From isgtw: “Desktop power helps map protein dance”

“Proteins are part of a complex social network, and rarely act alone. Protein-protein interactions is the term used to describe when two or more proteins ‘partner-up‘ and bind together to carry out a different biological function. While experimental techniques are used to identify the relationships between one protein and another in its cellular neighborhood, computational simulations are still needed to uncover the more complex web of connections for multiple protein partners.

Neuromuscular disease is a generic term for a group of disorders (more than 200 in all) that impair muscle functioning either directly through muscle damage (muscular dystrophy) or
indirectly damaging nerves. It affects one in 2,000 people. These chronic diseases lead to a decrease in muscle strength, causing serious disabilities in motor functions (moving, breathing etc.). The most well-known is muscular dystrophy. In cases of muscular dystrophy contraction of the muscle leads to disruption of the outer membrane of the muscle cells and eventual weakening and wasting of the muscle. Dystrophin is part of a protein complex that connects the cytoskeleton of a muscle fiber to the tissue framework surrounding each cell through the cell membrane. This complex does not form correctly in muscular dystrophy. (Image courtesy Alessandra Carbone).

Distributed computing power from the World Community Grid (WCG) has recently aided the Help Cure Muscular Dystrophy (HMCD) project in capturing all the possible molecular and atomic connections between 2,280 human proteins. The analyzed proteins include those that are known to mutate and induce different forms of neuromuscular disorders, including Muscular Dystrophy.

HCMD is part of a larger-scale venture, the Decrypthon Molecular Docking Project. This is an alliance between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research) and IBM, who are using the World Community Grid resources to help them decipher and map all the functions of interacting proteins found in humans to a worldwide repository of information such as the Research Collaboratory for Structural Bioinformatics (RCSB) protein databank.

The first phase of the HMCD project, completed in June 2007, scrutinized relationships among 168 proteins using molecular docking simulations. The researchers predicted that it would have taken over 14,000 years of computational time on a 2 GHz PC to reveal and rule out all possible docking confirmations for all 168 proteins. However a ‘distributed calculation’ allowed them to considerably reduce the processing time. Over 6,000-8,000 donor machines meant the task took under 26 weeks. However, to test 2,280 proteins on a one-to-one basis for phase II of the project, researchers needed a method to significantly reduce the number of configurations they would have to check. Molecular docking data from analysis of the 168 proteins (known to form 84 complexes) helped them develop a fast docking algorithm to predict potential partners for this large pool of proteins.”

See the full article here.

The World Community Grid is comparable to one of the world’s top 15 supercomputers [ curently at 590.673 TeraFLOPS]. Its software has been downloaded onto over two million computers, which together have completed almost 700,000 years of scientific computation.”

World Community Grid (WCG) runs on BOINC software from Berkeley Open Infrastructure for Network Computing from the Space Science Lab at UC Berkeley.

iSGTW is an international weekly online publication that covers distributed computing and the research it enables.

“We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

In its current incarnation, iSGTW is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

You can read iSGTW via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

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From Gizmodo: “This Wind Tunnel-Cooled Computer Is Helping Conquer Cancer”

World Community Grid

I got my first glimpse of the subject here at a WCG forum post. I followed the links and was blown away.
I was given permission to use this copyright protected material and I will do my best to honor that permission.

Jan 4, 2013
Andrew Tarantola

Distributed, crowd-sourced computing platforms—doesn’t matter if it’s Indigogo or SETI@home—are only as useful as the individual systems connected to them. And for IBM’s World Community Grid, a single system can do a lot, especially when it’s a purpose-built 4.5GHz calculation-crushing super computer.

Mike Schropp, the Total Geek behind the Total Geekdom website, built the Wind Tunnel Computer after grid computing piqued his interest in 2011. As Schropp describes:

‘The idea that I could build a computer, or use existing computer resources and donate their power so scientists and researchers could process medical and humanitarian research was extremely interesting. By donating computer processing time, you actively contribute towards a great cause. World Community Grid has numerous projects available; finding cures and treatments for cancer, AIDS, malaria, muscular dystrophy, etc.

In particular, Schropp was struck by IBM’s World Community Grid which combines the extra cycles of member machines into a virtual super computer. The organization has also recently begun implementing GPU- rather than CPU-based processes (such as the Help Conquer Cancer project) which is significantly faster when used in massive parallel applications—reducing computational times from hours to minutes.

The rig he built is composed of an Ivy Bridge 3770K CPU running at 4.5GHz, a pair of Radeon HD 7970 graphics cards, 8GB of 2133Mhz of RAM, and a Gigabyte Sniper M3 motherboard. With all these overclocked components running 24/7, heat generation is a major factor—but that’s where the wind tunnel comes in….”

And that is where you should go to the full Gizmodo article which is very instructive.

All we can say is Wow!

For a step-by-step photo review, visit Total Geeekdom’s article.

Thanks to Jesse for the permission to use this material.

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

Computing for Sustainable Water

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

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My BOINC

From Einstein@home: " Einstein@Home passes 1 Petaflop of computing power!"

Bruce Allen is an American physicist and director of the Max Planck Institute for Gravitational Physics in Hannover Germany and leader of the Einstein@Home project for the LIGO Scientific Collaboration. He is also a physics professor at the University of Wisconsin–Milwaukee.

“Congratulations and thank you to all Einstein@Home volunteers: sometime shortly after January 1st 2013, Einstein@Home passed the 1 Petaflop computing-power barrier. To put this in context, according to the current (November 2012) Top-500 computing list, there are only 23 computers on our planet that deliver this much computing power.

(One Petaflop is 1,000,000,000,000,000 floating point operations per second.)

Congratulations and thank you again, and keep on crunching!”

Bruce Allen
Director, Einstein@Home

A diagram of a pulsar showing its rotation axis, its magnetic axis, and its magnetic field.(NASA Goddard)

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience. BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

Einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

My BOINC

ScienceSprings is powered by MAINGEAR computers

BOINC Announces Asteroids@home Project

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience. BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

BOINC has announced a Happy New Year surprise, a new project, Asteroids@home.

Here is a description from the projects own home page

“Project Asteroids@home

Asteroids@home is a volunteer distributed computing project developed at the Astronomical Institute, Charles University in Prague, in cooperation with Radim Vančo from CzechNationalTeam. The project is directed by Josef Durech. It runs on the Berkeley Open Infrastructure for Network Computing (BOINC) software platform and uses power of volunteers’ computers to solve the lightcurve inversion problem for many asteroids.

Why distributed computing?

With huge amount of photometric data coming from big all-sky surveys as well as from backyard astronomers, the lightcurve inversion becomes a computationaly demanding process. In the future, we can expect even more data from surveys that are either already operating (PanSTARRS) or under construction (Gaia, LSST). Moreover, data from surveys are often sparse in time, which means that the rotation period – the basic physical parameter – cannot be estimated from the data easily. Contrary to classical lightcurves where the period is “visible” in the data, a wide interval of all possible periods has to be scanned densely when analysing sparse data. This fact enormously enlarges the computational time and the only practical way to efficiently handle photometry of hundreds of thousands of asteroids is to use distributed computing. Moreover, the problem is ideal for parallelization – the period interval can be divided into smaller parts that are searched separately and then the results are joined together.

Why to study asteroids?

The large discrepancy between the huge number of all known asteroids and the small number of those with known basic physical parameters (shape, spin, period) is a strong motivation for further research.

Knowing the physical properties of a significant part of the asteroid population is necessary for understanding the origin and evolution of the whole solar system.
Thermal emission of small asteroids can significantly change their orbit (Yarkovsky efect), which can be crucial for predicting the probability of their collision with the Earth. To be able to compute how the thermal emission affects the orbit, we have to know the spin (and also the shape, to a certain extent) of the object.

Scientific objectives

The aim of the project is to derive shapes and spin for a significant part of the asteroid population. As input data, we use any asteroid photometry that is available. The results are asteroid convex shape models with the direction of the spin axis and the rotation period. The models will be published in peer-reviewed journals and then made public in the DAMIT database.”

Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

My BOINC

ScienceSprings is powered by MAINGEAR computers

From Einstein@home – is a PetaFLOP a Possibility?

From Einstein@home:

“The computing power of Einstein@Home has exceeded 950 Teraflops for the first time since the project was begun in 2005. Based on the rate that our computing power has been growing, I am hopeful that Einstein@Home will pass the 1 Petaflop barrier before the end of 2012. Einstein@Home volunteers: please keep your computers running over the holiday season, and please sign up any new ones that you might receive as a gift!

Bruce Allen
Director, Einstein@Home

Einstein’s screen saver, just in case you love really cool screen savers. When it runs, the globe rotates. Like I said, really cool.

You can help. Visit BOINC, install the software, and attach to the Einstein project. Who knows, you may be the next “cruncher” to tag a pulsar.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience. BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

My BOINC

ScienceSprings is powered by MAINGEAR computers

From GPUGrid.net via BOINC: “GPUgrid.net announces AIDS breakthrough”

From GPUgrid.net

Crucial step in AIDS virus maturation simulated for first time

“Bioinformaticians at IMIM (Hospital del Mar Medical Research Institute) and UPF (Pompeu Fabra University) have used molecular simulation techniques to explain a specific step in the maturation of the HIV virions, i.e., how newly formed inert virus particles become infectious, which is essential in understanding how the virus replicates. These results, which have been published in the latest edition of [Proceedings of the National Academy of Sciences, could be crucial to the design of future antiretrovirals."

HIV proteasa cutting the poly-protein chain. Source: IMIM

Using ACEMD a software for molecular simulations and a technology known as GPUGRID.net, Gianni De Fabritiis’ group has demonstrated that the first 'scissors proteins' can cut themselves out from within the middle of these poly-protein chains. They do this by binding one of their connected ends (the N-terminus) to their own active site and then cutting the chemical bond that connects them to the rest of the chain. This is the initial step of the whole HIV maturation process. If the HIV protease can be stopped during the maturation process, it will prevent viral particles, or virions, from reaching maturity and, therefore, from becoming infectious.

This work was performed using GPUGRID.net, a voluntary distributed computing platform [running on BOINC software] that harnesses the processing power of thousands of NVIDIA GPU accelerators from household computers made available by the public for research purposes*. It’s akin to accessing a virtual supercomputer. One of the benefits of GPU acceleration is that it provides computing power that is around 10 times higher than that generated by computers based on CPUs alone. It reduces research costs accordingly by providing a level computational power that previously was only available on dedicated, multi-million dollar supercomputers.”

[*Rest assured, while a small number of projects run on GPU processors, most projects running on BOINC software are CPU based and do not use GPU processing.]

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience. BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

My BOINC

ScienceSprings is powered by MAINGEAR computers

From Einstein@home: “Our paper got two positive referee reports from Physical Review D, the scientific journal that it is submitted to for publication :-)”

WE LOVE IT WHEN PROJECTS NEAR AND DEAR TO OUR HEARTS CAN REPORT POSITIVE RESULTS IN THE FORM OF PAPERS PUBLISHED, THE SUCCESS OF NEW MEDICATIONS, AND THE LIKE.

So, here we have notice of a successful paper from the Einstein@home project.

From the project web age:

“Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than three dozens new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

From the Paper:

“(Submitted on 31 Jul 2012 (v1), last revised 4 Aug 2012 (this version, v2))
This paper presents results of an all-sky searches for periodic gravitational waves in the frequency range [50, 1190] Hz and with frequency derivative ranges of [-2 x 10^-9, 1.1 x 10^-10] Hz/s for the fifth LIGO science run (S5). The novelty of the search lies in the use of a non-coherent technique based on the Hough-transform to combine the information from coherent searches on timescales of about one day. Because these searches are very computationally intensive, they have been deployed on the Einstein@Home distributed computing project infrastructure. The search presented here is about a factor 3 more sensitive than the previous Einstein@Home search in early S5 LIGO data. The post-processing has left us with eight surviving candidates. We show that deeper follow-up studies rule each of them out. Hence, since no statistically significant gravitational wave signals have been detected, we report upper limits on the intrinsic gravitational wave amplitude h0. For example, in the 0.5 Hz-wide band at 152.5 Hz, we can exclude the presence of signals with h0 greater than 7.6 x 10^-25 with a 90% confidence level.”

The notice is here from M.Alessandra Papa, Project Scientist

Visit the Archive site for a PDF download. Then settle down to an astonishing read.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

My BOINC

ScienceSprings is powered by MAINGEAR computers

NASA FERMI Announces a Team at Einstein@home

NASA FERMI has announced a team crunching Einstein@home. You can view the team page. This is a huge testament to the significance of Citizen Cyberscience, Public Distributed Computing, and BOINC.
Me? Crunching Einstein@home on CPU and GPU, and, I might say, looking for my own pulsar find.

ScienceSprings is powered by MAINGEAR computers

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.

MAJOR PROJECTS RUNNING ON BOINC SOFTWARE

SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

The famous SET@home screen saver, a beauteous thing to behold.

einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

These projects are just the oldest and most prominent projects. There are many others from which you can choose.

There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

My BOINC

ScienceSprings is powered by MAINGEAR computers

From the WCG Clean Energy Project at Harvard: The IBM Contribution

The Clean Energy Project (CEP2) at Harvard University gives us the look into IBM’s contribution to the betterment of Society via World community Grid (WCG).

Watch this short video.

You can visit the WCG web site (link is above), download the BOINC software agent, and attach to the Clean Energy Project. We would love to have you.

From the project:

Mission
The mission of The Clean Energy Project is to find new materials for the next generation of solar cells and later, energy storage devices. By harnessing the immense power of World Community Grid, researchers can calculate the electronic properties of hundreds of thousands of organic materials – thousands of times more than could ever be tested in a lab – and determine which candidates are most promising for developing affordable solar energy technology.

From The Human Proteome Folding Project at WCG

The Human Proteome Folding (HPF2) project at World Community Grid (WCG) has announced the publication of a paper:

21 Jun 2012
Paper published in the journal Genome Biology and Evolution using Human Proteome Folding project results

Category: Human Proteome Folding
Tags: Project Update , Research Papers

Summary
Researchers have published a paper in the journal Genome Biology and Evolution, which documents their findings studying a number of plant genomes, their proteomes, evolution and protein structure.

Paper Title:
“The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families”

Lay Person Abstract:

Melissa Pentony et al. have presented work considering components of proteins exhibiting faster-than-average evolution in the proteomes of five major plant species, including rice (Oryza sativa) and Arabidopsis thaliana (an important model organism for plant study). They describe new information on the relationship between evolution and protein structure in plants.

The World Community Grid has contributed to this study by providing a much more structurally complete view of unknown and understudied proteins from five plant families than was previously available. The results from the Human Proteome Folding project produced 29,202 protein structures contributing to this project, of which 4,764 were very high-confidence. This should eventually assist agricultural scientists to better understand important plant and food crops, how to breed them for disease resistance, better nutrition and to better handle environmental stress.

At the News web page, there is a technical abstract for anyone interested, and a link to the paper.

“World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

WCG projects run on BOINC software from UC Berkeley.

BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BETCHA!!

“Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

Please visit the project pages-

Say No to Schistosoma

GO Fight Against Malaria

Drug Search for Leishmaniasis

Computing for Clean Water

The Clean Energy Project

Discovering Dengue Drugs – Together

Help Cure Muscular Dystrophy

Help Fight Childhood Cancer

Help Conquer Cancer

Human Proteome Folding

FightAIDS@Home

Computing for Sustainable Water

World Community Grid is a social initiative of IBM Corporation
IBM Corporation

IBM – Smarter Planet

My BOINC