Things I noticed #11

October 29, 2006

Todays edition of Things I Noticed is brought to you from the HUPO congress in Long Beach, CA. We kick off with a bit of an ode to open access. The new PLoS badge in the sidebar only re-affirms bbgm’s support of open access.

PLoS ONE is almost here

As Pedro announced the other day, PLoS ONE is will soon go live. The journal is a ” high-volume, efficient, and economical system for the publication of peer-reviewed research in all areas of science and medicine” and will utilize web 2.0 technologies extensively. For more you can always get it from the horses mouth. They have well over 200 submissions and an editorial board of 179 scientists. I, for one, can’t wait to see if the journal takes off. It is a unique approach to scientific publishing. While I still don’t quite understand where it fits in with all the other PLoS journals, it is a laudable effort, and as much as possible, I hope to participate.

HHMI hearts open access

In another sign that new open publishing models are gaining ground, HHMI is considering a plan that would make it mandatory (sub required) for its investigators to deposit papers in a public database within six months of publication, otherwise they would not count against the investigators renewal application.

Instant science

An interesting post out at Seed magazine talks about the impact of the blogosphere on the speed of science and any conclusions. With blogs and the aforementioned PLoS ONE around, the question arises. Is this a good thing? I think so.

Plagiarism in Indian science

Nonoscience is carrying a rant against questionable publishing ethics back in India. Sadly, I am not surprised. This is another area, as stated in the post where open source publishing might be a solution (not a panacea)

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Posted by Deepak Singh | Filed Under Admin, Life Science, Science, Software & Internet, Weekly Roundup 

I just “protein-ed” him

October 27, 2006

Imagine an excited postdoc telling his/her PI that they had just sent of a bunch of protein structures to a collaborator using a phone. That scenario is part of the goal for Greg Quinn and others at the mobile data visualization laboratory at the San Diego Supercomputing Center. A couple of years ago, someone (I don’t recall who it was) from the lab showed me a protein viewer running on a PDA. At the time I remember thinking about the utlity of such a viewerga, but today, I can certainly appreciate the value. The time is not far when laptops will not be a mandatory part of the traveling persons kit, but rather a lot of tasks will be handled using smart phones, PDAs and shared online services accessible from any computer, and being able to share scientific data using handhelds might just find some use (That said, I am still an ardent supporter of the laptop. I need the 15″ monitor). The funding for the project, formally the Mobile Life Sciences Platform, came by way of Microsoft, which is definitely making a push into the Life Science area. The pilot project is focussed on the co-resident Protein Data Bank. It will be very interesting to see how the project can be extended to other data types. Structures have their unique challenges, but looking at complex statistical analysis on a small screen probably has a completely different set of challenges that will take some very smart people a good chunk of time to figure out. Currently, version 1.0 is schedule for a second quarter, 2007 release.

I am curious if some day, a crystallographer at a cyclotron somewhere will be able to use a handheld to collect data and send it off to a cluster or grid somewhere and then view the data when it has been crunched.  I can certainly see medicinal chemists with PDAs looking up compounds and perhaps even publications on handhelds. Only time will tell.

Source: Bioinform

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Posted by Deepak Singh | Filed Under BioIT, Innovation, Life Science, Science, Software & Internet, Technology 

Google custom search

October 23, 2006

Google announced a brand new custom search engine today. I have one set up for bioinformatics/computational biology related searches at my favorite sites. Still a work in progress, but feel free to give it a try. It’s also visible on my sidebar

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Posted by Deepak Singh | Filed Under Off Topic 

BioIT needs to re-invent itself on the fly

October 22, 2006

Microsoft just announced a whole new bunch of new participants for its BioIT alliance and a second proof-of-concept project, this one focused on biomarkers. The announcement got me thinking about the future of BioIT, at least in the medium to long term.

While the volume of data available today seems unmanageable, it is nothing compared to the disparate types and gargantuan volumes of data that will be available faster than most people probably realize. Data will be generated by a number of sourced, including all kinds of omics research, patient records, clinical trials and other sources that I probably can’t even think of right now. An emphasis on pharmacovigilance and a general acceptance of translational medicine will result in the need to correlate data from the most basic of research to the impact of drug treatments several years into a treatment regimen. This means a fundamental change in how we approach data itself. The fact is that even today, cheminformatics and bioinformatics are quite poorly integrated and people pursuing either activity tend to stay in their own silos. Even more challenging is the lack of integration between bioinformatics and medical informatics. As the emphasis of research moves towards understanding systems, these data will need to be readily available and understood not just by expert informaticians, but by clinicians and bench scientists alike. The electronic healthcare system is not yet a reality, but steps in that direction are being taken.

If I were a CIO at a pharmaceutical or healthcare company, my concerns would be to try and build an infrastructure that is ready to adapt as the needs of the users and regulatory industry evolve. On the flip side, vendors (software and hardware) and scientists need to continue to work together to develop appropriate standards. I still feel that the W3C should be involved at some level, since they have shown the ability to maintain and propogate a standard that is more widely used than genomic data ever will be.

Virtualization might be an overused buzzword in IT circles, but its a good one. For most applications, assuming security and privacy are maintained, does it matter where a calculation or search is carried out? In a perfect world, the end user should be concerned only with what he/she needs. Everyone should have access to the same types of data (with varying levels of access). Proprietary data should have the same format as more widely accessible data, making it easy for licensed content to be distributed and accessed. How the data are made available should be dependent on the context. In other words, the clinician and the basic researcher in a biotech company might query the same data source, and might even run similar queries, but what they see might be different as each has different goals. Compute power is no longer the bottleneck in achieving these goals. The bottlenecks and challenges lie in network speeds, security, accessibility and of course building an onotology for all aspects of healthcare, beginning from the genome all the way to patient data.

Which brings us back to the CIO. Contrary to popular perception, the role of information services in the future of healthcare is going to be absolutely critical. The efficiency of entire healthcare networks might depend on how effect information services are. The role of the life science community should be to make their lives a little bit easier.

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Posted by Deepak Singh | Filed Under Admin, BioIT, Business, Computing, Healthcare, Informatics, Infotech, Innovation, Life Science, Omics, Science, Software & Internet, Technology 

Things I noticed #10

October 21, 2006

I can’t believe that I actually made it to edition #10 of Things I Noticed, but here we are. It was actually quite a busy week, but most of what I wanted to bring to attention are things I want to write some additional commentary on, so keep watching this space.

The “new” postgenomic

Postgenomic.com has a new look and I believe a new codebase. I definitely like the new look. The site has not quite become the techmeme of the science world, but I think it can get there (in the limited world of science bloggers).

… as does techbizmedia

Techbizmedia.com, a site that I occasionally contribute to also has a nice new look, and some new contributors.  Keep an eye on things.  I have a feeling the site is going to take off.

Microsoft refreshes the BioIT Alliance

The rougly year old BioIT alliance announced new members and a second project, one focussed on biomarker identification and validation.

The Omics World is back

Hari has been off the blogosphere for a while, but he promises he’s back.

Now this is a lab

First seen on Neil Saunders’ blog was a post about the Redfield lab. Not only does the website have some panache, but everyone has a blog. Wonderful!!!

The bio::blogs icon challenge

I have no capabilities as a graphic designer, so I am going to pass, but Pedro would welcome some help.

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Posted by Deepak Singh | Filed Under BioIT, Blog, Life Science, Omics, Weekly Roundup 

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