A virtual symposium
November 29, 2006
Found this wonderful thread over at Postgenomic about the First Online EMBL PhD Symposium, which looks quite interesting. I will be on the road when it starts but hopefully will find some time to attend, since pretty much every session is right up the personal interest alley. Speakers include Roland and Leroy Hood. I quite liked Pedro’s suggestion of holding the conference at the Nature Island in Second Life. Would be great if we could do this over some form of Skypecast or something along those lines
Update: The organizers keep an eye on the blogosphere (surprise surprise!!). Following Pedro’s suggestion, there will be a session at the Nature island on Second Life
Technorati Tags: Virtual Conference, Symposium, Leroy Hood, EMBL
Genomic patents
November 26, 2006
Omics Omics recently added some very pertinent commentary on gene patents. The post is a response to an article published in Parade. Keith points out that the article carries several factual errors, such as statements by Michael Crichton on the percentage of genes that have been patented. I am not fond of the IP policies in the us, both for software and scientific knowledge. I believe, rather strongly, that the system is flawed, and the number of flawed patents is too numerous.
However, taking the kind of alarmist view that the Parade article does, serves no useful purpose. What is important is to have a rational dialog in the community and with regulatory agencies to try and understand what kind of IP protection really aids innovation, and what is socially and ethically appropriate. I am probably on the side of those who think that genes should not be patentable, but then, that is a very grey area. Should knowledge of the gene and its implication in disease, as it relates to a specific treatment mechanism be protected? I think so. After all that is intellectual pursuit. It’s broad-based, non-specific patents that I have issues with. This is a debate that’s only going to return to the fore as genomic medicine becomes reality.
Technorati Tags: Intellectual Property, Genomics, Genes, Patents, PTO
IT and research - A clash of cultures
November 26, 2006
BioIT world pointed me to a Computerworld story entitled Cultures Clash as IT Takes Control of Research Systems. The headline alone was enough to garner my interest and the story touched on an interesting subject. One of the subjects that Joe Landman and I have been covering in recent months has been the phenomenon of accelerated computing and such products and Windows Compute Cluster Server. The goal of these products is to bring superior computing into the hands of individuals or small workgroups. The story in computerworld goes in the opposite direction and talks about how the expansion of high performance computing (HPC) systems into organizations is bringing computing resources more into the control of IT groups, leading to some interesting problems. I believe this topic came up at the recent SC06 meeting. It would be interesting to hear from someone who was there.
HPC is definitely going mainstream. Perhaps it is the failing of the HPC community that there still remains a barrier to deployment and maintenance that makes it necessary to have a significant amount of specialized IT involvement. Having worked with some great IT groups in the past, I can appreciate the importance of great IT managers. After all as a researcher or algorithm developer, the last thing one wants to worry about is the maintenance of HPC infrastructure. What is needed however is more accessibility for researchers and more flexibility within IT groups. Research by its very nature cannot be very rigid, and in a fast changing world, sometimes operating systems and other features need to be changed rapidly and not always in a stable environment.
Personally, I think some of the problems, such as the one described by Goran Pocina can be avoided. This is where accelerated computing can make a huge difference. By deploying cheaper, easier to maintain accelerated systems at the departmental level, or even virtualized blade centers, and larger, centralized resources for large scale projects and heavy duty number crunching. I also see another issue. Many IT departments are meant to manage standardized solutions (desktop PCs and workstations, networking, backup, etc). HPC is a different beast, and access to cheaper hardware brings the problem right to the forefront.
Sharan Kalwani has it right. Many IT groups are bureaucracies, and too many companies look at IT as part of business solutions, not as a route to innovation. Hopefully this is a temporary problem caused by access to HPC systems becoming less of a privilege than it was just a few years ago.
Further Reading
“Accelerated Computing” - The floodgates
Drinking the Koolaid
Technorati Tags: High Performance Computing, Information Technology
Software tools - A question to the blogosphere
November 26, 2006
I suspect that many of the readers of this blog are more aware than I am of the tools of the web development trade, so I am posting this public question.
I want to get really serious about website design, and plan to develop a site that incorporate widgets, RSS feeds, rich media elements (e.g. flash). At this point of time, I am completely text editor based. What development environment would people suggest for XHTML/CSS/PHP/AJAX/Rails development? I am still not sure of the final direction, but it will be within that realm. Obviously, I am no pro, but I would like an extensible environment that can grow as my knowledge grows.
My first instinct is Eclipse, but there is also the possibility of using the Adobe/Macromedia Studio 8 bundle, which I would rather avoid if I could. Anything other suggestions?
Update: I am pretty much set on going with Eclipse at this time. It just fits my way of working, or so it seems.
We are back, but not quite fully functional
November 25, 2006
The blog has been moved over, but there are some issues that need to be resolved, so for now, comments are off and I am using the default wordpress theme. Updates to follow. I might keep posting.
Update: Comments are back on. Hopefully things will be smooth from here.
