Two years, a new year and a look ahead
December 31, 2007
It’s New Years Eve and bbgm just turned two in its incarnation as a self-hosted wordpress blog. By now you’ve all seen the new (and still in progress) design. It harks to bbgm being more of a website and not just a blog. I hope to write some informational content this year and doing specific video material that is a driver for the change. So what else can we expect in 2008?
For starters an emphasis on the three subjects shown on page one, specifically personalized medicine, the web as platform and open science/open data. I also hope to write more about molecular modeling and simulation and not just about informatics. Must of the focus will remain as before will the usual geeky stuff, but I want to try and do some more commentary around issues I have been thinking about for a long time and their relevance, commercially and socially.
One hope in 2008 is to start a weekly live broadcast, perhaps with a co-host, which will be available for offline viewing on bbgm.tv. Grand plans, but we’ll have to see what time permits.
That’s about it. Happy New Year folks and so keep reading and commenting. Here’s a short screencast pointing to various elements of the new design
Blog is back up - New theme, etc
December 30, 2007
Hi folks
As you may have noticed, I have a new theme up at bbgm, Revolution. Will take me a few days to work out the kinks, but as you can see, the blog now has a landing page with an emphasis on video and regular columns (the three topics I plan to stick to in 2008). In other words I am making bbgm a little less bloggy and more of a website. Should have everything up and running smoothly in a few days, but the feeds, etc should be working fine.
Comments, etc are always welcome on the new look. It’s quite a drastic change, but I do have plans down the road which fit this change.
See you in 2008
Blog upgrade in progress
December 30, 2007
Upgrading bbgm. Comments are turned off as well
A look back at 2007 and a peek into the future
December 24, 2007
This is probably my last blog post of the year. I had all these posts planned, but am going to defer them to the new year. December 31st will be the second birthday of bbgm, reflecting the day I moved the blog from Blogger to its own domain and decided to focus on science and technology. If you’d indulge me, I’d like to look back at some of the highlights of the year and reminisce a little.
The highlight of the year for me would the launch of Bioscreencast. I am the least active member of the Bioscreencast team, focusing any efforts on the blogging side of things, but as one of the few sites on the web marrying video, new media and science, Bioscreencast is a source of great pride. Of course, the real people who make it happen are Suresh, Hari, Geeta and Shailja, so all credit goes to them. Given that between us, we barely, if at all, have one full time person working on the site, it’s come a long long way.
At a personal level, the most memorable moment was getting invited to Scifoo. It was even better than I could have ever imagined. Not only did I get to spend time with some of the smartest, most creative minds in the world, but I met a number of people I had wanted to for a long time, and was able to make new connections and friends. It was a source of inspiration (yes I will start the project some day) and ideas. It was also the start of my entry into video, since it was at Scifoo that I started doing daily broadcasts on Kyte.tv.
Speaking of video, it’s probably been pretty obvious that it is a medium that I am increasingly fascinated by. While I still haven’t completely figured it out, over the past few months, I have been able to incorporate video into my blogging. Only a lack of time has prevented further incorporation of video. It’s probably been the biggest change in how I think about information and making it available. In my opinion, blogging as a medium is poised for its next push. A push where our content evolves from simple chronological text to multiple media types. We also have a lot of choices. Not everyone has to blog. Some use multiple forms of communication, blogs, tumblelogs, twitter, etc, others have the option of picking one. I still argue that if you have something meaningful to say, you should have an online presence, otherwise you are doing yourself no favors
Science also adopted video in 2007. While nowhere close to mainstream, the launch of SciVee and the increased visibility of sites like JoVE, DNAtube, etc make me believe that video is going to play an ever increasing role in science. It feels good to be part of that trend in a small way.
Switching gears to some topics that highlighted 2007. Personal Genetics, driven by high density SNP arrays and next-generation sequencing made a huge leap this year, with commercial consumer genetics companies hitting the market. If nothing else, the volumes of press and blog attention that 23andme, Navigenics, etc received this year gives us a hint of the promise, challenges and dangers of knowing a little bit of our own genetic makeup. I have a feeling that this subject is not going anywhere in 2008
The consumer is king and science is getting closer to the consumer. Healthcare search engines, healthcare networking sites and personalized health records were all hot topics in 2007. Healthcare search is one of the hotter areas in the field, with a number of companies making their move, including Google and Microsoft. In addition, you have a number of startups offering search engines or social networking capabilities, marrying the best of web 2.0 with our need for more information about our own health. The natural progression of this need is the personalized health record. While Google’s efforts are still mostly under wraps, Microsoft fired the first salvo, announcing HealthVault. The release probably left us with more questions than answers, but it is clear that the big boys see PHRs as big business. There will be a lot of policy and regulatory decisions over the next few years. How will these changes impact healthcare search, PHRs, consumer genomics, etc? We don’t know, but there will be an impact, that could alter business models and the success of some of these companies.
Computing made some major strides this past year. There are three companies that I would like to point to; Amazon, Google and Yahoo. A couple of years ago, Amazon made the decision to provide its computing resources to anyone who wanted to use them on a a utility basis, i.e. you pay as you go. Utility computing is not new as an idea, but this was one of the first examples of a consumer web company opening up its infrastructure. What made it work in the end was the adoption of Amazon’ web services by a legion of developers and startups, and it is clear by now that Amazon is making their web services group part of their business model as an enabler of startups. They’ve added to the offered services, funded startups and done a great job of capturing the imagination of developers everywhere. At Bioscreencast, we have adopted S3 and hope to add EC2 to the mix early next year.
The second company to acknowledge is Google. By now many people have realized that Google’s computing infrastructure is a huge competitive advantage, and the systems they have built on top of that infrastructure, like MapReduce and the Google File System are excellent examples of how large scale distributed computing can be deployed and leveraged. Along with Google, Yahoo has adopted distributed computing very visibly, championing Hadoop, which both Google and Yahoo are using for educational efforts targeted at training a generation of developers who know how to leverage lots of compute resources.
I end with something that most of this blogs readers are passionate about. If there was one recurring theme on this blog, especially in the first part of the year it was open science and open data. The need to make data available and the publishing process more transparent. If there is a reason I blog about open science less these days, there is a good reason; it’s in great shape and in good hands. We have a long way to go, but efforts from publishing houses like PLoS, scientists like Jean-Claude Bradley, Cameron Neylon, Peter Murray-Rust and Pedro Beltrao, etc are going the lead the way to what appears to be inevitable; an open scientific environment, with an emphasis on growing our scientific knowledge and a more transparent, vibrant environment. Perhaps the announcement of a Protocol for Implementing Open Access Data, something I called a monumental achievement, will be a catalyst in driving open science and open data access forward.
Looking Forward: What are we likely to see in 2008? Here are some topics I will be tracking
- The debate around consumer genomics and personal health records
- The continued evolution of open science and open data access
- Video in science and next-generation scientific communication
- Next-generation sequencing is going to have a huge impact on science over the next two years. Will we start seeing a tangible impact as early as 2008?
- Distributed computing and adoption in the sciences
- The changing landscape of the biopharma industry
- Molecular modeling has taken a step back in recent years. Will it make a comeback?
- Data pipelining and workflows
- The semantic web, meta-data and information management
- The web, life science and business models
You’ll see changes in BBGM, mostly around how content is presented, more screencasts and video, and some other potential ideas I have been playing around with. In the meantime I leave you with a list of my top 5 visited blog posts in 2007
- GFS, MapReduce and Hadoop
- SciVee.tv
- The Mythical WebOS
- Google and large scientific datasets
- Microsoft, Google and Healthcare
and the top 5 search keywords (not including my name, or the blogs name)
- gapminder
- scivee
- google healthcare
- 23andme
- protein simulation
and in the words of the immortal Bugs Bunny - That’s All Folks
Have a great 2008!!!
gopubmed: bringing pubmed and the semantic web together
December 22, 2007
I first noticed gopubmed when Berci mentioned it in a blog post a few days ago. It sort of fell off my radar until AltSearchEngines pointed to a new screencast explaining how the site is used.
My reaction was much the same as Berci’s. Wow!!!. gopubmed, developed by Transinsight in Germany, marries Pubmed to the semantic web to give you rich information about the searches you’ve performed, using a pretty neat interface. The interface does have its quirks, but it’s pretty slick and easy to understand.
Results are neatly organized by category dervived from MeSH terms and GO terms. You also get a list of top authors, top journals and date sorting, all in a very elegant navigation. All query terms also come with statistics, which can be very interesting on their own. The example below is one of the graphs from the statistics on the query “MM-PBSA”
All in all, I highly recommend the site. You get the Pubmed results you are used to, just with a lot more information content and in a more pleasing interface. There is an enterprise version as well which allows you to integrate patent searches and corporate intranets as well.
Technorati Tags: gopubmed, semantic web, search, life science
