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Link of the week - Why humans don't crash, but computers do

The hierarchical organization of the transcriptional regulatory network of bacterium E. Coli, left, shows a pyramidal structure compared to the Linux call graph, which has many more routines controlling few generic functions at the bottom. Image courtesy of Yale University.

If the human genome is our operating system, then what is it about it that prevents it from crashing as frequently as computer operating systems?
To answer that question, a team of bioinformatics researchers at Yale compared the transcriptional regulatory network of bacteria with the Linux call graph. According to the Yale press release:

The molecular networks in the bacteria are arranged in a pyramid, with a limited number of master regulatory genes at the top that control a broad base of specialized functions, which act independently. In contrast, the Linux operating system is organized more like an inverted pyramid, with many different top-level r

Link of the Week - Kudos for cloud programming

No, coding while in a plane does not count.
Cloud and moon image courtesy of Leonardini. Code added by iSGTW.

According to Technology Review, cloud programming is one of the top ten emerging technologies of 2010.
Do we mean cloud computing? Nope! Joseph Hellerstein, a researcher at the University of California-Berkeley, is working on a creating a cloud programming language called Bloom, which his team hopes to release in late 2010. They are also preparing a number of domain-specific demonstrations.
Erica Naone of Technology Review writes:
His big idea is to modify database programming languages so that they can be used to quickly build any sort of application in the cloud--social networks, communication tools, games, and more. Such languages have been refined over the years to hide the complexities of shuffling information in and out of large databases. If one could be made cloud-friendly, programmers could just think about t

Link of the week - Did you know?

Image courtesy YouTube

At Sony’s Executive Conference a few months ago, they played this video to bring home the sense fo the rapid progress of information technology and the changes it wrought in our times.
It has since gone viral on YouTube.
The video starts with small tidbits of information, called “Did you know,” which mention, for instance, that “The top ten in-demand jobs in 2010 . . . did not exist in 2004.”
Or that “the U.S. Department of Labor estimates that people in school today will have been in between 10 and 14 jobs by age 38.”
Or that “the volume of unique new information we will generate this year (4 exabytes) is greater than produced in all of the past 5,000 years of human history.”
It also claims that the amount of new technical information doubles every two years — meaning that by the time someone enters the third year of a four-year technical program, half of what they l

Link of the week - Scientific Computing April-foolery

As usual, this year’s April 1 saw the web littered with pranks and jokes of varying quality. iSGTW scoured the web for the best April Fools stories related to science, computing, and scientific computing. Enjoy browsing the stories we found!
Story categories:

Cloud computing
Computer security
Information science
Science culture
Science

Image courtesy of Box.net

CLOUD COMPUTING
Space Computing from Box.net
It’s the new cloud computing! Interplanetary file redundancy, WarpTravel CDN to speed up file transfers, and secure file deletion via black holes are just some of the advantages of Space Computing. Not to mention the option of warming other planets instead of our own! We also dug the gorgeous website design – even if FaceBook’s Mark Zuckerberg wants to redesign the page.
Amazon’s Quantum Compute Cloud, QC2
Using the “spooky action at a distance” pro

Link of the week - eScience and Google Summer of Code

This summer marks the sixth edition of Google Summer of Code. Around 1000 student programmers from around the world will be offered a $5000 stipend to work with one of 152 open source mentor organizations, creating a substantial body of new open source code.
Last week Google announced this year’s list of participating open source projects, and a number of them are closely tied with grids, clouds, or computer-assisted science.
Is your project missing from this list? Email us to have it added!
ASCEND – A software program for solving small to very large mathematical models, including non-linear equations, linear and non-linear optimization problems, and dynamic systems expressed in the form of differential/algebraic equations.
Encyclopedia of Life – A single portal providing information on all 1.9 million known species by aggregating data from thousands of sites using novel informatics tools. Sponsored by the Marine Biol

Statistics of the week - To lease or buy CPU-hours: that is the question

The cost per CPU-hour is based on a four-year project. More details on how these numbers were calculated is available via both the IEEE and USENIX papers.

Ever wonder if you should just outsource all your cyberinfrastructure needs to your friendly neighborhood cloud provider?
That’s exactly what Edward Walker is researching. So far, it looks like in most cases, the answer is “no.”
“The key take away in the article "The Real Cost of a CPU Hour" is that cluster utilization is a very important factor in determining if leasing from a cloud vendor, or purchasing your own cluster, is cheaper,” said Walker, who is the HPC software group leader at the Texas Advanced Computing Center.
“However, the USENIX ;login: article serves as a cautionary note: the performance that can be achieved in doing science on a cluster, optimized for doing high-performance computing, can be quit

Link: And the winner is . . .

Computer Engineer Barbie. Image courtesy Mattel

About a month ago, we ran a story in this space that mentioned the “Vote for your favorite Barbie career” contest, in which we noted that “computer engineer” was a nominee for the first time.We quipped that “if all 5,806 iSGTW readers voted, we could swing the Barbie election.”
Apparently, some of you took this to heart.
According to Mattel’s official Barbie vote website, the Popular Vote Winner is . . . Computer Engineer, whose outfit and accessories you can see at right.
The company’s press release says that to create an authentic look, “Barbie designers worked closely with the Society of Women Engineers and the National Academy of Engineering to develop the wardrobe . . . Computer Engineer Barbie is geek chic.”
Preliminary responses from iSGTW readers ran the gamut. One wrote that “She looks cooler than most computer engineers

Blog post of the week - LOLCats get on the Grid

Could transmitting these inane yet adorable pictures be the future of large-scale data movement? Find out at our blog post of the week. Image courtesy of mikenmar

What do the LHC grid, LOLCats, and Avatar have in common? More than you might think, according to our blog post of the week.
It turns out that creating the three dimensional IMAX film required a tremendous amount of computational power. Special effects company Weta Digital used the combined power of seven supercomputers. The system is no slouch; it includes the computers ranked by top500.org as 193 through 197, 274, and 449. Together, they have nearly 40,000 processors. And the final cut of the film took up over 17 gigabytes per minute.
Agent Utah, a.k.a. science writer Calla Cofield, muses about the massive amounts of data being moved around the Internet in the form of movies, commercial sites, Google, and LOLCats:
“It's pretty amazing how fantastic we humans are at pr

Word of the week - Multithreading

A single-core machine multithreading is much like a good juggler: you may only be doing one thing at once, but you have to be really good at switching between balls or you’ll drop one! Image courtesy of Guillaume Riesen

Until recently, most computers had a single processor (CPU) which contained a single core. Computers could execute only one task at a time.
Then multi-threading came along. top500’s glossary of terms describes multithreading as:
A capability of a processor core to switch to another processing thread, i.e., a set of logically connected instructions that make up a (part of) a process. This capability is used when a process thread stalls, for instance because necessary data are not yet available. Switching to another thread that has instructions that can be executed will yield a better processing utilisation.
Not all CPUs can do multithreading, and not all applications follow the multithreading programming model. Both must be

Link of the week - Climate Wizard

A screenshot of the Climate Wizard website.

Now anyone can play with climate models using an online tool called Climate Wizard.
Climate Wizard is an interactive website where visitors can browse maps of historical climate data and future predictions of temperature and precipitation.
“Climate Wizard does not simulate future climate. Rather, it analyzes General Circulation Models in a way that makes them more accessible to non-climate scientists,” said Evan Girvetz, a Senior Scientist with The Nature Conservancy Global Climate Change Program.
General Circulation Models are a type of mathematical model of the general circulation of a planetary atmosphere or ocean.
“The Climate Wizard takes climate projections from 16 GCMs, each of which are 3-dimensional databases of latitude, longitude, and time,” Girvetz said. “It analyzes each of them to determine the rate of change over time for each grid cell, then combines the maps of

Word of the week - Transparent

Image courtesy of ilco at stock.xchng.

All too often, common words take on new and unexpected meanings within a scientific or technical discipline. And to the uninitiated, this can be incredibly confusing.
The word ‘transparent’ is a great example of such a word. The most basic definition for transparent is ‘see-through.’ In other words, allowing light and information to pass through.
When journalists say that we should strive to be transparent, we mean that we should strive to provide readers with details on how we got our information and reached our conclusions.
In the computing world, however, the word takes on an entirely different meaning. In fact, you could say it takes on the opposite meaning.
When a developer says that a science gateway should be transparent, that means that the scientists who use the gateway should not need to know anything about how it works. Any black box system would be considered likewise ‘tran