Computing in the cloud and science
September 30, 2007
I have previously written about 3Tera, a company provides other companies with an infrastructure for on-demand computing. Read/Write Web, which pointed me to 3Tera in the first place, has a new post about 3Tera getting into online gaming. However, it is the rest of the post that caught my attention.
Back in the day, we had to purchase supercomputing time and then run jobs till you ran out of your allocation. In todays world you can purchase time as you go along. Companies like 3Tera, Amazon, Google, Sun, IBM, etc have infrastructure that supports on demand computing. However, in the scientific world, we have not really started to take advantage of all these computing resources. Nor have we begun to look at the existing large scale computational infrastructure as an on demand cloud. In a way, this is somewhat curious, because buying supercomputing time was something a lot of groups routinely did in the past, and probably many do so even today. I wonder if anyone is writing “x hours of computing on EC2″ into their grants today. If nothing else, perhaps supercomputer centers should look at joining hands and offering on demand resources, at least if they have excess capacity (it might be that they don’t).
There is a golden opportunity here if the market does come about. I can see commercial software companies offering software services with “pay per use” licensing to customers, where they could leverage 3rd party hardware and other infrastructure resources. Will such an ecosystem ever come about? Only time will tell.
Further reading:
Computing in the cloud
IBM deep computing on demand for the life sciences
Picture courtesy Skimaniac via a Creative Commons license
Technorati Tags: On Demand Computing, 3Tera, EC2, IBM, Sun
Dr. Beltrao hosts Bio::Blogs #15
September 29, 2007
Pedro, who defended his Ph.D. recently is hosting the latest edition of Bio::Blogs. You have all weekend to get something in.
Technorati Tags: Bio::Blogs, Pedro Beltrao
Really cool video on silicon microchips
September 29, 2007
Via JoVE
I wish there was a way to embed the video into this page. Sangeeta Bhatia does really cool work in the bioengineering. I got interested in some of her work in regenerative medicine some time ago during my nanomedicine days (She was at UCSD at the time). This is an excellent example of how video can be used to showcase experimental/fabrication procedures.
Technorati Tags: Bioengineering, Cell-cell interactions, JoVE, Sangeeta Bhatia
The future of PLoS - Community and science
September 28, 2007
Following the release of PLoS One, the future of PLoS journals was always going to be interesting. Pedro, in a comment earlier this week, mentioned that new PLoS journals were unlikely. Well, I believe we have a pretty decent idea of where PLoS is going, following the announcement of the release of the PLoS Hub for Clinical Trials. What is it?
Launched in September 2007, the PLoS Hub for Clinical Trials collects PLoS journal articles that relate to clinical trials. The Hub is a destination site for researchers to share their views and build a dynamic, interactive community.
Currently, the PLoS Hub for Clinical Trials features articles originally published in PLoS Clinical Trials, along with clinical trials articles from PLoS ONE.
In the future, this new resource will expand to include articles from all the PLoS titles that publish clinical trials. It will also feature open-access articles from other journals plus user-generated content.
The new site is built on the Topaz platform, and therefore allows you to comment, annotate, rate, etc.
This is obviously not the last such hub (just note the url and menu options). I really like what PLoS is trying to do. By building communities around topics, aggregating information and providing a web-based platform for their activities, PLoS is pushing the envelope of online scientific publishing. I hope other publishers take note of the efforts of PLoS and Nature, which are streets ahead of the rest of the game.
I do have one request. Open ID/XFN support (the latter might already be there)!!!
Further reading
Nature Precedings
PLoS One
Topaz
Technorati Tags: PLoS, PLoS, PLoS Hub
Folding@home gets the Pirillo treatment
September 27, 2007
I remember when Folding@home first showed up around 7-8 years ago. Seti@home was all the rage at the time, but I really wanted to use my spare CPU cycles for my something that I really cared about, and Vijay Pande’s project was just the right balance between geek, cool, and my favorite scientific problem at the time. There have been many other interesting screensaver projects since then. The Berkeley Open Interface Network (BOINC) service on which Set@home now runs has a bunch of relevant projects, including Rosetta@home (running David Baker’s famous ab initio prediction program), and Predictor@home from Charlie Brooks. Others I have run at various time through the years are IBM’s World Community Grid, which includes a number of cool projects, and now defunct precursor of the World Community Grid that was a joint project of IBM, United Devices, Accelrys and others (Disclaimer: I used to work for Accelrys at the time).
Anyway, getting back to the title of the post. Essentially instead of writing a long response to Chris Pirillo’s broadcast on what he calls an “E-charity”, I figured I’d write something here. Chris asks “What other E-charities are you involved in? Do you believe the work these places are doing is above excellent and the wave of the future?”
I answered the first earlier. I have also been known to be skeptical of grid computing in pharma companies. However, I do believe that one day we will do a lot of computing in the cloud, and through grids. In the meantime, I agree wholeheartedly that screensaver projects like the ones described about are quite useful, as the success of Folding@home has shown.
Of course, since it’s Chris, I answer in kind
(Apologies for the screen reflection in my glasses and the low volume. Still not a video guru)
Technorati Tags: Grid Computing, Protein Folding, Folding@home, Protein Structure Prediction
