MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'business|bytes|genes|molecules' source. Wed, 19 Nov 2008 22:41:01 +0100 http://feedproxy.google.com/~r/mndoci/~3/vCvMtY5Vjt8/ I am sitting at RDU airport, waiting for my plane to board heading back to the Pacific Northwest for a day before heading out to Supercomputing 08. Yesterday was a blast. Chris Lasher and Co pulled out the red carpet and were wonderful hosts. I was also able to take part in some very interesting discussions on everything from cloud computing to social networks with graduate students and faculty alike. I really have no idea how the talk went. It was a new talk, something I hope to extend over the coming months as I spend more time fleshing out this idea that big science, data-driven science needs to be built upon collective intelligence on the fabric of the World Wide Web. But the discussion afterwards and later at dinner, etc convince me that there is hope as the grad students of today get... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1960824 Sat, 15 Nov 2008 10:06:52 +0100 1960824 http://feedproxy.google.com/~r/mndoci/~3/sDz-EwWfF9Q/ The first attempt at distilling some of my thoughts on Big Data and the Networked Future of Science. Thanks to Chris Lasher for the invite to speak at VA Tech. I had fun, although in my jetlagged, uber-caffeinated state I spoke at 200 mph Science Big, Science Connected View SlideShare presentation or Upload your own. (tags: science science2.0) (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1960825 Fri, 14 Nov 2008 22:17:31 +0100 1960825 http://feedproxy.google.com/~r/mndoci/~3/nXKC6L1tVPg/ Dropped the latest podcast earlier today. Heavy discussion around the Saunders principle and the tension between bioinformaticians and bench scientists (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1960826 Thu, 13 Nov 2008 00:40:34 +0100 1960826 http://feedproxy.google.com/~r/mndoci/~3/t-m_eJ4liSY/ Looks like Allen Roses has a boutique consultancy focussed on pharmacogenetics. For those who don’t know Allen Roses, he is a former head of genetics research at GlaxoSmithKline and Director of Duke University’s Deane Drug Discovery Institute. The latter came to my attention when I saw an article on PGx Reporter (might require a sub) about the Drug Discovery Institute which called the institute a new model designed to fill the void between academic drug discovery and translational medicine. The whole idea of a virtual pharma has been floated around by different people under different guises and something I’ve alluded to often over time, but I definitely liked the mindset behind Roses’ thinking. The idea is to build a think tank with knowledge of every step of the drug d... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1960827 Wed, 12 Nov 2008 02:17:48 +0100 1960827 http://feedproxy.google.com/~r/mndoci/~3/Y7ALURwZraI/ On episode 28 the Stack Overlow podcast Joel Spolsky talked about something Adam Bosworth mentioned to him after Bosworth moved from Microsoft to Google. Apparently Bosworth said something along the lines of “Google uses Bayesian filters like Microsoft uses the IF statement”. The discussion went on to discuss how that mentality allows Google to always think in the mindset where they know that there are a million things being returned from search, but these are the ten that the person might be looking for. That got me thinking about life science search. When we are looking for a paper, or some scientific topic, what are we looking for? What do we expect back? The challenge here is context. The same query under different contexts might/should return different results. In the abs... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947272 Tue, 11 Nov 2008 04:51:07 +0100 1947272 http://feedproxy.google.com/~r/mndoci/~3/wAAwvPMEChQ/ Programmable Web is now tracking 1000 APIs in it’s directory. That’s quite an achievement. The blog post specifically points to a number of APIs considered disruptive, including APIs from ebay, Amazon (including Amazon Web Services), Google Maps API, Twitter, etc. Recent APIs like the ones from the New York times only point to the importance of allowing people to use data or functionality from one source in all kinds of new contexts. Programmable Web tracks a few life science APIs (under the Medical category) It’s a small number and missing some for sure. What I see missing are APIs from Nature, Elsevier, PLoS, etc. Also missing are APIs to tools, not just data sources. Wonder why not? Related articles by Zemanta Let A Thousand Web APIs Blossom (Source: business|bytes|g... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947273 Mon, 10 Nov 2008 00:18:25 +0100 1947273 http://feedproxy.google.com/~r/mndoci/~3/ugJtSUgvJsQ/ I’ve always liked , especially the interface and the distributed service driven model. But this is nothing to do with that. They have an iPhone app I already use the Molecules app on the iPhone and recently saw someone launch a sequence alignment job on EC2 from an iphone. I think the day of using mobile devices as part of regular scientific workflows is not that far away. (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947274 Sat, 08 Nov 2008 21:03:26 +0100 1947274 http://feedproxy.google.com/~r/mndoci/~3/oO9a1yYs-JI/ Next week, I head to Virgina Tech to give a talk as part of the Genetics, Bioinformatics and Computational Biology (GBCB) guest lecture series. I think Chris Lasher needs a stern talking to about his speaker choices, but it gets me to talk science so can’t really complain. The topic of my talk is Science Big. Science Connected. I am still working through the slides, but the talk is an extension of many of the things I talk about here at bbgm. In my head that is best represented as Big data and the networked future of science But that’s not what I wanted to really talk about. The best part about the whole thing is the flyer that Chris and Co came up with. click to see full version They used my delicious feed to build a tag cloud using Wordle. The results are wonderful and give ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947275 Sat, 08 Nov 2008 20:44:42 +0100 1947275 http://feedproxy.google.com/~r/mndoci/~3/CSawukl9BX4/ The current meme seems to be data to rule them all A bunch of blog posts out there discussing the importance of data, all pretty much screaming out for the importance of open data. First a couple of posts on Nodalities. In A data-centric view, Zach Beauvais talks about a rather fascinating blog post over at Flickr, where they have used the vast amount of geotagged data to generate mostly accurate contours for various places. The part that Zach homes in on the fact that the folks at Flickr didn’t go around planning this project. It sort of fell out from the data available to them. Rather “they re-used data they were already capturing, and brought out something very interesting indeed.” This is why open data in science is so important. Not everyone gets the same ideas when ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947276 Fri, 07 Nov 2008 05:41:27 +0100 1947276 http://feedproxy.google.com/~r/mndoci/~3/mppBZBXbC18/ Be stubborn on vision and flexible on details – Jeff Bezos Those words, which I heard recently, have stuck in my head (or rather in Evernote, as I typed them on my iPhone furiously as I heard them). Over the years, I have seen too many in the life science industry, even pharma in recent years, lurch around, almost trying to figure out what they need to be doing as companies as they go along. That’s why so many fail. Let’s say you are running a small biotech or bioinformatics shop. You need to be sure what your vision is, identify the actionable milestones that you need to achieve and then figure out what you need to do to hit each milestone. It’s not just for a company. If you’re a product manager, think about your product line, and so on. The time... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947277 Thu, 06 Nov 2008 05:35:45 +0100 1947277 http://feedproxy.google.com/~r/mndoci/~3/iKWhRTFiQGs/ So far so good. Episode 2 of Coast to Coast Bio is now up. More riffing on matters somewhere in the continuum between biology and programming. Also available via iTunes (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947278 Thu, 06 Nov 2008 00:34:02 +0100 1947278 http://feedproxy.google.com/~r/mndoci/~3/Gj0d_xsp6EY/ Image via WikipediaI am not a lawyer, and while I have some opinions and some knowledge of FDA guidelines, I want to use the current pharma story du jour to highlight something that we need to do. I am sure anyone who listened to NPR today heard about Wyeth’s anti-nausea drug, Phenergan. To cut a long story short, the drug was administered to Diana Levine, a musician from Vermont, via the IV-push method, which has a small risk of inducing gangrene (if pushed into the artery). At issue, whether Wyeth should have changed the label having known about the issue. I won’t go into what Wyeth should have done, or not. That case is now before the US Supreme Court. I want to talk about the importance of pharmacovigilance, about the need to essentially never end clinical trials. We often ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933315 Tue, 04 Nov 2008 05:22:15 +0100 1933315 http://feedproxy.google.com/~r/mndoci/~3/7n4wB0Oihf8/ Image by mndoci via FlickrI should start with a disclaimer. My studies in the US have been limited to graduate school, so a lot is hearsay and gut feeling. Fred Wilson writes about hacking education. First, he echoes something I believe in strongly education is possibly the most important thing we can do for our world and our children. Education is the ultimate equalizer, at least a good one, and more importantly, the right now. The one that is composed for formal school education, informal/extracurricular education, and what we learn from our parents. Fred believes this is something children in this country are not getting from a badly broken public education system. Being from India, I can’t really say much about that. Myself and most of my peers are a product of India’s priv... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933316 Mon, 03 Nov 2008 01:18:40 +0100 1933316 http://feedproxy.google.com/~r/mndoci/~3/E4Qk0GRYi5A/ Interesting post by Frank Gibson on the Triumvirate of Scientific Data. He postulates that there are three properties of scientific data that are fundamental to the understanding of the curation, standardization and representation of scientific data, specifically Content, Syntax and Semantics. I think Frank encapsulates many of the points that we have been talking about for a while. I am not sure I necessarily agree on the labels as is, but the key points are the problems we are trying to address and I believe to solve them, there are a few things that we should not forget 1. Context. A key for any piece of scientific data is context. What does a particular protein mean in the context of the problem we are trying to solve, or question we are trying to answer. I’ve been in many cases ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933317 Sun, 02 Nov 2008 07:28:10 +0100 1933317 http://feedproxy.google.com/~r/mndoci/~3/ehhZKUlLXgM/ Freebase just had a major update, both cosmetically and in terms of features. Not sure when this got in, but Kingsley Idehen notes that Freebase is finally on the linked data web, one of the complaints that even those of us who have liked the service have had over time. (Update: Finally found the link to the Freebase RDF service) One of the more interesting changes is the concept of Bases. What is a base? From the blog post A base is a way to gather together information about a subject you’re passionate about. It’s a homepage for your structured data, and a community hub for people who share your passion. Interestingly you can give a base a nice endpoint, e.g. yourbase.freebase.com. Existing methods for data modeling and schema creation stay in place. What I am trying to figure out if ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933318 Sat, 01 Nov 2008 06:50:01 +0100 1933318 http://feedproxy.google.com/~r/mndoci/~3/IJsBUiHX4K4/ Lots of chatter about Adaptive Blue’s Glue this week. I’ve been meaning to blog about it for a while, because it does one thing in particular that really resonates at this end. First, a quick intro. Glue is a new service that continues Adaptive Blue’s quest to bring context to our actions on the web, hence the usual label as a “semantic” service. The following video probably does the best job of describing the new service Glue Overview from AdaptiveBlue on Vimeo. In a nutshell, Glue adds a bar to your browser in the context of a particular page for various categories, e.g. books, friendfeed, etc You can choose to annotate the page, like something, see who else might have seen that, and use those as a launchpad to find other interesting material. That&#8217... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933319 Fri, 31 Oct 2008 03:23:09 +0100 1933319 http://feedproxy.google.com/~r/mndoci/~3/vhNHWahTpx8/ Lots to blog about, so I will just put up something that came to me in the flight from LA to SEA that I took earlier today. First time this sort of occurred to me was a couple of weeks ago at work. Like many geeks, I carry a moleskine notebook around with me (a small one in my travel bag, a bigger one at work) to scribble down notes just in case, especially in situations where a laptop might be inappropriate or inconvenient. With the iPhone and Evernote, I seem to have stopped doing that. On the plane today, I was writing down all kinds of ideas, except that I wasn’t writing, but typing and this time, the notes would actually be legible afterwards. Just an example of how our devices and web services are changing our habits, especially as we get better at the interface of online and o... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933320 Thu, 30 Oct 2008 21:31:34 +0100 1933320 http://feedproxy.google.com/~r/mndoci/~3/ygdU1WO4pVg/ For a long time Hari and I have been talking about doing a podcast. We finally went ahead and started one. Coast to Coast Bio is a podcast that will evolve over time, but it’s a couple of geeks, who don’t always agree on things, bantering about biology, programming and all kinds of stuff. You might see a screencast or two in there as well. Episode 1 went live today. Still rough around the edges, but hopefully will tighten up as our workflow gets more streamlined. (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1933321 Thu, 30 Oct 2008 01:00:59 +0100 1933321 http://feedproxy.google.com/~r/mndoci/~3/IVP2tCNh1-Q/ I am getting frustrated by the number of people calling any HTTP-based interface a REST API. Those words come from the man who put REST on the map, one Roy Fielding in a bit of a rant against what people call REST today. The post is worth reading for anyone who is into the REST architecture (or isn’t). Also wanted to point to a couple of responses to Roy’s post. Sam Ruby, who co-authored the book that exposes most of us to REST, is amused by people’s attempts to try and figure out what Roy is saying. You have to read Leigh Dodd’s post as he channels WALL-E to present his understanding of REST. Me, I am still trying to get my head around Roy’s post (his writing style isn’t exactly one that lends itself to easy understanding). The one thing that’s cl... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1908835 Sun, 26 Oct 2008 06:27:35 +0100 1908835 http://feedproxy.google.com/~r/mndoci/~3/Yj5zU-tWmTU/ The New York Times continues to innovate. They have announced the TimesTags API. What is this? The API returns official NYTimes.com tags that match your search string. Even better, it ranks the results from most commonly used tags to least. That means you can quickly see what’s making news, how a company’s name has evolved, or which Baldwin brother currently has the biggest spotlight. The Times has some powerful dictionaries underlying their data, which makes the metadata more powerful, e.g. it allows you to disambiguate tags like Turkey (the country vs. the bird). They also clearly have bigger fish to fry. As the blog post says We see our tags as a contribution to existing metadata discussions and efforts, such as Freebase, Topic Maps, Fuzzzy and similar projects. If TimesTags can al... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905971 Wed, 22 Oct 2008 03:41:48 +0100 1905971 http://feedproxy.google.com/~r/mndoci/~3/BoUDbNCtOD8/ Shirley picks up on a topic near and dear to my heart, physics-based simulation, specifically a couple of questions What are high impact biomedical arenas that offer exciting challenges for physics-based simulation? What are new areas of computational research in physics-based simulation that will have a major impact on biology? The way I see it, our computational platforms will evolve, whether it be virtualized cloud infrastructures or GPUs as they always have. The real challenge is in methodology. I have fretted in the past about the lack of innovation in molecular simulation and lack of advances. Oh for sure, there is some innovation, not in the least from Shirley’s own institute. The key though, as pointed out, is in multiscale modeling. That’s an area I explored to quite... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905972 Wed, 22 Oct 2008 02:52:46 +0100 1905972 http://feedproxy.google.com/~r/mndoci/~3/qCTTsHwr5hA/ Image via WikipediaEver wondered what you might want to use a triple store for? Well, wonder no more. Toby Segaran has put one to good use to essentially capture his personal stream for the month of September. That stream includes phone records, email history, contacts, calendar and Facebook friends. Of course, being Toby, it’s not just about getting the data in there, but also doing something with it. At this time, it involves some clustering, and seeing the groupings of the connections. Toby’s right. We have lots of applications which, rightly so, are optimized to do a certain task well, but few ways of capturing information across applications. In a world where you can output data streams in XML or JSON, or RDF, or whatever easily parsable format we choose, we need approach... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905973 Tue, 21 Oct 2008 06:26:47 +0100 1905973 http://feedproxy.google.com/~r/mndoci/~3/d0drHV7usiA/ Via a post on Hacker News I ran into the Tulane School of Medicine Student Portal. As one of the developers writes on Hacker News Our goal is ‘making med school easier, one less click at a time’. We have no business model, just trying to make our own lives easier. There is further description on the site Hello, and welcome to the Tulane University School of Medicine’s Student Portal! This website came into existence over the course of the latter part of the 2007-2008 school year through the hard and volunteered work of a group of students concerned with making the lives of TUSOM medical students a bit easier. Our university community is a dynamic place with much do, and many resources to use on a daily basis. In an effort to reduce the amount of time and energy required to a... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905974 Sun, 19 Oct 2008 20:25:20 +0100 1905974 http://feedproxy.google.com/~r/mndoci/~3/Blem5wpU4MI/ The real big opportunities are changing the infrastructure of society – Vinod Khosla Venture Hacks highlights an interview with Vinod Khosla, where he talks about big opportunities, multi-billion dollar markets. The kind of change that literally impacts how we live. Wait, there’s more We are an investor that tries to build companies. We make money by building entities over the long term. We’re not in the business of transacting or doing deals. We don’t even allow that word here. It’s not buying and selling, that’s a transaction. You don’t invest in something and say I can sell it tomorrow or next year. We take a five year, ten year view and say we can build a company that can significantly change the landscape. Now if you happen to do that, you build companies of la... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905975 Fri, 17 Oct 2008 04:37:35 +0100 1905975 http://feedproxy.google.com/~r/mndoci/~3/fPrmyHVi_AM/ Image by Getty Images via DaylifeNick Carr points to an article by Andrew Sullivan that sheds some very interesting insights into blogging, points that are even more important for scientific writing and journalism Some of the key points made Quoting Matt Drudge, Sullivan writes … the key to understanding a blog is to realize that it’s a broadcast, not a publication. If it stops moving, it dies. If it stops paddling, it sinks. If you are serious about blogging, either as a writer, or just a casual blogger, you have to continuously be on top of your game, constantly being aware of what’s going on, of responding to comments or what others write. It’s not easy. Yes blogs are superficial, but in their superficiality they have power But the superficiality masked considerable ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905976 Thu, 16 Oct 2008 03:52:17 +0100 1905976 http://feedproxy.google.com/~r/mndoci/~3/_aBD2SvjU9w/ The New York Times just released an API, one for Campaign Finance. Marshall Kirkpatrick calls this significant because “steps like this are going to prove key if big media is to thrive in the future.” To me this is another data point into something I have been thinking a lot about lately. We’ve often talked about a web of data. We’ve also talked about how data is pretty much useless until you can do something about it. This actually fits in well with my theory that raw data on it’s own doesn’t really have any value. It’s what you do with it that makes it valuable. That leads us to the next evolution of the web and the data-centric age; a web of data services. This is also the answer to the question Tom Tague asks, How will we interact with the web ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905977 Wed, 15 Oct 2008 13:00:00 +0100 1905977 http://feedproxy.google.com/~r/mndoci/~3/YLB7xTe3mTU/ Image via WikipediaMy favorite source of hardware acceleration commentary returns to that subject. Joe asks My question now is, given the intent of Intel in this market, will Larrabee be able to get traction in the graphics world? And therefore, effectively displace nVidia (and to a lesser extent, AMD) as the accelerator king? IMO, if Intel nails the programmability issue, they can make a huge dent into nVidia’s leadership. It’s all about the programming at this stage Related articles by Zemanta Intel’s Larrabee Aims to Take on Nvidia and AMD (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905978 Wed, 15 Oct 2008 02:21:12 +0100 1905978 http://feedproxy.google.com/~r/mndoci/~3/_gBqo0x0wqA/ So today is Open Access day. I am writing this late in the evening, following a busy day at work and away from the computer. Writing this as late as I am, there have been some great posts already, none better than that by Neil. Tough to add to what he wrote. Open Access has taken a special meaning for me as I have moved away from science. I come from a heritage where the favorite journals included journals by the ACS, an organization that has come to epitomize closed access to me. Back in the day, sitting in universities with free access to papers and journals, that journal access wasn’t democratic never really registered. Then I started working in industry, at a startup, and suddenly you had to be careful about which journals you could subscribe to as a company. As I moved further ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905979 Tue, 14 Oct 2008 04:20:58 +0100 1905979 http://feedproxy.google.com/~r/mndoci/~3/v_kb1iYs9Do/ Bret Taylor has posted some graphics that he presented at the Future of Web Apps conference. The slides seem to explore the concept of signals in a virtual river of information, i.e. Friendfeed. We’ve talked about trust and filters a bit in recent days and the slides, even in the absence of context of the entire talk, suggest some ideas about how we can try and find trusted sources of information. I will include the slide that makes the most sense to me As I have said before, the challenge comes when we go beyond the first layer of connections that we have and traverse the graph of connections. I almost feel like we need an agent in the middle, continuously getting feedback and analyzing signals being sent from various nodes of an ever expanding graph, making the “keep this&#8... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905980 Mon, 13 Oct 2008 13:00:31 +0100 1905980 http://feedproxy.google.com/~r/mndoci/~3/3n_aBbsvj8k/ Zooming interfaces are cool. This week I have had a chance to see Zoomii in action, a Microsoft Surface, and of course, I use the multitouch zooming of the iphone quite regularly. In an interview with Jon Udell, Kristin Tolle, who works on biomedical computing at Microsoft Research had this to say Yeah, and we have these cool technologies. I think the WorldWide Telescope could be redeployed in many environments, and I think healthcare is one of those killer applications. We were talking with the National Cancer Institute, and one of the things they’d like to do is take a slice out of the liver while the patient is still on the table and be able to zoom in and zoom out — it’s the same technology. This was in response to a question on our abilities to make sense of complex ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1809826 Sat, 20 Sep 2008 00:19:46 +0100 1809826 http://feedproxy.google.com/~r/mndoci/~3/T7qWhCPPqDI/ No, contrary to popular belief no aliens are involved in my longest blog silence in a long time. Thanks to a hectic road trip, mostly at Web 2.0 Expo, haven’t had much of a chance to write about anything. In the meantime, the internet stayed up, the financial markets are in a mess, AWS made a huge announcement, and Tim O’Reilly gave a rather though provoking talk that I have to blog about soon. Oh, and the new Zemanta is sweet. Got a chance to meet Jure this week too :). Related articles by Zemanta O’Reilly: Stop throwing sheep, do something worthy (Caroline McCarthy/Webware.com) O’Reilly signals Free Web 2.0 party is over? (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1809827 Fri, 19 Sep 2008 12:10:25 +0100 1809827 http://feedproxy.google.com/~r/mndoci/~3/IDofgGzGIuY/ We wonder whether the traditionally do-it-all, own-it-all from every part of the value chain is sustainable. It’s certainly a risky and costly model That quote comes from Elliot Sigal, the CSO at Bristol Myers-Squibb. Bio-IT World has an article where it talks about Sigal’s proposal to make BMS a next generation biopharma company. Hmmm, wonder what that means. As far as I can tell it means taking some of the blue sky research ethos of biotech and marrying it to the scale and commercial expertise of pharma and the ability to work in multiple therapeutic areas. Somehow I find that underwhelming, even distressing. Both are cliches to the core, and just words to a degree. What the industry needs is for people to think differently, not just talk about stuff that people talk about all th... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1788754 Fri, 12 Sep 2008 13:00:47 +0100 1788754 http://feedproxy.google.com/~r/mndoci/~3/LawSxZy1k4c/ it’s just striking how some very basic kinds of data friction keep getting in the way of ever-more-amazing possibilities for analysis and insight. – Jon Udell I don’t think I need to add anything to this line (at the end of a typically great post by Jon) I wonder what kind of data friction life scientists have to fight through. Back in the day, it was all the non-standard terms and slight changes that used to show up in the PDB. In recent times, I have heard of datasets (same kind of data) from different groups that had one column of different with no directions on what the different column meant. Try designing a schema for that. Of course, the need to come up with yet another data format is the favorite pastime of most life science data creators. Related articles by Zemanta ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1786011 Fri, 12 Sep 2008 00:41:46 +0100 1786011 http://feedproxy.google.com/~r/mndoci/~3/RnekOoDyLjI/ I hope Bret and co are paying attention. I’ve heard people say that Friendfeed is too noisy, that they don’t get the value, etc. The tech world has the unique ability to make anything too noisy and the worlds ultimate echo chamber. The scientific community on the other hand (life scientists, physicists, librarians and technologists) have made it a second home. We use it to discuss ideas and ask questions. Of course, every conference seems to get it’s own backchannel on Friendfeed, e.g. ISMB, BioBarCamp, Science in the 21st Century, Science Blogging 2008, etc. We even have rooms for programming and development efforts now, e.g.for Ruby for Python and for the Chemistry Development Kit. It’s a classic example of successful micro-communities, all coming together, driven... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1786012 Wed, 10 Sep 2008 05:08:25 +0100 1786012 http://feedproxy.google.com/~r/mndoci/~3/BGi-CnvI0jo/ Image via CrunchBase, source unknown Did 23andme just cut prices? Update: Apparently they did A new blog post suggests that they’ve dropped prices to $399 (unless I am being completely dense and that’s an upsell). That information is part of the launch of 23andme v2. With the introduction of v2, our next-generation analytical platform, 23andMe customers will have access to an even more powerful set of the SNPs we use to probe their unique genetic composition. Can anyone with a 23andme account, or in the know, tell me what the potential and scope of the “analytical platform” is. I also suspect that v2 is on the 1M chip.. From the press release, it appears they are using the new Quad+ Beadchips The price reduction is largely made possible following technological adva... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1786013 Tue, 09 Sep 2008 05:23:31 +0100 1786013 http://feedproxy.google.com/~r/mndoci/~3/yTNffD_PEto/ Image via Wikipedia Science was always about mashing up, taking one result and applying it to your [work] in a different way. The question is ‘Can we make that as effective [for] samples [of] data and analysis as it [is] for a map and set of addresses for a coffee shop?’ That is the vision. — Cameron Neylon Those words, found on a great post at the Science Commons blog, have been stuck in my head since I saw them. I’ve talked about mashing up science many times. In my time in the bioinformatics industry, the need to do “integrative genomics” comes up again and again, yet the approaches we adopt to solve those problems are either too heavy and complex, or simply abandoned due to the inherent gaps in our data. Mashups, e.g. the ones with Google Maps that we are a... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1786014 Tue, 09 Sep 2008 04:51:09 +0100 1786014 http://feedproxy.google.com/~r/mndoci/~3/_LFt--0G5rg/ Image via Wikipedia I love wikis. From the time I was exposed to them as part of software development efforts to Wikipedia (where I make little changes every now and them) and Citizendium, to more vertical wikis like EColiHub, the wiki has been a platform that has made a lot of sense for all kinds of activities. For Bioscreencast, the Bioscreencast Wiki has always been a key part of the site, as a general resource. An interest in Wikis as a collaborative platform was why a wiki was the most obvious platform for The Biogang. One of my goals for 2008 had been to move away from my current shared hosting to more virtualized hosting and development environments, which is why I got rid of my desktops, and am now using my macbook pro, a slice on Slicehost and Amazon Web Services (quite literally ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1773250 Mon, 08 Sep 2008 00:00:32 +0100 1773250 http://feedproxy.google.com/~r/mndoci/~3/Fn56L0H1-is/ Just futzing around with Dipity. Here is an alternative to your normal list based RSS feed and fits in with the mood of the visualization theme earlier on Friendfeed Dipity first caught my attention due to its utilization of Freebase Related articles by Zemanta Dipity Do Da - An Interactive Collaborative Timeline To Track Wiki Contributions (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1768956 Sat, 06 Sep 2008 06:41:34 +0100 1768956 http://feedproxy.google.com/~r/mndoci/~3/9eJg_S49A3A/ The Broad Institute just got a donation of $400 million from Eli and Edyth Broad. The donation is the formal start of an endowment, making the Broad Institute a permanent, standalone biomedical institution. I have bemoaned the death of such bastions of innovation like Bell Labs in the past. But there is a trend in the biomedical sciences that is encouraging. Non-profit institutes and research centers like the Broad, The Wellcome Trust Sanger Institute, Janelia Farms, The Institute for Systems Biology, etc, with funding from powerhouse funders like the Wellcome Trust and the Bill and Melinda Gates Foundation are leading a trend towards independent research centers. Given the requirements for focussed cross-disciplinary research, I have a strong feeling that many of the innovations of the n... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1768957 Fri, 05 Sep 2008 06:33:38 +0100 1768957 http://feedproxy.google.com/~r/mndoci/~3/UGL9udivD24/ Image by St Stev via Flickr Over the last 14 years, I have flirted with nanotechnology at three different times; during my Masters in India, during the initial part of my PhD, and a couple of years ago when I was trying to figure out software solutions for nanomedicine. Each time, I have walked away feeling strangely unsatisfied. I have always found nanotech fascinating, still do. It’s incredibly cool and geeky. I have seen some wonderful examples of the success of nanotech, and the promise, and have friends actively involved in the field, but reading an article in Tech Review on nanotubes for drug delivery brought back some of those old feelings of dissatisfaction. Why? Well, when I saw the post, I thought I had found an old article from 2006. There just seems to be a lot of proofs ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1768958 Thu, 04 Sep 2008 06:23:19 +0100 1768958 http://feedproxy.google.com/~r/mndoci/~3/zXOTlT2fFBY/ What are the things that evolution has at its disposal to define a creature, to mix and match the parts, and eventually come up with a unique organism that’s going to live its life and try to reproduce? – Will Wright, gaming innovator Every time I take a “how big a geek are you” test, I fail, since I am not a gamer. That’s by choice. If I ever start, I am doomed. There is not enough time for all the things I care about as it stands, especially music, so gaming has always been kept at arms length. That said, cool games, and ideas in games are always of interest. Spore, which gets released on Sunday, has to be among the most highly anticipated, most hyped games since, well I suppose, GTA IV. Well, when you bring a cool game and genetics together, you get my attenti... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1750234 Tue, 02 Sep 2008 06:20:50 +0100 1750234 http://feedproxy.google.com/~r/mndoci/~3/_mFqhF0qXrU/ This is an atypical bbgm post. I am going to talk about “scientific blogging” in light of various recent events and discussions on the web on the subject. I started blogging over two and a half years ago, mostly as a way to write about material in my head. I used to label myself a “blogger”, but since I also dabble in video/screencasts, podcasts, maintain a wiki, etc, that label is one of convenience. The point is, that by painting blogging, including scienceblogging, with one big brush, we are selling ourselves short. Some people use a blog as a diary of observations. Others talk about specific scientific experiments (which might also go up on a wiki). Some record screencasts of their work, while some might choose to go with putting up material on slideshare, or in... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1750235 Mon, 01 Sep 2008 20:52:28 +0100 1750235 http://feedproxy.google.com/~r/mndoci/~3/WahpnKVCmbk/ Image via Wikipedia I discovered a new blog today, FlowingData, at least I don’t recall having seen it before. The blog is all about the meaning of data. How did I find it? One of my Google alerts took me to a post on How Open Should Open Source Data Visualization Be. The part that I went straight to was the part on the three aspects of open source data visualization; Open Tools, Open Code, Open Data. I don’t necessarily agree with some of the discussion in the post, at least from a scientific perspective, where data visualization is a key to data interpretation, although it’s possible I am misinterpreting the author who seems to be favorable of openness. Again, it’s not always possible to satisfy all three. While R does achieve that, but you can’t always use ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1746365 Sat, 30 Aug 2008 20:25:40 +0100 1746365 http://feedproxy.google.com/~r/mndoci/~3/fahDh4mi8Lo/ bioinformatics: acquiring, collating and rearranging information already available elsewhere? That is from a Tweet by Neil. My reaction was somthing along the lines of “boy that sounds like the definition of a mashup”. Bioinformatics is a broad field, but part of it, a good part of what a bioinformatician does is exactly what Neil describes. The work of a bioinformatician is built on data collected by many people around the world and deposited in a variety of data bases. A lot of what we do is take information from one and try and match it up to information from a second source, presumably with the goal of getting additional insights. It might sound crude to call it that, but I think if we start thinking of bioinformatics as a mashup, we could start thinking about making those... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1742800 Fri, 29 Aug 2008 13:54:07 +0100 1742800 http://feedproxy.google.com/~r/mndoci/~3/VqCtCy5-11o/ I have been thinking a lot about distributed identity lately and what it means for scientists. This was fueled by a bunch of things, including the recent news about OAuth, and discussions around social networks in science. We keep talking about how to connect information together. In the general web world, you have various services that, with varying degrees of success, bring things together into a common namespace. What we need to do in the scientific space is something similar. We have standards in place to make sites and services talk to each other. If we could figure out how to move our scientific identity, i.e. our collaborators, our communications (formal and informal, peer reviewed or otherwise), and our interests across services, while maintaining control over the communications, w... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1739239 Fri, 29 Aug 2008 05:36:52 +0100 1739239 http://feedproxy.google.com/~r/mndoci/~3/qqXyebg4uy4/ Image via Wikipedia All of you know about it already, but I shall happily add to the noise. Last evening I had one of those “Holy S**t” moments. Was sitting in a coffee shop, catching up with the days news, when I saw a flurry of activity on Friendfeed around Ubiquity. Turns out Ubiquity is a new project by Mozilla Labs, which for want of a better description is like Quicksilver for the browser, a mini command line available with an Alt-space. Ubiquity for Firefox from Aza Raskin on Vimeo. Ubiquity is still young, and may never catch on although I have a feeling it will, at least among the geek crowd, and being a Firefox plugin = low friction. But you can see the promise right away. You can, very quickly, using simple commands access search, Wikipedia, maps, insert material int... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1739240 Thu, 28 Aug 2008 05:13:52 +0100 1739240 http://feedproxy.google.com/~r/mndoci/~3/PZoJiFz4LRI/ Image via Wikipedia I was one of the lucky few who was given access to a dump of “social” statistics for PLoS One (my term). The data were given to us to analyze as we please, to glean from them what we may (I don’t really know who all the others were). To give some context, we need to look back at Euan’s post on commenting. He does a great job of slicing and dicing the data from BMC. My first instinct was to do a similar analysis of data from PLoS One, but in the end decided to go in a slightly different direction and look at some trends that might give some semi-quantitative insights into the scientific mind and commenting, and provide some commentary on what this really means, if anything. In the time since the first comments on PLoS One, in December 2006 (I show... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1739241 Wed, 27 Aug 2008 14:00:27 +0100 1739241 http://feedproxy.google.com/~r/mndoci/~3/T0JTNsJyFg4/ Organizations that sit tight tend to get verry comfortable with sitting, and they don’t move when they need to move. They want proof that the direction is the right direction, they study it, consider it, test it, and the next thing you know, they are fourth in a three-person market. Those are words from a recent blog post by Seth Godin. His point is actually a simple one; don’t flit, don’t get into waiting mode. What’s important is to keep executing in pursuit of a vision to believe in. My experience tells me much the same. Yes, you need to listen to people and be somewhat pragmatic, but that is part of execution, but you should set yourself targets and do your level best to achieve them. I equate this to agile programming paradigms. Your market, your customers need... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1734054 Wed, 27 Aug 2008 03:15:49 +0100 1734054 http://feedproxy.google.com/~r/mndoci/~3/HPHWvx0E8_Q/ Image via Wikipedia One of the talks I wanted to attend at OSCON, but missed in the blur of booth duty and conflicting sessions was Aaron Thul’s talk on Electronic Medical Office Logistics (EMOL). The talk was a talk on PostgreSQL talk, but wrapped around what it takes to develop an EMOL solution. The good news is that a lot of the OSCON talks are available online. Check out the pdf for Aaron’s talk, or follow on for some comments (based on just the slides) or do both. The talk essentially goes through how a FLOSS stack (with one notable exception) can be used to build a system that can collect data from EMRs and other data sources, while maintaining regulatory standards and providing a degree of automation. I remember the first time I was sitting in on a talk on EMRs some year... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1734055 Tue, 26 Aug 2008 03:47:22 +0100 1734055 http://feedproxy.google.com/~r/mndoci/~3/31RWuy1_BVc/ I’ve covered image mining in scientific literature in the past (here and here). Bioinform points us to another image search engine. The Yale Image Finder is a search engine that uses the text inside figures in addition to other features such as captions, etc Check it out and the others. I don’t have a sense for how successful the engine is for various kinds of images. I had more success using “captions” for molecular dynamics. The results for “image text” were not satisfactory. It is good to see a few things; decent performance (at least at this time), decent site design, and an effort in the community to try and develop tools of relevance. In an image heavy field like the life sciences, relevant image search is going to be important, so such efforts ar... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1726408 Sat, 23 Aug 2008 04:01:45 +0100 1726408