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mercredi 19 novembre 2008
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In recent months, the concept of 'cloud computing' was all the buzz. European researchers think about another name, the World Wide Grid, which could run on top of the Internet. In an article to appear soon, ICT Results will report about the g-Eclipse project. As the scientists said, 'the g-Eclipse project aims to build an integrated workbench framework to access the power of existing Grid infrastructures. The framework will be built on top of the reliable eco-system of the Eclipse community to enable a sustainable development.' The project started in July 2006 and was successfully completed in June 2008 for a total cost of €2.5 million including a EU contribution of €1.96 million. You can submit today jobs to this grid, but read more...
Here is a link to the g-Eclipse project homepage. You can see above a diagram describing the g-Eclipse architecture. (Credit: g-Eclipse project) This figure was extracted from this poster (PDF format, 1 page, 1.52 MB).
As I mentioned above, there are plenty of 'computing clouds' these days. Once you're working with one like Amazon, it's not easy to interoperate with another one such as Google. Even if these 'clouds' mereley exist in 2006, this was this lack of interoperability which created the need for the g-Eclipsea project. "As things stand at the moment there are a series of isolated grids which allow the resources of clusters of computers, at different universities for instance, to be shared. Each of these grids is usually based on its own proprietary middleware which makes interoperability impossible. Middleware is a type of software which connects hardware resources to a grid. There are different middlewares available, each tailored for different scientific, commercial or industrial usage. Another barrier to the development of the grid system is its difficulty of use, requiring as it does now knowledge of specialised computer languages and coding skills."
Here is a quote from project coordinator Mathias Stümpert. "Entering and using a grid has been too difficult for most people, so we are developing a system which allows the ordinary student to use grid resources. Until now, these have only been available to academics and scientists able to enter complicated command lines. Instead of something that takes months to learn, we are developing a graphical user interface (GUI) which can be operated by anybody with a basic knowledge of computing."
So how did the consortium develop a middleware independent system? "'You can think of g-Eclipse as a browser for what will become the World Wide Grid,' says Stümpert. 'It searches for and displays the resources that are available, and allows the user to access them. Complicated computing jobs which need more processing or storage than are available on the user's system can be sent to the grid. Data can be transferred from the local computer to the grid and workflows can be managed.'"
The team decided to base its efforts on the Eclipse platform in order to be operational as soon as possible. "'We chose Eclipse as our medium because it allows us to create a user base and it also means anybody in the world can contribute. Eclipse projects are really transparent and open, more so even than Linux, and source code can simply be reused between Eclipse programmes,' [Stümpert says.]"
For more information, you can read these documents. You also can take a look at these screenshots. And if you want download and install the g-Eclipse framework, please visit this page.
Finally, the ICT Results website doesn't mention future articles, but its search engine shows them. Here is a link to Foundations for the World Wide Grid which should appear soon.
Sources: ICT Results, November 20, 2008; and various websites
You'll find related stories by following the links below.
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mardi 18 novembre 2008
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The Firefly mission is the second project under the new U.S. National Science Foundation (NSF) CubeSat program. The goal of this program is to provide a low cost access to space research. Firefly will be launched in 2010 or 2011 and will try to 'solve the mystery of the most powerful natural particle accelerator in Earth's atmosphere: TGFs, or terrestrial gamma-ray flashes,' according to this NSF news release. As I wrote recently, satellites can cost several hundreds of millions of dollars. But the Firefly represents a new kind of satellite. It is small -- the size of a football (4" by 4" by 12") and the cost to develop, launch, and operate it for three years during its science mission is expected to be less than $1 million. Read more...
You can see above a rendering of the Firefly CubeSat satellite which will investigate 'Terrestrial Gamma Ray Flashes' (TGFs) when it launches in 2010. "Scientists theorize that TGFs are linked to lightning and result when high-energy electrons are accelerated upward over thunder storms."(Credit: Universities Space Research Association (USRA)) Here is a link to a larger version of this picture and to USRA news release about the future Firefly mission.
So Firefly will study TGFs. But what are they? Here is NSF answer. "TGFs are short, powerful bursts of gamma rays emitted into space from Earth's upper atmosphere. The gamma rays are thought to be emitted by electrons traveling at or near the speed of light when they are slowed down by interaction with atoms in the upper atmosphere. These events may occur much more often than realized and may be associated with a significant fraction of the roughly 60 lightning strokes per second that occur worldwide. They could have a large effect on the upper atmosphere and near-Earth space, scientists say."
And here is what the NSF says about the future Firefly mission. "'This mission could provide the first direct evidence for the relationship between lightning and TGFs, and addresses an important research question in atmospheric electricity,' said Anne-Marie Schmoltner, head of NSF's Atmospheric Sciences Division's Lower Atmosphere Research Section. 'Identifying the source of terrestrial gamma ray flashes would be a great step toward fully understanding the physics behind lightning and its effect on the Earth's atmosphere.' To accomplish these goals, Firefly will carry a gamma-ray detector along with a suite of instruments to detect lightning."
Now, let's look at a NASA news release about Firefly for more information about these space thunderstorms. (Laura Layton, NASA's Goddard Space Flight Center, November 17, 2008). "Massive energy releases occur every day in the upper reaches of Earth's atmosphere. Lightning may give rise to these bursts of radiation. However, unlike the well-known flashes of light and peals of thunder familiar to Earth-dwellers, these energy releases are channeled upward and can be detected only from space. Our atmosphere protects us from the effects of this radiation, but the mechanisms at work can impact Earth's upper atmosphere and its space environment."
Here are additional details about TGFs. "TGFs are likely produced by beams of very energetic electrons, which are accelerated in the intense electric fields generated by large thunderstorm systems. Before CGRO [NASA's Compton Gamma Ray Observatory, many scientists thought these very energetic types of radiation could be generated only near the Sun, or in black holes, large galaxies, or neutron stars. 'These electron beams are more powerful than any produced in near-Earth space, and understanding their acceleration mechanisms will shed light on a physical process that may occur on other planets, or in astrophysical environments, as well as in the sun's corona,' said Doug Rowland, principal investigator for the Firefly mission at NASA Goddard's Space Weather Laboratory."
Good luck to the Firefly mission -- and to all the students involved!
Sources: U.S. National Science Foundation (NSF) news release, November 17, 2008; and various websites
You'll find related stories by following the links below.
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lundi 17 novembre 2008
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According to this article from Technology Review, U.S. researchers have developed an integrated blood barcode chip which can identify what's in your blood in less than 10 minutes. Instead of going to a lab, having a shot, and waiting for results for a day or two, this new chip will allow physicians to practice sophisticated exams in their offices by using a single drop of your blood. And these tests will be very cheap compared to existing procedures. If this chip becomes widely available, you might one day enter your physician's office and learn a few minutes after that you have a cancer. Of course, such blood chips are a good thing, but they also are frightening. Read more...
You can see above the design of an integrated blood barcode chip (IBBC). This figure depicts "plasma separation from a finger prick of blood by harnessing the Zweifach-Fung effect. Multiple DNA-encoded antibody barcode arrays are patterned within the plasma-skimming channels for in situ protein measurements." (Credit: California Institute of Technology (Caltech) research team)
This blood chip has been developed by Caltech chemistry professor James Heath and his colleagues, and by Leroy Hood, the president and founder of the Institute for Systems Biology in Seattle. Hood is already known for his participation of the invention of the high-speed DNA sequencer that made the Human Genome Project possible.
With other researchers, Heath and Hood have founded a company called Integrated Diagnostics to commercialize this new blood chip. Here are some additional details provided by Xconomy about this startup that will spot tiny cancers in blood (Luke Timmerman, September 26, 2008). The article says that the new company is still keeping a low profile, and doesn't have a website yet.
Let's go back to the Technology Review article to learn about this cheap new chip. "'We decided to make things dirt cheap: it costs a nickel a protein,' Heath says of the current device. Such rapid and cheap tests requiring only a drop of blood should allow doctors to monitor more proteins more frequently, enabling earlier detection of diseases like cancer and better preventive care for the elderly. The new diagnostics should also be more accurate, says Heath. Traditional blood samples sit for hours or even days before the measurement process is completed, allowing plenty of time for them to degrade."
And how this new chip work? It "starts the analysis process with some simple microfluidics. A drop of blood is pulled down a microscale channel by the application of a small external pressure. This first channel branches off into narrower ones, which exclude blood cells and admit the protein-rich blood serum. In typical blood tests, this separation step requires a centrifuge. The narrower channels are patterned with what Heath calls a protein bar code -- lines of DNA bound to antibodies that capture proteins of interest from the serum. After the serum and cells are flushed out, antibodies bound to red fluorescent proteins are flushed in, lighting up captured blood proteins. The protein bar codes can be read under a fluorescent microscope or a gene-chip scanner. The identity of the captured blood proteins can be determined by the location of red lines in the bar code relative to a green fluorescent reference line."
This research work has been accepted by Nature Biotechnology under the title "Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood." The article is available since November 16, 2008 as an advance online publication.
Here is a link to the abstract. "As the tissue that contains the largest representation of the human proteome, blood is the most important fluid for clinical diagnostics. However, although changes of plasma protein profiles reflect physiological or pathological conditions associated with many human diseases, only a handful of plasma proteins are routinely used in clinical tests. Reasons for this include the intrinsic complexity of the plasma proteome, the heterogeneity of human diseases and the rapid degradation of proteins in sampled blood. We report an integrated microfluidic system, the integrated blood barcode chip that can sensitively sample a large panel of protein biomarkers over broad concentration ranges and within 10 min of sample collection. It enables on-chip blood separation and rapid measurement of a panel of plasma proteins from quantities of whole blood as small as those obtained by a finger prick. Our device holds potential for inexpensive, noninvasive and informative clinical diagnoses, particularly in point-of-care settings."
For more information, d the full article is also available (PDF format, 6 pages, 490 KB). The above figure has been extracted from this paper.
Sources: Katherine Bourzac, Technology Review, November 17, 2008; and various websites
You'll find related stories by following the links below.
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dimanche 16 novembre 2008
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According to ICT Results in 'The Network of Everything,' wireless experts estimate that our personal networks will include about a thousand devices in 2017, including dozens of sensors checking our health and our home. This is why European researchers have launched in 2006 a networking project called 'MAGNET Beyond.' The name is an acronym for 'My personal adaptive Global NET and beyond.' The article suggests that the researchers have in fact built the Smart Personal Network, which integrates the concepts of Personal Networks (PNs) and Personal Area Networks (PANs). Read more to discover the results already achieved...
The EU-funded MAGNET Beyond project was completed in June 2008 by a consortium of 35 companies from 16 countries. The EU provided about €10 million for a budget of over €17 million. The picture above shows the 'MAGNET Beyond' architecture. (Credit: MAGNET Beyond) Here is a link to a larger version of this diagram and another one to a page giving additional details.
But first, where does this number of a thousand devices in a personal network come from? "In reality, it is hard to know what kind of devices or technology might be around for sure, but one thing is certain… there will be a lot of them. Hence the Wireless World Research Forum's (WWRF) prediction of 7 trillion devices for 7 billion people by 2017 -- in other words, around a thousand devices for every man, woman and child on the planet."
How is this possible? "In the future, there will be hundreds, even as many as a thousand devices in a PN. It may seem an impossible figure, but in the near future the number of personal devices will multiply enormously. One person might have dozens of sensors, monitoring vital signs like heart rate and temperature, and even the electrolytes present in perspiration. And then there are sensors and actuators in the home, including light switches, and more again in cars. People will be able to link with TVs, stoves and spectacles, which could double as a personal TV screen, and even clothing. They will have a home gateway, to manage all their home devices, and a car gateway while driving."
Let's admit that our PNs contain a thousand devices? How will be these devices be connected together? "Right now, PNs usually involve fiddling around with Bluetooth settings and crossing your fingers. If it does work, users typically try to complete simple tasks by trial and error, like hunting for photos on your mobile or trying to transfer a tune from your computer to a PDA."
What will be different if we use the MAGNET approach? "In the MAGNET model, users are able to easily set up their Personal Networks with all their devices. 'We have a user-centric approach,' reveals Professor Liljana Gavrilovska, Technical Manager of the MAGNET Beyond project, 'with the overall objective to design, develop, demonstrate and validate the concept of a flexible PN that supports resource-efficient, robust, ubiquitous personal services in a secure, heterogeneous networking environment for mobile users.'"
This sounds more like marketing than anything else. But let's look at how the project was managed. "Four fundamental principles guided the consortium's work: ease of use, trustworthiness, ubiquity and low cost. 'For example, the system is designed to be user friendly, with little or no training required and no need for system administrators,' Gavrilovska explains. 'It will ensure security and protect privacy, and it will work everywhere, even without any additional infrastructure, but still be able to exploit any available resources, like wifi or cellphone networks, for example.' The key elements to achieving these goals were personalisation and a tailored security, privacy and trust framework, including identity and the management of credentials. Credentials establish the trustworthiness of services outside the PN.
Finally, ICT Results writes that "The Network of Everything" is "part one of a three-part feature on MAGNET Beyond." If you use the site own search engine, you'll see that the other parts should appear on the homepage on November 18 (Technology behind the Personal Network) and on November 24 (Up close and personal networks).
Sources: ICT Results, November 15, 2008; and various websites
You'll find related stories by following the links below.
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vendredi 14 novembre 2008
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The first satellites were launched about 50 years ago as a way to conquer space. Now, satellites are essential for our civilian and military communications. But they remain large and expensive, some of them costing several hundreds of millions of dollars. This is why researchers from the University of Florida (UF) are building small satellites able to work as a team to take multiple and distributed measurements or observations of weather phenomena for example. These small satellites should cost only about $100,000 to produce. The first one should be launched next year by a NASA rocket and should not be larger than a softball. The goal is to mass-produce these satellites to even reduce their costs. But read more...
The picture above shows the expected benefits of multi-satellite systems. (Credit: University of Florida) Here is a link to a larger version of this chart.
And you can see above "a prototype of a 'pico satellite' being designed and built in a mechanical and aerospace engineering laboratory at the University of Florida. [...] The completed pico satellite, nicknamed SwampSAT, expected to be launched in 2009, will be about the size of a softball. This prototype is slightly larger than a basketball." (Credit: University of Florida) Here is a link to several other pictures of these small satellites and the man behind them.
This research project has been initiated by Norman Fitz-Coy, an associate professor of mechanical and aerospace engineering. Fitz-Coy is also the director of the Advanced Space Technologies Research & Education Center (ASTREC) established by the U.S. National Science Foundation (NSF) at the UF College of Engineering.
But will these $100K small satellites replace $100M ones? Not at all. "Fitz-Coy said small satellites are not anticipated to totally replace larger ones, but rather to complement them by adding new capabilities. For example, he said, 'swarms' of small satellites could take multiple, distributed measurements or observations of weather phenomena, or the Earth's magnetic fields, providing a more comprehensive assessment than is possible with a single satellite. 'People are looking toward these to not totally replace the big satellites but to supplement what the big satellites are doing,' he said."
It's interesting to note that it's easier to control large satellites than small ones. Fitz-Coy uses an analogy with cars. "The smaller the satellite, the harder it is to manage its flight path and attitude, or orientation in space -- for example, which directions its instruments point, a critical parameter in spacecraft design. 'It's similar to you driving an SUV down the road or a sub-compact,' Fitz-Coy said, explaining that while inertia helps large satellites, it is not enough to keep small satellites on track and properly oriented. 'The SUV is a lot more stable than the sub-compact.'" Yes, but it costs more...
So what will happen in the short term? The first launch should happen in 2009 "aboard an unmanned NASA rocket carrying other payloads as well. The satellite will fly at an altitude of between 600 and 650 kilometers, or from 373 to 404 miles, and will remain in orbit for several years, Fitz-Coy said. A container that could be standardized for use in transporting the small satellites aboard the rocket also is being developed. As with the satellites themselves, the goal is mass production – to be able to transport satellites to outer space much the same way that ships and trucks transport goods around the terrestrial world now, Fitz-Coy said."
Sources: University of Florida News, November 13, 2008; and various websites
You'll find related stories by following the links below.
6:19:47 PM
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jeudi 13 novembre 2008
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The northern lights are beautiful when you see them from the ground. But they can be dangerous for your life if you're in a plane crossing an area where they are active. This is because your plane can lose radio contact for a long time when flying above the northern polar region. This is why a Norwegian professor of physics is about to launch a rocket to discover the mysteries of the northern lights. The 9-meter long rocket should be launched between November 28 and December 7, 2008. It should reach an altitude of 350 kilometers and its flying time will be only 10 minutes. Let's hope that the embarked sensors function correctly. But read more...
You can see on the left a picture of Jøran Moen in front of the rocket that will try to uncover some of the mysteries of the northern lights. "'If we succeed in flying through the northern lights, we will set a world record in measurements of highly dissolved electronic precipitation in these lights,' Professor Moen points out." (Credit for photo: Yngve Vogt, University of Oslo) Here is a link to a larger version of this picture.
Moen is Professor of Physics and a member of the research group for Plasma and Space Physics in the Department of Physics at the University of Oslo.
But why did Moen start this project? Here are some of his motivations. "Because of the curvature of Earth, the airplanes flying the polar routes have to use high-frequency radio communication. The radio signals are sent via the ionosphere, which lies between 80 and 500 kilometres above the landscape. This consists of a layer of gas with electronic particles that reflect the signals back to Earth. When the northern lights are active, they create so much turbulence in the electronic clouds that the radio signals are cut off. In addition it is not unusual for solar storms to cause inaccuracies of up to 100 metres on the GPS. Professor Moen is planning to use the registrations from the rocket to gain a better understanding of the connection between the northern lights and the disturbances to navigation systems and radio signals."
Now, how will this experiment work? "The rocket is equipped to measure the electric fields and waves of the northern lights, particles of low and high energy in these lights, and fine structures in the electronic clouds. Until now it has only been possible to examine the dissolution of electronic structures of a few hundred metres of a northern light. The rocket instruments from the University of Oslo can concentrate on structures down to a few metres."
And what kind of results can we expect? "The rocket is filled with advanced instruments. In its basement at the Institute of Physics, the University of Oslo has developed a new instrument for measuring the fine structures of electronic clouds. The European space organisation (ESA) is interested in using this instrument in satellites for forecasting space weather. 'The importance of better forecasts of space weather will increase with the escalating offshore activities in the Barents Sea. Offshore is dependent on stable radio and satellite connections and precise navigation,' Professor Moen explains."
I'm a little bit frustrated by the lack of details about this rocket. One of the obvious reasons is that I don't read Norwegian. If you have access to more details, please drop me a note. Thanks.
Sources: Yngve Vogt, Apollon Magazine, University of Oslo, November 11, 2008; and various websites
You'll find related stories by following the links below.
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mercredi 12 novembre 2008
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Canadian scientists have recreated a famous painting from Vermeer on the microscale by using a new protein patterning technique. In fact, they've used a new laser method to draw protein pictures. And to illustrate the precision of their protein patterning technique, the research team reproduced 'Girl with a Pearl Earring,' a masterwork of Dutch painter Johannes Vermeer. But the real goal of this work is to replicate the brain's complex cellular environment. The research team said their new laser method is 'a major discovery, since the new laser technology can encourage and guide the growth of finicky nerve cells.' But read more...
You can see above two very different pictures. On the left is a reproduction of the Girl with a Pearl Earring painting by Johannes Vermeer circa 1665. This painting measured 44.5 x 39 cm. (Credit: Wikipedia) On the right, you can see how the Canadian research team reproduced this masterwork "in the miniature dimension of 200 microns wide or about the thickness of two hairs." Credit: Santiago Costantino, Université de Montréal) Here is a link to a larger version. Anyway, I'm pretty sure that the vast majority of you prefer the original to the copy.
This research work has been led by Santiago Costantino(page in French), a scientist at the Université de Montréal and Maisonneuve-Rosemont Hospital Research Centre. On his personal homepage, you'll discover that Costantino also used his method to create a micro-image of Albert Einstein.
Here are some quotes from Costantino about this research project. "We have created a system that can fabricate complex methods to grow cells. [...] We see this technique as being very relevant to neuroscience and immunology research. With this system, we laid down a chemical gradient to guide the growth of nerve fiber, which is very useful in studying nerve damage and repair. [...] The flexibility, precision and ease of this technique will hopefully lead to increased access in protein patterning, which could lead to major advances in science. [...] Our next goal is to extend laser-assisted protein adsorption by photobleaching to fabricate more complex protein combinations and distributions. We want to improve our imitation of the chemical environment found in the early stages of developing organisms."
This research work has been published in Lab on a Chip under the title "Patterning protein concentration using laser-assisted adsorption by photobleaching, LAPAP" on October 30, 2008. Please note that LAPAP is an acronym for "laser-assisted adsorption by photobleaching" even if it's not apparent from the title of the article.
Here is a link to the abstract, which should be understandable only by specialists. "The study of cellular responses to changes in the spatial distribution of molecules in development, immunology and cancer, requires reliable methods to reproduce in vitro the precise distributions of proteins found in vivo. Here we present a straightforward method for generating substrate-bound protein patterns which has the simplicity required to be implemented in typical life science laboratories. The method exploits photobleaching of fluorescently tagged molecules to generate patterns and concentration gradients of protein with sub-micron spatial resolution. We provide an extensive characterization of the technique and demonstrate, as proof of principle, axon guidance by gradients of substrate-bound laminin peptide generated in vitro using LAPAP.
Here is another link to the full paper. And here is an excerpt from the conclusions. "The studies presented demonstrate the versatility and potential of this simple approach. Nevertheless, chemotaxis in a living organism implies complex distributions of a plethora of guidance cues and to understand and manipulate this requires a means to generate more complex protein distributions and combinations. Our current studies aim to extend LAPAP to link more than one guidance cue by increasing the number of fluorescent tags and laser lines, and additionally to carrying out functional chemotaxis assays using full-length proteins. In conclusion, we report a novel assay for precise and flexible generation of protein distributions on cell culture substrates. LAPAP provides a relatively straight forward method that allows the generation of graded distributions of substrate bound protein at subcellular levels of resolution."
Sources: University of Montreal news release, November 11, 2008; and various websites
You'll find related stories by following the links below.
6:17:13 PM
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© Copyright
2008
Roland Piquepaille.
Last update:
19/11/2008; 18:44:19.
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