Integrating NGS data into clinical practice
Category Archives: Science 2.0
Science meets Web
Using the internet for open science
A few days ago, PLoS hosted a talk by Michael Nielsen at their San Francisco offices. Nielsen, author of the book “Reinventing discovery”, due late this year from Princeton Press, is a strong-voiced proponent of the need for a change in the way we share data.
The Polymath project, his opening story, is one of the best examples of how and why open science works. Tim Gowers, a Fields medalist, posted a famous mathematical problem on his blog, an open invitation to anyone interested to try their hand at solving it. For the first 70 hours, nothing happened. Then a math professor left a comment, quickly followed by a high school teacher, another Fields medalist and so on. In the span of 37 days, over 800 comments collectively solved the problem. How many conferences and scientific papers, peer reviews boards and editorial revisions would it have taken to even get these diverse minds thinking together in the same space? Nielsen describes it as the difference between “driving and pushing your car”.
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Merrily, We Tag Along…
By Anoop Grewal
The work of a curator never ends. Sometimes I anthropomorphize the raw data I’m about to work with, imagining it eating potato chips and lazing away on a couch in desperate need of conditioning. “Alright data, get ready for a little exercise,” I say and start it off with some stretching, or more accurately, assessing the quality of the data by examining the experimental design and sample annotations. Next on the program is weight lifting which consists of applying the appropriate statistical analyses to process the data. Don’t think we neglect aerobic activity! To this end, the NextBio Curation team runs each comparison through rigorous tagging by applying relevant biological labels. At this point, the resulting comparisons (now called biosets) are finally fit and ready to be imported to the NextBio platform where they can be scored against the thousands of other datasets.
The aerobics, or tagging of datasets with biomedical terms, goes a long way in helping us achieve our mission of rendering the huge volume of public domain data to formats that better serve the needs of all researchers. Typically experimental results are tagged with multiple biological concepts. For example, a leukemia study in which B-cell acute lymphoblastic leukemia is compared to acute myeloid leukemia using human blood samples would be tagged with the source tissue, peripheral blood mononuclear cells, as well as with the two diseases. And the terms used for tagging aren’t just any biological terms that come to mind. Rather they are derived from accredited biomedical vocabularies.
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Enhanced ScienceDirect Goes Live
- Lisa Green
Remember my blog post NextBio Elsevier Partnership telling you that Elsevier was going to use NextBio technology to enhance ScienceDirect? Well, the updated version of ScienceDirect went live yesterday and now you can see the enhancements for yourself!
ScienceDirect users who are logged into their account will now see a box titled “Relevant Terms extracted from this Article” beneath the familiar “Article Toolbox” box.
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The Four Musketeers
- Hope Leman
As I try to grasp the revolution in scientific and medial research that Science 2.0 and Medicine 2.0 are effecting I often find that I am literally being rendered sleepless by trying to keep up on the writings of the leading thinkers on the subject such as Cameron Neylon, Jean-Claude Bradley, Michael Nielsen and the new kid on the block, Steve Koch.
It is quite daunting to try to keep up with the many fascinating things they have to say and the many links they provide to their colleagues in the field such as Bill Hooker and Rich Apodaca (How I wish that the latter two would add “Follow me on Twitter” buttons to their blogs. They have fascinating things to say and I find that the best way by far to keep up with thinkers and doers is via Twitter. RSS is so 2006.)
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NextBio Elsevier Partnership
- Lisa Green
Last week the partnership between NextBio and Elsevier was officially announced!
Elsevier will be using our technology to enhance ScienceDirect. Elsevier is the biggest player in scientific publishing and ScienceDirect is used by millions of researchers. Their decision to incorporate our technology into their platform shows that they recognize the value of NextBio’s tools and we are very pleased to have the endorsement of such an influential company.
The new, enhanced ScienceDirect will utilize NextBio’s ontological framework so that users can search ScienceDirect’s literature along with publicly-available, experimental data, clinical trials, and news articles. There is a growing trend in the scientific community towards integrating multiple types of information. I believe that Elsevier’s decision to integrate literature, experimental data, clinical trials and news on the ScienceDirect platform is a big step in the right direction. Hopefully, we’ll soon see other vendors join the bandwagon.
The NextBio engineering team let me see a sneak peek of the enhanced ScienceDirect. Not to let the cat out of the bag, but there is a great interface that will let users easily navigate through the different types of content. You’ll be able to see the new ScienceDirect for yourself when it goes live later this summer!
Is it becoming dangerous to NOT blog?
- Jean-Claude Bradley
It wasn’t so long ago that the big discussion about scientists blogging was whether or not it would hurt your career. Granted, some the examples used involved personal content that would have been problematic on any platform. Still, many scientists chose to blog anonymously, even for the most uncontroversial scientific musings.
Recently I have noticed a change in the tone. The question doesn’t seem to be “Is blogging bad?” anymore but rather “Is blogging a waste of time?”. Often this involves the rather ironic situation of naysayers using a blog to express their opinion that blogging is a waste of time. There are many examples of this but a particularly controversial discussion took place on Nature Network recently.
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FriendFeed and Twitter
- Hope Leman
It is 5:10 a.m. I am working on a netbook in a hotel room in San Francisco. I am attending the Web 2.0 Expo and covering it for the blog AltSearchEngines. While I am attending that event, I have been invited to a dinner sponsored by Microsoft Live Search. Yesterday I attended sessions about Web site monitoring and about how to build online social communities.
All of these activities tie into the world of Science 2.0 and Open Science. For example, the presenter on the online social communities asked what we would leave disappointed about if it were not addressed. I immediately shouted out, “FriendFeed!” because the Science 2.0 and Life Scientists rooms of FriendFeed are fascinating venues for those of us interested in how science is being conducted in the age of Web 2.0.
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The Future of the Web
- Lisa Green
Recently, I watched Sir Timothy Berners-Lee’s TED talk The next Web of open, linked data . Berners-Lee is the inventor of the World Wide Web and the talk is extremely thought-provoking.
Today’s internet is something we frequently take for granted – as if we have always had the power to access a trillion hyperlinked documents. But listening to Berners-Lee makes you consider the time before the web was born. In the 1980s, Tim Berners-Lee was frustrated by the difficulty in unlocking the enormous potential of his lab’s data, methods, devices and protocols. He sought a way to easily share documents and link information and eventually came up with the idea of using the internet to link hypertext documents.
Notes From The Molecular Medicine Tri-Conference
- Lisa Green
On Friday I attended the Molecular Medicine Tri-Conference held in San Francisco. It was an exciting day of talks including the announcement of the transfer of a large amount of Merck data into the public domain through the new non-profit entity, Sage.
Many of the conference talks addressed the problem of accessing and connecting massive amounts of biological data, including the talk given by my colleague, NextBio cofounder Ilya Kupershmidt. I’ll readily admit I am biased – I think Ilya is the bee’s knees – but I thought Ilya did an exceptional job addressing these issues. He detailed the challenges of effectively leveraging the ever-increasing collection of biological data in a clear and logical manner and then went on to present a compelling approach.
While the last day of a conference generally tends to be fairly low energy, Ilya’s talk created an audible buzz and several enthusiastic conversations. It could be that the vaguely coffee-flavored beverage served by the conference center was actually some kind of GMO supercoffee, but my bet is that the energy was brewed up by Ilya’s talk.*
*My apologies to those who do not share my love of bad puns