Around the Web - May 10, 2008
May 10, 2008
Linkfest
- NASA workshop on massively parallel supercomputers
- Aviary - I am out of accounts, but this is sweet
- NY Times - Pursuing the next level of AI
- McKinsey surveys the new software landscape
- Yahoo Design Pattern library
- hackystat - “A framework for collection, analysis, visualization, interpretation, annotation, and dissemination of software development process and product data”
- From the NY Times’ brilliant OSS blog - dbslayer (github repository)
- Erlang vs. MPI
Multimedia & Presentations
- Andrew’s presentation from XTech
- Is it time to throw away your servers
- Abstractions for handling large datasets
Blogspotting
- Greg Linden - This one is from the archives and for all of you interested in computer science, personalized search etc
Self Assembly
Once again, life is very hectic, so not much to report. Follow me on Friendfeed, twitter or check out the Tumblelog, where I am have been putting up some cool stuff lately
Around the web - May 4, 2008
May 4, 2008
It’s been a while, so will jump right into it.
Linkfest
- chip-ruby
- SEQanswers.com - Discussion forum for next gen sequencing (was down when I was writing this)
- In perpetual pursuit of context
- Open Metabolomics Data
- EquityEdit is an interesting organization. They edit and translate biomedical manuscripts and the compensation funds small, innovating, global health organizations (with a focus on the developing world, e.g. Nyaya Health). Don’t know too much about them, but the financial model is definitely interesting.
- WIkiPatents
- Interview with Paul Graham
- Subversion & Git
- Stagerat - a site for live music fans
- Data stores and BI
Multimedia & Presentations
- Bio2RDF do SPARQL
- Nodalities becomes a magazine
- Twitlive.tv - Watch out for what Leo is up to
- The stackoverflow podcast. This is a must listen. Can’t wait to see what the site turns out to be
Blogspotting
- Hypebot - A music 2.0 blog
Events
- BioBarCamp or ScienceBarCamp, regardless, there is a strong chance that prior to SciFoo 2008 we will be hosting a gathering of science geeks in the Bay Area
Self Assembly
Not much really. Had fun at Bio-IT World, which is the perfect conference for me, a place where I can combine work with subjects (and hardware) that really get me excited. Someday, Bio-IT World will be a mix of the current Bio-IT, Web 2.0 Expo and Gnomedex; a gathering of minds and industry folk.
I do have my macbook pro now and wishing I hadn’t taken the bad Windows/Dell detour late last year.
New business models for life science content
April 28, 2008
Let me start of by pointing everyone to the standard disclaimer.
Now to the good stuff. I have blogged about NextBio in the past. A couple of weeks about I was on the site and noticed that I could use the search engine without having to log in and get some pretty interesting results fast (well presented, well laid out, etc). I also registered and got an account for enhancements to the search experience. So when I got an advance copy of a press release announcing the formal public launch of the NextBio search engine. From the release
Using NextBio, any researcher or clinician can search the world’s public life sciences data and literature - over 10,000 experiments, 16 million articles, and literally billions of data points. Moreover, users can import their own experimental data into the NextBio search engine, share it with the community, and collaborate with others as never before
The release offers more details. There are over a billion data points, tens of thousands of study results and millions of scientific articles. There is a really neat autocomplete feature. Perhaps most importantly one can make correlations across six species, comparing animal models to human data.
Here are some screenshots. What I like most about the service is just the look and feel, very “Googley” if I might say.
For me the more interesting part is the business model. The NextBio model is essentially the freemium model that so many have advocated. They offer a quality free search engine, but revenues are going to be driven by commercial services, both hosted search and local installs. Transinsight, with GoPubMed, is doing something similar albeit not quite at this scale.
I like the direction life science content is taking. It’s only going to be better for science and for the companies working in this space
Hopefully I will get a chance to see the presentation tomorrow here at Bio-IT World. Check the site out, I would love to hear what all of you think.
Further readingh
Searching biological information at NextBio
Technorati Tags: NextBio, Search, Biological Content
Your personal health: The Personal Genome
April 24, 2008
Last evening, I had a chance to attend an interesing panel discussion on The Personal Genome. The Symposium featured Eric Lander, George Church, Leena Peltonen and Bill Gates and was moderated by Maynard Olson.
My take away from the discussion, which was fueled by questions submitted by the audience and via the web, was that there is so much uncertainty at this time. We know so much, yet so little. At some level, we do not understand the implications of what we know, ethical and medical, at the same time, we underestimate the ability of our own genetics to withstand changes.
Perhaps one of the things that jumped out at me was the general popular belief (which is hardly surprising) that it is a gene or a few genes that can be altered or fixed to address a “problem”. We’re just beginning to grasp the relevance of pathways, of epigenetics, etc, so the long term implications of what we know (and don’t) are still a little fuzzy.
I didn’t get a chance to record or take notes, but I was Twittering the whole thing. Unfortunately, I forgot to use a hashtag, which was silly. Much of the backchannel discussion was on the subject of designer babies. Leena Peltonen made some good points about the impact of genetic selection (we will not be able to alter germ lines), and whether it was desirable from the evolutionary perspective. George Church pointed out that people were going to do it anyway, much as they do today for sex selection or during IVF.
Bill Gates had an interesting opinion on the question of what a personal genome really means. He differentiated between an individual with money getting themselves genotyped or sequenced and between the ability to sequence individuals cheaply and in large quantities. The latter for him was much more important since it will help advance science and medicine. He is quite right of course, and it will be interesting to see how the ability to sequence individuals cheaply has an impact on research and clinical studies, where, in theory, in a few years it will be possible to just sequence everyone.
More on Sandra Porter’s blog
Image via Wikipedia
Technorati Tags: Personal Genomics, Personal Genetics, Ethics
Around the web - April 19, 2008
April 20, 2008
Linkfest
- I am sure there is something profound to be said about writing a gazillion books algorithmically, but it mostly escapes me
- Michael Barton riffs on Git and Github (and yes I have an account)
- Cascading is a large dataset build tool and a processing API for Hadoop
- Sun Microsystems has a Platform as a Service? Check out Project Caroline
- MetaBase - the place where life science databases go meta
- Papyrus, a student oriented feed reader
Multimedia
- Hadoop Summit - Tons of great material
- Social Graph Foo Camp videos - See previous
- Word for scientific publishing
Blogspotting
- Toby Segaran’s blog
- Venture Hacks - A long time favorite
Events
Self Assembly
Well, you’ve already heard about my appearance on Jon Udell’s podcast. Probably one of the highlights of recent times.
I’m still recording the bbgm daily on a nearly daily basis. We’ve also got a thriving bio community these days on Twitter and Friendfeed
