Utility computing, web applications and computational science
September 27, 2006
I forget the source that pointed me to this piece posted at Read/Write Web (all due apologies to the original poster) about 3Tera, a company based in California, that has developed a “disposable infrastructure” for on-demand computing. Specifically, the company’s product, AppLogic, has been positioned as a grid operating system. I must say that the product description page reads like a laundry list of information technology cliches, but reading between the lines this writer sees a framework that is targeted squarely at the SaaS market, and is positioned to take advantage of commoditized computing and virtualization (I can do cliches too) in a way that seems to make sense.
So why does this interest me? Bioinformatics, at least a good chunk of it, is evolving into a service industry. I use the term industry loosely, but strongly believe that tasks like sequence analysis, homology modeling, functional annotation and various database searches are best deployed using a web services model, whether that be freely available services or paid services. Using appropriate APIs, software developers should be able to plug their applications to query such databases for information. For many institutions and organizations, something like AppLogic should help them with high quality deployment. This should especially benefit content providers, and potentially metaservers, that run a number of tools to help researchers annotate sequences or build homology models, etc. I still feel that scientists are not quite taking advantage of some of the more recent developements in the information technology industry and hopefully applications like AppLogic will lower the barrier to entry for scientific developers.
As David Berlind said recently, and Read/Write Web notes, for most cases in the not too distant future computing will be outsourced by all but the biggest companies. With virtualization and deployment frameworks designed to make product deployment and access easier, companies like 3Tera definitely fill a space that is currently empty. A place between the Websphere’s of the world and do-it-yourself developers
Technorati Tags: 3Tera, Virtualization, Grid Computing, Bioinformatics, SaaS, Web Services, Scientific Computing, Software Development
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Things I noticed #7
September 24, 2006
Let’s kick off this week’s roundup with some good old computing
Much ado about APUs
Scalability.org has a number of posts on APUs (of which FPGAs are a subset). A couple of weeks ago, there was a post about some discussions the scalability folks had with VCs. More recently there was commentary on APU programming and a discussion on the APU market and possible success factors. As I have said before, I like the concept of accelerator cards, and the potential processing power they bring to the table. What makes me more circumspect are the various barriers to adoption, and the need (or realization of one) for APUs in the mainstream scientific computing market. I just feel that the way they are marketed is somewhat limiting. Vendors need to find applications that show a clear benefit and also ways to make code development a lot easier and scalable (the latter is an area where scalability.org is as good a resource as any)
The next 2.0
With all the 2.0’s around, I believe that some sort of compendium is required, so that the world can keep pace. Which is why a recent Bio-IT World headline entitled Revolution 2.0 made me chuckle a little bit. The article in question is about Gene Network Sciences, a biosimulation company with origins in Ithaca, NY. Regardless of the title, the article is an interesting read, and covers other players in the field, some of the different approaches, and the sheer challenges of being a company in the still young, albeit fascinating, field. I should send out a shout to the company that first attracted me to this field, Physiome Sciences (now part of Predix). Some of the original Physiome people now run the BioAnalytics Group
THe FDA under fire
When the Institute of Medicine rips the FDA, one has to to take the issue seriously, and the FDA is certainly taking the report seriously. I am sure there are some obvious things in the report, but in the long term everyone will benefit from patient, carefully thought out changes. I always worry about kneejerk, politically driven changes, which usually backfire badly.
The Tripoli Six
Normally I avoid politics like the plague, but Declan Butler’s article was the final straw. I just wanted to add my voice of support.
Technorati Tags: FPGA, Biosimulation, Tripoli Six, FDA, Drug Safety, Regulation, Scientific Computing, High Performance Computing
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The onslaught against scientific publication
September 20, 2006
Well not quite that, but it makes for a better headline. The scientific paper and the process of peer review as you and I have known all of our scientific lives is facing something of a grassroots revolt. The Scientist is carrying an article on the subject by Mark Gerstein and Michael Seringhaus, with an equally provocative title.
They argue that the science of today, with its mountains of data and ambitious scale, has outgrown the traditional scientific manuscript. Since scientific information today comes in multiple levels and in different guises, they believe that the paper is somewhat optional. Betraying their bioinformatics roots, they strongly favor databases and other repositories as sources of scientific information. In their opinion, the “paper” must be just one part of a submission, data deposition should be required and a unified nomenclature should be enforced. They go on to make numerous other suggestions, all leaning towards open and complete access of data, web-centric access and formats, and believe that a publication should be a living document with all its entities in complete sync.
In general I agree with them that the article model of scientific publication is somewhat outmoded. To me a paper should be concise, with a list of goals, methods, results and analysis. The supporting data and data analysis should be included and accessible online. The peer-review process is the other side of the coin, one that Seringhaus and Gerstein do not not discuss in significant detail, but the experiment currently underway at Nature has received more coverage lately, as noted by Timo, including an article in Wired. In the Pipeline also has an interesting take on the project. People should have the right to, within editorial guidelines, debate the authors, offer counterargments, etc. When a rebuttal, update or counteropinion is published, a web presence means that the reference should be directly to the original article. Hyperlinking would make life so much easier. I also think a wiki format is a great idea as instead of padding their paper count, researchers could publish updates right with the original paper. A mechanism I like is the online submission of a paper to a pre-print server. There the paper can be read, but not commented upon. The peer reviewer selection process should be random and from a database which would evolve with time. Following publication, the paper should be opened up for public debate. Seems like a good starting point at least.
Whatever the merits or demerits of the Nature efforts, the fact remains that it is a step in the right direction. Is it the right model? I don’t think its perfect. That will take time, but it will work itself out. Whether it is Nature or PLoS ONE, something will work out in the end. How quickly depends a lot on the community. Most people are happy being consumers and not participants.
Technorati Tags: Peer Review, Nature Magazine, PLoS ONE, Peer Review Debate, Scientific Publication, Communication
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Things I noticed #6
September 16, 2006
It has been a rather hectic two weeks, but the blogosphere is still here, so what better way to announce a return to the mainstream with a new, albeit brief, edition of Things I Noticed
IRIX … RIP
Scalability.org is one of my favorite blogs. Joe Landman is opinionated and knowledgable, a perfect combination for good blogging. He has a lot to say about the demise of SGI and recently he blogged about the company ending IRIX and MIPS. Back in the day IRIX used to be my favorite *NIX distribution. Very stable, easy to use, and oh the graphics. Come to think of it, I should have ackownledged the company in my dissertation, a lot of which was done on two trusty SGI Octanes. They were wonderful machines
Of course all good things come to an end. For various reasons, and Joe covers many of those issues in various posts, SGI was not able to keep up with the competition. The rise of Linux, faster x86 (and now X86-64) chips, and high quality graphics on other plaforms pretty much took the steam out of the company, and even diehards like me eventually moved to Linux (and some to OSX)
Science and Blogging
Nonoscience is another of my favorite blogs and this post on the role of blogs as a means of science communication is arguably the best one there yet. Science and blogging are still far removed from each other. While a number of scientists have adopted such tools as Connotea and del.icio.us, blogging as a scientific communication medium is a long way from mainstream adoption. The comments in the post are also worth a good read.
Wikis, education and texts
Wikis were around before Web 2.0 became the overused phrase it is. Now the University of Georgia is using Wikis to try and pool collective knowledge into a series of online textbooks. In a way, it’s a little ironic that a tried and tested format like Wikis are turning out to be one of the more successful mediums of communication and content development in the scientific community.
Mashup season
A really cool mashup of pubmed and postgenomic, and another mashup between pubmed and connotea, and it doesn’t end there. There is one between pubmed and citeulike as well.
Technorati Tags: SGI, Science Blogging, Blogging, Wiki, Education, Books, Mashups
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Finding my way back and a new blog carnival
September 14, 2006
This is going to be a month of fits and starts. Just as the pacific northwest decides to show its true colors (the past few days have been sunny, but the rain is finally here), this blog will soon be back to its regularly scheduled programming. In the interim, I leave you with a wonderful new blog carnival aimed squarely at the physical sciences. Inspired by Tangled Bank, Charles Daney has started (and is hosting) the carnival Philosophia Naturalis. I am pleased to see that one of my all time favorite posts made it there as well.
To learn more about the carnival and how to contribute, just read this
Technorati Tags: Blog Carnival, Physical Science, Science, Physics, Engineering, Mathematics, FEM, Protein Modeling
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