The DNA Network |
| Posted: 11 May 2008 03:08 PM CDT As you may have read in the national press, the university where I work, Washington University in St. Louis, is honoring the anti-feminist activist Phyllis Schlafly with an honorary doctorate at the university's commencement this week. |
| Systems Biology - I'm coming around to it [The Daily Transcript] Posted: 11 May 2008 12:14 PM CDT Friday I was supposed to meet up with Mike Springer from the Kirchner lab. At some point Mike and I had set up a collaboration in order to figure out what was so special about little regions of the genome that encode signal sequences. (To read more on my paper and what we did click here). In any case Mike had emailed me that Alex van Oudenaarden was giving a Systems Biology "Theory Lunch" and that he had to postpone our lunch. Having heard Alex once before and being impressed, I decided to check it out. It was one of the best seminars I've attended in quite a while. |
| The Open Data licensing issue [business|bytes|genes|molecules] Posted: 11 May 2008 12:05 PM CDT A little tied up this weekend, so will keep it brief. I have added a number of comments on Friendfeed to posts I have shared from Google Reader about what the licensing of data should be. The whole thing started by Antony Williams announcing CC support for data on ChemSpider. That was followed by a chain of events and a ton of confusion. Let me add my voice to this debate, since Open Data is near and dear to my heart I classify scientific data into the following categories
I can’t but agree with John Wilbanks. Here is the part that all of us should read again and again
The public domain is the natural place for raw scientific data. That’s where it belongs and always has been. We, myself included, have been guilty of making things more complicated than they need to be. There is a data commons already. Our goal should be to make sure people respect it, and make data available in ways that we can take advantage of it. Our discussion on content licensing should be limited to processed data, i.e. what we do with data in the public domain. There, we need to allow people to make choices, but keep the raw data unfettered. Those who want to associate copy left licenses with raw data are being dogmatic. Scientific data doesn’t have to be viral or anything like that, it’s there for the greater scientific good, and there’s only one logical mechanism for it. In fact, I would argue that putting copy left on it (a sequenced genome doesn’t belong to anyone) is as wrong as full on copy protection. You may have some embargo on making it publicly available, especially with things like structures where you might want to do something with it before anyone, but in the end the data belong in the public domain I would like to thank John for putting this down so emphatically and clearly. A lot of us have been saying the same thing for a while, but this is the most clear distillation that I’ve read yet. That does not mean we don’t have to have a discussion around how we make content (not raw data, but follow on content) available and the implications. Antony was confused for good reason. Further reading More from John  |
| Programming HPC for the domain [business|bytes|genes|molecules] Posted: 11 May 2008 10:24 AM CDT
So in an era with more scale available, clouds to tap into, accelerators, and new data and distribution models, are we going to see a shift? I still feel that the underlying scientific research has to come from academia. They have the resources, time and incentive to do so, but I think industrial think tanks and expertise can contribute back by working with academia on advanced problems of relevance, e.g. in the area of computing. Will we tap into some of the new domain specific development being done today as a scientific community? It can’t be done by one side or the other. But rather we need to identify approaches as a community and understand what works best, without trying to duplicate efforts. Of course, we need people who understand these new methods and paradigms to implement them. There will always be a tension between academic research efforts and commercial need. In the life sciences it is especially tough for industry specific apps to be developed from an economic point of view, which is why I believe it will have to be a joint effort. Your thoughts? Image via Wikipedia Technorati Tags: High Performance Computing, Parallel Programming  |
| A silly meme… [Mailund on the Internet] Posted: 11 May 2008 09:27 AM CDT Ok, so I was tagged to do this by my good old friend Thomas Widmann. Who, by the way, stood me up once in Oxford, claiming he was ill or something… PJC and myself were meeting up for a drink (Peter coming all the way from Bremen, taking time off his busy schedule building space rockets) and Widmann didn’t even bother to show up… Anyway, apparently the idea now is:
Now, the closest book means I have to dig through the piles of paper on my desk. I am assuming closest is in Euclidean distance and not in time it takes to get at it. On my desk I have a few books that I have had here for ages and never use — a few manuals that I never look at because Googling is much easier, and a dictionary that I haven’t used since I discovered Webster online. So, the closest book, once I made it through piles of papers I should have read but never got around to, is: Oxford Advanced Learner’s Dictionary. It was a gift from my sister — I have the big, red, massive Webster myself, but I got this from here when she finished her studies and decided she would never need it again… In my version — which doesn’t look like the picture at Amazon I linked to above — page 123 is bole to bona fide. Sentence five is:
The next three are:
Wasn’t that a senseless exercise? Now I need to pick five others to tag. I’ll stick to people AU people who probably knows Widmann as well: Peter JC, Peter Ahé, Kristian Høgsberg, Søren Sandmann and Michael Westergaard. Now, where exactly am I supposed to leave a comment, Widmann? |
| Connecting the world [Mailund on the Internet] Posted: 11 May 2008 05:54 AM CDT Just in follow up to my previous post, where I wrote a bit about my amazement of how the Internet has connected the world, here’s a TED talk on that exact topic: |
| Pangea Day [Mailund on the Internet] Posted: 11 May 2008 04:49 AM CDT Yesterday was Pangea Day. Imagine a world-wide film festival? I continue to be baffled about how information technology has changed the world. Two-three years later, everyone had an Internet connection at home, and a little bit later, when Google showed up on the scene replacing AltaVista, Yahoo etc., the Internet replaced the encyclopaedia as the place you would find information (they may not like me saying this, but Google really did blow the competitors out of the water). I cannot really imagine living without the Internet and search engines any more. When I am not connected, I feel almost handicapped. In my work, I need to look up stuff all the time, and going through books and manuals is so much harder than just googling. A little later, I was myself working in Australia, first at the University of Adelaide, a bit later at the University of South Australia — both times for shorter stays of a few months duration — and using instant messaging I could work interactively with people at home, and talk to friends. With my cellphone, I could talk to my friends while I was walking through a park in Adelaide and they were getting ready for bed in Denmark. It was a bit expensive, but it was possible.
Hell, I’m posting this sitting in my garden, connected over a wireless connection. I wouldn’t have believed this possible ten years ago. There’s some drawbacks to this as well, of course, such as Jotun Hein never really understanding time zones and calling in the middle of the night from New Zealand to discuss a project… It happened a couple of times while Jotun was on sabbatical there. Mike Steel told me at a bbq that he had the same problem when Jotun calls him from the UK. But all in all, it is a great thing, in my opinion. Information technology has made the world into a global village. It is said a lot, but in some sense it is true, and if you stop and think about it, it really is amazing. Well, not the entire world has joined the village. The majority of people are not connected. I don’t know the numbers, but I wouldn’t think a billion people are connected (and we have just passed 6,666,666 billion people worldwide). |
| Gene Genie #31 at Adaptive Complexity [ScienceRoll] Posted: 11 May 2008 02:21 AM CDT The 31st edition is up at Adaptive Complexity. A great compilation of articles and blogposts about human genetics and personalized medicine. Thank you, Michael White, for hosting Gene Genie. Gene Genie is the blog carnival of genes and gene-related diseases. Our plan is to cover the whole genome before 2082 (it means 14-15 genes every two weeks). We accept articles on the news of genomics and clinical genetics. The news and articles of personalized genetics are also included. Check out Gene Genie for more about this unique field of medicine.
The next edition is due to be published on the 25th of May but has no host at this time. If you are interested in hosting Gene Genie, drop me a mail. Don't forget to submit your articles via the official page. Here are all the issues of Gene genie:
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| Capitalists, Genetic Tests and Your DNA [adaptivecomplexity's column] Posted: 10 May 2008 11:43 PM CDT  Everyone knows there is a lot of crazy stuff on the internet, but did you know there is a lot of great writing about genes, genetics, and human diseases? And believe it or not, sometimes these pieces are written by people who know what they're talking about. If you're looking for what's new in human genetics, you've come to the right place. Welcome to the 31st Gene Genie, a blog carnival dedicated to great blogging about human genes and how they impact our health. This Mother's Day edition includes an in-depth highlight of the growing industry of personalized genetics. |
| Around the Web - May 10, 2008 [business|bytes|genes|molecules] Posted: 10 May 2008 08:51 PM CDT Linkfest
Multimedia & Presentations
Blogspotting
Self AssemblyOnce again, life is very hectic, so not much to report. Follow me on Friendfeed, twitter or check out the Tumblelog, where I am have been putting up some cool stuff lately |
| Workman's Compensation, Stereotypes and GATTACA [The Gene Sherpa: Personalized Medicine and You] Posted: 10 May 2008 08:01 PM CDT Have you ever had back pain? Almost everyone has. Who has sciatica? Sciatica a very common condition accounts for a significant amount of lost work days, medical costs and psychologic stress.... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
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