons Tranche is one of the cooler resources on the web. Ever since I met Jayson Falkner, I have liked their approach to open data, and their early support for CC0. Looks like Tranche has hit the big time with the announcement that the resource has been chosen to host all mouse model proteomics data collected by the National Cancer Insititute. From the press release (which you can read in its entirety here).
The innovative scientific file sharing network and data repository, Tranche, has been chosen to host all Mouse Models proteomics data collected by the National Cancer Institute (NCI) Mouse Proteomic Technologies Initiative (MPTI) for public release.
In collaboration with Dr. Philip Andrews, University of Michigan, Department of Biological Chemistry and the Tranche team, the NCI MPTI project consortia deposited their mass spectrometry data sets into the Tranche data repository for storage and secure data sharing among participating research labs. See details about the MPTI projects below.
The mouse model data sets are already available on Tranche
Further reading
MPTI
Science Commons blog
Technorati Tags: Proteome Commons Tranche, Jayson Falkner, Open Data, Open Science, MPTI, NCI
Non-commercial research usage
April 2, 2008
I was just on the CAMERA site, a really nice resource for metagenomics. On the registration page you get the following text
By registering to use the CAMERA web site and associated services, you acknowledge that the genetic information available through the website may be considered to be part of the genetic patrimony of the country from which the sample was obtained, and that countries may claim intellectual property rights arising from commercial use of such data. It is your responsibility to familiarize yourself with these conditions. In general, countries place no restrictions on the use of the data available within CAMERA for non-commercial research purposes. To the extent possible, the CAMERA project will provide notice of those countries that impose conditions for commercial use. CAMERA is not in a position to assess the validity of such claims and, therefore, cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained within.
Now I understand that there are global treaties and the like in place here, but I want to use this example to illustrate something more general. The CAMERA data is raw data, in my book. In many cases such resources normally prohibit commercial use of the data. If we agree that raw data by itself powers discovery, but by itself has limited information, why are we limiting the commercial use of these data? Why can’t a group of people develop commercial apps based on data stored in resources? Yes the data could be acquired via public funding, but other than a few big companies, very few people other than the government have the resources to acquire such data.
I really wish that as a community we approached data differently. Yes there are gray areas and everyone must agree for this to work, but access to raw data should be made freely available and then we should let people run with it.
Technorati Tags: Open Data, CAMERA, Metagenomics
Nextgen sequencing adds another player
February 10, 2008
Pacific Biosciences joins the nextgen sequencing club, which is growing faster than I ever imagined and in a year or two is likely to go through another round of consolidation (following last years acquisitions of nextgen companies by some of the big boys).
I won’t comment too much about the viability of PacBio. It seems they are targeting the next generation of nextgen with a targeted release date of 2010. Will that be too late as George Church seems to think? The company has the money, with Kleiner Perkins being one of the investors. The differentiator seems to be the long read size. Can the company make the cost competitive? The speed? As nextgen moves to the mainstream, those are the questions that the company will need to address. As with any market, once price wars start companies need to differentiate themselves and try and lower cost. This is not the biggest market in the world so there is bound to be some stabilization (there are already way too many consumer genomics companies).
For more on Pacific Biosciences, read David Hamilton’s excellent analysis
The nextgen sequencing wars are just starting, both technologically and to find out who remains standing. Will be very interesting to return in five years time and see where we end up.
Please read this standard disclaimer
Technorati Tags: Nextgen Sequencing, Pacific Biosciences
Loic Le Meur with Linda Avey at Davos
January 25, 2008
Wanted to link to a post on Seesmic by Loic Le Meur, where he interviews chats with Linda Avey from 23andme
Technorati Tags: 23andme, Linda Avey, Loic Le Meur
Wallstrip on Illumina
January 13, 2008
I hadn’t visited Wallstrip for a while, but I have to share Lindsay’s over the top take on Illumina.
I always find watching and reading about Wall Street’s and the media’s take on the life science/genomics industry somewhat amusing. Folks there’s a lot more to Illumina than 23andme. That makes me wonder. How do investors end up making investment decisions, if they don’t really understand an industry?
Unfortunately, Lindsay is leaving Wallstrip for another CBS show. She was good. Let’s see how Wallstrip does without her.
