The DNA Network |
| Posted: 11 Jun 2008 03:25 PM CDT Hey students: if you are looking for a summer internship in marine metagenomics and you can get your application together before June 16th, Jonathan Eisen posted information about an open position on his blog. It also looks like he's looking for post-docs (see the side bar on the right of this page.) Read the comments on this post... |
| Using XMPP for lab management [business|bytes|genes|molecules] Posted: 11 Jun 2008 03:14 PM CDT
Now lets move to a pharma company or a big lab. You have a number of instruments, lab processes, potentially robots. Or you could be a big sequencing, or microarray facility. What if you could create XMPP agents for each machine/instrument/long computational process and have them communicate with a central LIMS controller. IMO, if we combine RSS and XMPP we have a pretty powerful lab management framework, built upon open standards. What gets included in the messages becomes the implementation challenge, but even that could be solved if the vendors decide to make that part of their design process. Also allows you to integrate and manage things more easily.
Check out slide #42 Further reading Image via Wikipedia Technorati Tags: XMPP, LIMS, Research Streaming  |
| CLC bio’s Next Generation Sequencing solution just released [Next Generation Sequencing] Posted: 11 Jun 2008 02:28 PM CDT I am happy to announce that we have just released version 1.0 of our solution for analyzing and visualizing Next Generation Sequencing data: CLC Genomics Workbench It includes user-friendly, high quality, high speed reference assembly and de novo assembly of Solexa, SOLiD, 454, and Helicos sequencing data, to name a few key features. Here you can read [...] |
| An Open Access pioneer - Trent Reznor [The Tree of Life] Posted: 11 Jun 2008 02:18 PM CDT Normally, everything I write about here is at least indirectly connected to science in some way. However, today I am drifting into the world of music. The New York Times had an article a few days ago about Trent Reznor (Trent Reznor's Frustration and Fury - Take It. It's Free). Trent, the brains behind the band Nine Inch Nails (full disclosure - I am a fan of his music), has been railing against the constraints of the music industry for year. And now he is going even further and in essence putting his music into the public domain as much as possible (see his web site NIN.com for more detail). For example "Mr. Reznor even posts online all the raw digital tracks from Nine Inch Nails albums for anyone to remix. "I'm done with them," he said. "Why not?"And he is doing this even though the $$$ for producing his music does not come from the government. He does it in part because he wants his ideas and music to spread and he wants to contribute to musical development. There are obvious parallels between what he (and others) are doing in music and those who develop Open Source software and those who release their data and publications to be as free as possible. I know I am not the first to discuss this, but just thought I would put it out there. |
| Three NGS sequencing companies have joined the 1000 Genomes Project [Next Generation Sequencing] Posted: 11 Jun 2008 02:12 PM CDT Leaders of the 1000 Genomes Project announced today that three firms that have pioneered development of new sequencing technologies have joined the international effort to build the most detailed map to date of human genetic variation as a tool for medical research. The new participants are: 454 Life Sciences/Roche, SOLiDApplied Biosystems and Solexa/Illumina Inc.. The three [...] |
| Posted: 11 Jun 2008 11:12 AM CDT The Marine-Microbiology Initiative at the Gordon and Betty Moore Foundation is looking a person to work there for the summer. This is "a short-term opportunity for an advanced undergraduate or graduate student who would enjoy delving into the genes and genomes of the microbes sequenced as part of the Microbial Genome Sequencing Project (a.k.a the "Moore 155")."For further details and links see the GBMF job ad. Note applications are due June 16, 2008. Here is more detail on what they are looking for:
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| Chris Smither on Darwin and Intelligent Design [The Tree of Life] Posted: 11 Jun 2008 10:47 AM CDT Entertaining little song by Chris Smither on Evolution/Darwin/Intelligent Design. Scroll to the 2:00 time point if you cannot wait. Thanks to Iddo Friedberg for the tip. |
| The 1000 Genomes Project: battle-ground for next-gen sequencers [Genetic Future] Posted: 11 Jun 2008 09:13 AM CDT  The 1000 Genomes Project is an ambitious international venture, launched back in January, that seeks to leverage advances in DNA sequencing technology to create a map of human genetic variation with unprecedented resolution.
The stakes are extremely high here. Involvement in the 1000 Genomes Project gives these companies an opportunity to prove their technology to the researchers in major sequencing facilities who will ultimately be some of their biggest customers, while at the same time providing some valuable public relations stories - Illumina got some good coverage with their "first African genome" back in February, for instance. The platforms that can prove themselves early in the game will have a serious edge over later competitors, simply by being well-established in the large facilities by the time young upstarts like Pacific Biosciences even have a product on the market. And when you think about just how much money there will be in the medical sequencing business within the next few years, Durbin's "exciting opportunity" starts to seem like classic British understatement.  Subscribe to Genetic Future. |
| Save Money on Gas [Sciencebase Science Blog] Posted: 11 Jun 2008 07:00 AM CDT
So what’s a driver to do? Save fuel that’s what! But, how? Money-saving expert and pragmatic tide-wad Martin Lewis has a few pointers on his MoneySavingExpert site. In fact, he reckons following his advice could cut your fuel spend by a third and it doesn’t involve overthrowing a government with a penchant for heavy stealth taxes. There are four key steps to saving money on fuel, Lewis explains:
The first of these involves removing any dead weight from your vehicle, detachable seats that never see a derriere could be stored offline, as it were. Roofracks and cycle racks should be taken down unless in use, and any trash, garbage, waste, rubbish lying in footwells, in the boot and trunk and elsewhere should be disposed of or recycled. Lewis reckons decluttering can save a couple of a percent, while ditching the roofrack and do the same. Other fuel savers include keeping tires at the correct pressure for your vehicle (up to 3% saving), keeping air-con use to a minimum (A/C uses between 4 and 8% of your fuel in hot weather). Lewis’ final efficiency tip is slightly less obvious and possibly doubtful - don’t fill your tank, he says. A car will run just as well on a half-full (half-empty) tank as a full one, apparently. He claims that the weight saving of not filling up every time you drive on to a garage forecourt (filling station), will boost efficiency by about 1%. I’m not so sure that this stacks up overall, however, because you will end up making twice as many journeys to the filling station, which itself will use fuel not only with the drive, but the stops and starts, and if you get stuck in traffic it could soon counteract that 1% saving. Especially given that being parked with Anyway, back to his list. Lewis next suggests that being a gentler driver, rather than a kid-racer can save you up to 60% fuel without cutting your top speed. It’s not about the theoretically optimal approach of accelerating gently up to 56 mph and then releasing the accelerator pedal and cruising back down to close to zero and then slowly accelerating up to 56 again. Rather, Lewis explains, you should ensure you’re driving in the appropriate gear (for stick shift drivers only) and that you should speed up smoothly. “When you press harder on the pedal more fuel flows, but you could get to the same speed using much less power,” he says, “a good rule is to stay under 3,000 revs [revolutions per minute, rpm].” Conversely, when you want to slow down, use the engine and ease down through the gears, reduce the need to stamp on the breaks. All that hard stopping and starting many drivers do simply wastes fuel. As my driving instructor told me at the start of my first lesson in decades past, “We’re all trying to get from A to B, but there’s no need to rush, be polite to other road users, and enjoy the ride.” (A good life philosophy in general, I thought). Lewis’ Point 3 means either doing some legwork and hunting down the best buys for fuel or using one of the many price comparison tools on the web. In the UK, we have the aptly and simply named petrolprices.com. Lifehacker recently highlighted GasBuddy and Gaspricewatch in the US. However, if you find a filling station 30 miles off your regular route that offers a fractional per gallon saving, then give it a miss, the extra 60 miles will most likely counteract the saving. In tip #4, Lewis suggests cashing in on loyalty cards, cashback credit cards, and company savings schemes, which could save a few quid (bucks) too. There are several other tips we might add to Lewis’ list. If you’re in the UK, agricultural vehicles avoid a certain amount of tax on their fuel, so becoming a farmer could save you money (and, of course, lose you it in other ways). You might be tempted to throw some magic potion, magnets or shiny beads into your tank in the hope of saving a few pennies. Don’t be. From a chemist’s perspective, I’d like to emphasise that drivers should avoid all such scams including so-called catalysts, magnetic gizmos, and shiny beads. Crystals, Reiki, and homeopathic remedies don’t work to fix human bodies, equally they are not going to let you squeeze extra juice from your car. Some observers suggest switching to compressed gas vehicles, hybrids, electric, and fuel cells etc. These are all well and good, although on the whole simply displace pollution elsewhere in terms of the fuels they use. However, the enormous overall energy and financial cost of replacing even an old car is far, far greater even than maintaining an old banger (lemon). Finally, here is the killer tip on how to save money on gas - walk or use a bicycle. Aside from the costs of extra carbs you’ll need to sustain you for the journey and the marginal increase in laundry costs for your Lycra cycling shorts, the broader outlook is for an almost 100% fuel saving. Of course, if you commute fifty miles a day, you’re going to have to set the early morning alarm just a little bit earlier to arrive at work on time, but just think of all those poor suckers paying $10 a gallon and listen to the dawn chorus and you’ll feel a whole lot better. A post from David Bradley Science Writer |
| Not quite Science Tuesday: Life after the lab [chrisdellavedova.com » Science] Posted: 11 Jun 2008 06:15 AM CDT
One of the things that I learned during my somewhat less than successful post-doc was that the traditional academic career path wasn’t for me. It wasn’t just the creeping feeling of dissatisfaction that greeted me every day I walked into the lab. One day, I was looking through our departmental website and realized that there were nearly four times as many post-docs as there were lecturers. I’m no mathematician, but it doesn’t take one to figure out that there are not a lot of jobs out there for your average Ph.D. In fact you’re pretty much waiting for the rare new faculty position or for an emeritus professor to wake up dead one morning. Even when a position opens up you’re competing with scores of other desperate Ph.D.’s, most of whom want it worse than you. From that moment on I pretty much new that I would never hold a faculty position and I started thinking about alternative careers in science.
As I write this post, I can say with some relief that I might have nailed it. I’m in a position right now to explore two of the aspects of science that I’m passionate about - communication and education. I’m going to be able to make some decisions about my career path and hopefully, in the long run, tailor a position for myself. I’m going to get a taste of the “real world” while still being able to relax in the cozy arms of a university. Best of all, I’m going to be able to support my family at the same time. May not see them much for a while, though. Nonetheless, right now, for this moment in time, it’s pretty damn good to be me. *A good suit doesn’t hurt. This posting includes an audio/video/photo media file: Download Now |
| Switching Disciplines [Bitesize Bio] Posted: 11 Jun 2008 05:08 AM CDT
Mine is a special case - I get the impression that most young postdocs cast wider nets (geographically speaking) with more narrow focus (their specialized field) in their job searches following grad school. But what about those who must, or choose to, open their search to related disciplines? In this case, I think that reaching back to your basic undergrad training becomes vital. It’s in undergrad that I achieved the breadth of instruction across disciplines in biology, afterall. How much attention you paid in lecture, and how hard you worked during lab courses, might pay off. It also helps if you had kept the course textbooks and notes, for you to look back on and use as a refresher. Of course, I sold my textbooks, discarded my notebooks after graduation, and lost focus at times, just as so many other students in undergrad at the time. Related article: Switching Disciplines, in the Chronicle for Higher Education (June 10, 2004) |
| What does DNA mean to you? #9 [Eye on DNA] Posted: 11 Jun 2008 03:06 AM CDT
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| Good luck Chris Gunter ... [The Tree of Life] Posted: 11 Jun 2008 01:59 AM CDT One of my favorite journal editors is moving on. Chris Gunter, who has been one of the genetics and genomics editors at Nature is moving to be the "Director of Research Affairs at the HudsonAlpha Institute for Biotechnology." She has been a big promoter of "free access" to articles within Nature and was at least in part responsible for (if not the major person behind) the fact that many genomics papers at Nature were freely available to all (note they were not always fully OA publications but at least they were free, which was more than many other journals, even non profit ones were doing). As for what Chris will do at HudsonAlpha, the press release says she "will work closely with Dr. Richard M. Myers, HudsonAlpha director, to raise awareness about HudsonAlpha and its research programs on a national level." RIck was the person who helped push me to formalize my ideas behind "phylogenomics" many years ago when we were both at Stanford and so now two of my favorite genomics folks will be in Alabama. I guess HudsonAlpha is a place to keep an eye on ... |
| Researchers update risk-of-death charts [Think Gene] Posted: 11 Jun 2008 12:33 AM CDT Researchers have updated charts that show an American’s risk of dying from a given cause over the next ten years, based on age, sex, and smoking status. The charts will be published online June 10 in the Journal of the National Cancer Institute. Although health information and the risks of various behaviors or conditions are frequently discussed in the media, the public rarely have access to enough information to adequately gauge the risk. To properly assess a risk, people need to know the absolute magnitude of a given risk and understand how it compares with other risks. To help physicians and patients assess an individual’s risk of dying from one condition versus another, Lisa Schwartz, M.D., of the Department of Veterans Affairs Medical Center in White River Junction, Vt., and colleagues used the National Center for Health Statistics Multiple Cause of Death Public Use File for 2004 to generate charts that show the risk of dying from a given cause within the next 10 years. To generate the updated charts, Schwartz and colleagues modified their previous methodology by including former smokers as a separate category to better account for a person’s smoking status. At all ages, men have a higher risk of death from all causes combined, relative to women. For both men and women, smoking increases the risk of death by nearly the same magnitude as adding 5 years to a person’s age. For men who have never smoked, the risk of dying from heart disease at any age exceeds the risk of dying from lung, colon, and prostate cancer combined. For men who currently smoke, the risk of dying from lung cancer is greater than the risk of dying from heart disease after age 60, and it is 10-fold higher than the chance of dying from prostate and colon cancer combined. For women who have never smoked, the chances of dying from heart disease and breast cancer are similar until age 60, after which heart disease becomes a bigger risk of death. For women who currently smoke, the chances of dying from lung cancer or heart disease are larger than the chance of dying from breast cancer after age 40. “The risk charts provide two basic elements that people need if they are to make sense of the health threats they face: the magnitude of the risk and some context,” the authors write. “We hope that the availability of these simple charts will facilitate physician–patient discussion about disease risk and help people understand where to focus risk reduction efforts.” In an accompanying editorial, Michael Thun, M.D., of the American Cancer Society in Atlanta and colleagues discuss the value of these charts and ways that physicians can best utilize them. For example, just posting the charts in the waiting room of a physician’s office may not be as effective as incorporating them into an interactive format of some kind. “The risk estimates provided by [Schwartz and colleagues] bring us a step closer to the goal of communicating effectively about risk in the context of routine medical care. The next steps could involve collaboration with other risk communication researchers to personalize this information and deliver it in ways that maximize its impact on health behaviors,” the editorialists conclude. Source: Journal of the National Cancer Institute |
| U of M researchers discover gene linked to adult-onset obesity [Think Gene] Posted: 11 Jun 2008 12:17 AM CDT Researchers at the University of Minnesota have discovered a gene that may provide a clue as to why obesity rates increase with age. The research was published today in the Proceedings of the National Academy of Sciences. Researchers in the lab of Kevin Wickman, Ph.D., associate professor of pharmacology at the University of Minnesota Medical School, removed a single gene from mice as part of an ongoing study to understand how the brain controls heart function. While some cardiac deficiencies were detected in these mice, the researchers unexpectedly found that these mice exhibited a predisposition to adult-onset obesity. By examining closely where this gene, termed Girk4, is expressed in the body, the researchers found particularly high levels in the hypothalamus, a brain region involved in regulating food intake and energy expenditure. Wickman speculated that disruption of normal function in the hypothalamus may underlie the obesity seen in the mutant mice, but he acknowledges that more research is needed to understand where and how this gene works, and consequently, why mice missing this gene develop obesity. The age-dependence of the obesity seen in this mouse model mimics human obesity patterns, researchers said. Indeed, the likelihood of people developing obesity more than doubles between the ages of 20 and 60. “This is a novel finding that may provide important new insight to the underlying cellular mechanisms that influence obesity,” said Catherine Kotz, Ph.D., co-author of the article, scientist at the Minneapolis VA Medical Center and adjunct professor in the Department of Food Science and Nutrition at the University of Minnesota. Source: University of Minnesota Josh says: Sometimes, the best discoveries in science are made by accident, though this isn’t exactly Nobel Prize worthy. Regardless, I’m still curious about the affects in humans and what the protein encoded by this gene normally does. |
Apologies if, like me, you’re a Brit and prefer to refer to petrol and diesel, then apologies for today’s post title. But, I’ve noticed a flurry of complaints from Americans about the price of vehicle fuel, recently, and just had to comment. Complaints about the price of gas? I hear the good folks of England, Wales, Scotland, and Northern Ireland exclaim! Yes, indeed, apparently, filling your tank Stateside now costs a staggering $4 per gallon (about 8 pounds sterling!) Pah! You say, us Brits are paying the equivalent of over $10 per gallon these days.
Regular readers may remember about a month of whinging and hand wringing about my lack of employment, demoralization and general shittiness. Funny, that. Just a week or so after taking on one job I’ve now been offered, and am likely to accept, a second. The writing gig is only part time, so I’ve been looking around for little bits to fill in the gap. Well, the little bits turned out to be fairly big bits when I got a phone call today offering me a full-time teaching position at one of Adelaide’s universities. So, in a couple of weeks I’ve gone from a state of panic about my potentially permanent unemployment to having one and a half jobs. I am a hugely relieved underwhelming correspondent today, folks. There was a fairly loud voice in the back of my head seeking to convince me that once I walked out of the lab that I was doomed to a life of McJobs.
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