Around the web - March 29, 2008
March 30, 2008
Another weekly roundup. Spent a good chunk of the week in airplanes and airports, so a little leaner than usual
Linkfest
- Microformats university
- The Tetherless World Constellation
- Friendfeed grid
- ConceptNet NLP toolkit
- Stories on maps (via O’Reilly Radar)
- Dan Roam’s Back of the Napkin - Everything indicates that this is a must have
- The Human Network
Multimedia
- Cluster computing for the classroom (you don’t have to have Silverlight for this. At the bottom there are links for mp3 and WMA)
- Jim Hendler talks to Paul Miller. This is a great great interview I loved it
Blogspotting
- The all new ambermac.com. I quite like the new design and how video is incorporated
- Tom Morris - Tom’s Blog (it’s almost a Tumblelog) is a reflection of the man. I don’t know him, but after hearing him talk to Danny Ayers I’m a fan. Might not agree with everything he says, but I like those who call a spade to spade and not just based on rhetoric
Events
- XTech registration is open. Just check out the schedule featuring such luminaries as Alf Eaton and Andrew Walkingshaw
- O’Reilly’s Velocity conference. There is a trend on conferences looking at web infrastructure, including
- Structure ‘08
- Yuri’s Night is right around the corner
Self Assembly
Here is a list of some feeds you could subscribe to
- bbgm
- bbgm - comments
- Tumblelog
- Kyte channel
- Videos from bbgm
- and last but not the least, the bioscreencast blog
In my Wiki, I’ve been trying to pen down my strategy to become a hacker again. There is a lot to learn and time is always the enemy. What I’ve penned there is roughly how things are proceeding as we speak. The key decision was to try and limit technologies and focus on developing on top of the Talis Platform. It’s more of a true web platform, and I’ve taken a real liking to the people involved. It’s been really slow going, but last couple of weeks things have begun to pick up just a bit.
What if?
March 28, 2008
Source: WikipediaWhat if the result of every docking result was published online, with associated metadata link to protocol, scoring function/docking function, etc)? What if we could search across this entire space to try and come up with some conclusions? What if every docking result was an addressable resource?
Just the kinds of questions we need to ask ourselves if we ever want to understand how to bring web-scale to our science.
Technorati Tags: Docking, Web-scale computing, Collective Intelligence
We were a little ahead of our time but we didn’t know
March 27, 2008
Source: WikipediaMy first job was at a startup, a little structural bioinformatics company, that no longer exists. At the time, SaaS was not exactly a common model for companies to deliver content to their customers, but when I think about it, we were ideally positioned to do that.
The company was developed on top of technology to identify function based on low-resolution structural modeling. While that was cool in itself, I think where we excelled was the infrastructure that we developed for internal use. Access to all applications was via web services, with a well designed database architecture and excellent software development approaches. We also were fantastic at using ontologies and at addressing the often gnarly problem of ambiguity in public data sources (especially in those days). Not only that, we had a killer data center, and support from IBM and could have really pushed the envelope in providing services to the scientific community for function identification and very advanced annotation.
Would it have worked? I don’t know. Platform was a dirty word in those days, and SaaS was not an established delivery model, especially for life science content. There were of course other challenges, like the validity of the key technology, but with all else that was built around it, at least today, it would have been a compelling offering with. It would have been interesting to formulate what we were offering.
You know what we were missing … a product manager :).
Note: Trying out Zemanta. First impressions. It’s an interesting entity extraction plugin. I already use Operator and Gnosis, which are entity extraction plugins for published data. Smartlinks also fall into that category. While it makes me do the editing inside Wordpress, something I don’t usually do, I can see myself saving a post as a draft and then zemantifying the post at the end. It seems to do a decent job at the picture end, and finding links. From initial impressions not too bad. It will be interesting to see the kinds of sources and links that are recommended as Zemanta begins to use the linked data graph that will be generated from all the blogger using the plugin. So all you bioinformatics types, start using it.
Technorati Tags: SaaS, Bioinformatics, Business Model
EC2 makes some important changes
March 27, 2008
From an email I received earlier today about two new pieces of functionality for Amazon’s EC2 service
Elastic IP Addresses are static IP addresses designed for dynamic cloud computing, and now make it easy to host web sites, web services and other online applications in Amazon EC2. Elastic IP addresses are associated with your AWS account, not with your instances, and can be programmatically mapped to any of your instances. This allows you to easily recover from instance and other failures while presenting your users with a static IP address.
Availability Zones give you the ability to easily and inexpensively operate a highly available internet application. Each Amazon EC2 Availability Zone is a distinct location that is engineered to be insulated from failures in other Availability Zones. Previously, only very large companies had the scale to be able to distribute an application across multiple locations, but now it is as easy as changing a parameter in an API call. You can choose to run your application across multiple Availability Zones to be prepared for unexpected events such as power failures or network connectivity issues, or you can place instances in the same Availability Zone to take advantage of free data transfer and the lowest latency communication.
More details on the AWS blog. These pieces of functionality and the new kernel functionality really make EC2 a more viable alternative for SMBs and not just startups.
Somewhat related, I am eagerly awaiting the official launch of Assay Depot, since to my knowledge they are the first life science company that is really using AWS consciously as part of their strategy. I had a chance to speak with Chris from Assay Depot at SOT and was quite impressed by what they are doing and even more so by how they are doing it.
Further reading
O’Reilly Radar
Rightscale on Fault Tolerance and Elastic IPs
Technorati Tags: Amazon Web Services, EC2, Assay Depot
Your personal health: Crowdsourcing healthcare - Pitfalls and possibilities
March 25, 2008
Thomas Goetz writes a wonderful article in the NY Times about Practicing Patients, where he talks about PatientsLikeMe. Like Trusera and to a lesser extent iMedix, PatientsLikeMe allows people to connect with other people, learn from their experiences and make informed decisions about their health. I think by now all of us Google our health conditions, almost using the web as a second opinion. That’s mostly a good thing.
The reason I liked Thomas’ article is that he also points out some of the pitfalls. There is a lot of data, not all scrubbed for reliability, and tons of anecdotal information, not all of which can be processed and correlated by the human mind, even less so one not trained to look at those data. Are we going to be in a situation where we will essentially make our physicians lives miserables by constantly second guessing them, or will we end up in a situation where physicians keep on top of things because our own expectations are raised because of our own knowledge?
PatientsLikeMe is rather interesting since they taken a quantitative and analytical approach to the social health space and everyone knows I have a soft spot for quantitative analysis. Given that and the ability to compare dosages, etc (i.e. going beyong anecdotal information), I am very curious about long term statistics and what kind of data mining potential is there and what consumers think about that.
One thing is clear - the train has left the station. Whether it be personal genetics, or social health, our efforts must focus on consumer education, consumer privacy and perhaps most of all data ownership. Who owns the data? That is the most important question. As has been said before in these parts, we essentially need some sort of license for personal health information that establishes ownership with the person whom the data belongs to, i.e. you or I and who has access and under what circumstances. That’s where education comes in. We need access to a lot of patient information and genetic profiles for personalized medicine to be successful. So the health community and consumers need to work together to ensure that we can be successful scientifically and as a society.
The second aspect is the underlying data. Just from the healthcare perspective, and the quantitative approach taken by PatientsLikeMe only enables that, there is a lot of useful information that can be used to improve how we get treated. If we can figure out some of the issues described above, there is value here that goes beyond finding out what our peers think.
Further reading:
Thomas’ comments on the article
Open Access News
George Laszlo on Patient (Self) Recruitment
Technorati Tags: PatientsLikeMe, HealthCare, Personal Health
