1. Please take 30 seconds to register your free account to remove most ads, post topics, make friends, earn reward points at our store, and more!  
    TalkBass.com has been uniting the low end since 1998.  Join us! :)

Alembic fans: got (CPU) time on your hands ???

Discussion in 'Off Topic [BG]' started by rockandroller, Mar 11, 2003.

  1. Join the "Alembic Club" GRID team, and donate yer spare background CPU cycles to this worthy cause:


    My puter runs 24/7 anyway, so I set it to run grid computations all night :)
  2. odie

    odie Supporting Member

  3. I've seen these things, I'd do it, but it's my parents computer ;)
  4. Its completely harmless, you just set it and forget it, basically... it activates itself and begins number-crunching whenever your machine is idle... and deactivates itself the moment you or your machine actually does anything. You can also set it to only activate when your screen-saver is active. You can configure it to only run at certain hours, and to only connect to the net (to gather new tasks and send computation results) at certain hours (handy if you are on dialup) .. does anybody out there still have to use dialup? If so, you have my condolences!
  5. geshel


    Oct 2, 2001
    I run that at home. It's been pretty unobtrusive. I used to run SETI @ Home - still have that one on at work.
  6. today's run looks a little more promising...

  7. Zon Bass

    Zon Bass

    Jan 20, 2002
    Dallas, TX
    I'm joining as I speak
  8. odie

    odie Supporting Member

    and later we find out we just supported a terror ring making new chemical and bio weapons.

    is this legit?:meh:
  9. Yes, its 100% legit - i checked it out! (i was more concerned about hacker backdoors and distributed ad-ware than conventional forms of terrorism....)
  10. john turner

    john turner You don't want to do that. Trust me. Staff Member

    Mar 14, 2000
    atlanta ga
    what's the purpose of this? what are they trying to find?
  11. Ívar Þórólfsson

    Ívar Þórólfsson Mmmmmm... Supporting Member

    Apr 9, 2001
    Kopavogur, Iceland
  12. geshel


    Oct 2, 2001
    The cure for cancer. Basically.
  13. from GRID.ORG:

    One in four of us will at some time suffer from cancer. The high mortality rate, the suffering experienced by patients from the side effects of existing treatments, and the high costs of treatment all contribute to making cancer a priority for drug research.

    A new way to help
    A landmark research project has begun that allows people to make a real difference in the fight against cancer.

    The United Devices Cancer Research Project is asking you to volunteer your PC to help process molecular research being conducted by the Department of Chemistry at the University of Oxford in England and the National Foundation for Cancer Research. To participate, you simply download a very small, no cost, non-invasive software program that works like a screensaver: it runs when your computer isn't being used, and processes research until you need your machine. Your computer never leaves your desk, and the project never interrupts your usual PC use.

    It's safe and easy
    There is no cost to participate and no impact on your computer use. The project software cannot detect or transfer anything on your machine but project-specific information. It just allows your computer to screen molecules that may be developed into drugs to fight cancer. Each individual computer analyzes a few molecules and then sends the results back over the Internet for further research. This project is anticipated to be the largest computational chemistry project ever undertaken and represents a genuine hope to find a better way to fight cancer.

    The computational power to perform research of this scale is only available through the generosity of individuals like you.

    The United Devices Cancer Research Project will advance research to uncover new cancer drugs through the combination of chemistry, computers, specialized software, and organizations and individuals who are committed to fighting cancer.

    The research centers on proteins that have been determined to be a possible target for cancer therapy. Through a process called "virtual screening", special analysis software will identify molecules that interact with these proteins, and will determine which of the molecular candidates has a high likelihood of being developed into a drug. The process is similar to finding the right key to open a special lock — by looking at millions upon millions of molecular keys.

    Participants in the United Devices Cancer Research Project are sent a ligand library over the Internet. Their PC will analyze the molecules using a docking software called LigandFit by Accelrys. The LigandFit software analyzes the molecular data by using a three-dimensional model to attempt to interact with a protein binding site. When a ligand docks successfully with a protein the resulting interaction is scored and the interactions that generate the highest scores are recorded and filed for further evaluation.

    LigandFit is a drug discovery software program.
    The program appraises each of hundreds of millions of molecules to see if they are likely to interact with a target protein. LigandFit calculates and studies the many positions, or conformers, the molecule might adopt interacting with the protein. This process is called virtual screening of the molecules.

    LigandFit explores the 3-dimensional position each molecule might adopt. Each new position of the molecule may help the right parts of the molecule interact with the protein target. LigandFit does this very fast-so fast your monitor can't show every conformation. The total number of conformations differs molecule to molecule. Some molecules may have more bonds or flexibility, and thus will have more conformers.

    Current molecule
    The 3-dimensional images on the right are representations of real molecules. The representations are made up of various elements, which appear as colored balls or rods. The "balls" or "rods" represent different atomic elements that make up the molecule, with different colors to represent specific elements.

    Molecular name
    There are hundreds of millions of molecules being processed. There are so many that identifiers, rather then names, are used to track them. The characters that follow the words "current molecule" indicate the molecule that LigandFit is currently screening.

    Current protein target
    The image at left of the screen represents a protein that the molecules may interact with. The protein has already been determined to be a possible target for cancer therapy. It is one of only a few protein targets that the millions of molecules are screened against for this project, so the same protein target will be featured on the screen saver for a while.

    Atomic legend
    What elements make up each molecule? You can map the molecules' elemental components by using the legend, which color codes the elements. There are several primary elements that make up most biological molecules, which can be seen on the legend: carbon, oxygen, hydrogen, nitrogen and sulfur.

    Hetero atoms
    Hetero means "different". Several primary elements feature strongly in biological molecules, but sometimes a molecule includes an atom that isn't one of the usual biological elements. A hetero atom could be any different atom that is not represented in the legend. For example, it may be chlorine, or it may be another element. That is, the hetero atom color signifies any other different atom that isn't one of the usual five atoms that make up most living matter.

    Progress meter
    The numbers along the bottom of the molecule graphic show how many ligand your PC has processed. A work unit is usually comprised of several hundred molecules. The molecules may vary considerably in size and number of conformers, with the more flexible molecules taking longer to compute. This variety in molecules is what accounts for the variety of time it may take to complete different work units.

    The buttons on the graphic interface allow access to more information about the project and the work your specific computer is doing. This includes information on how it compares to other computers, and what your Agent preferences are, which is how you want the Agent to run on your machine.
  14. The Smallpox Project

    Smallpox was eliminated from the world in 1977 by a World Health Organization campaign. Despite this, stocks of the variola virus are known to exist and its use as a weapon of bioterrorism remains a frightening possibility. With vaccination having ended in 1972, the world population is highly susceptible. The availability of drugs to counter the virus would be a major defense.

    There is a possible molecular target whose blockade would prevent the ravages of an infection. We intend to use grid computing to screen millions of potential anti-smallpox drugs against this target. This will involve the use of the United Devices Global Metaprocessor, which we have successfully used in the past towards cancer and anthrax research. The project can harness millions of computers belonging to people in over two hundred countries, all of whom will benefit from protection against smallpox.

    Join the Fight by Joining the Grid
    You yourself can participate and assist in this important effort. By downloading and running the UD Agent, you add your CPU to the global grid. Every time your computer is idle, you contribute your computing resource to the grid, accelerating the screening process while dramatically reducing the cost of the project. The result: Rather than spending years to screen hundreds of thousands of molecules, it will be possible to screen hundreds of millions of molecules in just months.

    The UD Agent itself will keep you up-to-date on several aspects of the project — ligands processed and their structure, and number of leads identified — so you can see the progress you're enabling and witness the power of this global computing grid.

    About the project
    Accelerating the Discovery of a Smallpox Cure
    The global threat of a smallpox outbreak as a result of a bioterrorist or military attack demands that scientists find new and faster ways to identify a cure. Now, accelerated drug discovery research — powered by commercial products from United Devices, IBM, and Accelrys — will make it possible to discover smallpox drug candidates at a record pace.

    The Challenge of Tackling Massive In-Silico Research
    The Smallpox Research Grid Project involves screening 35 million potential drug molecules against several protein targets — one of the largest computational chemistry project ever undertaken. Typically, a project of this magnitude is too great for any single organization to tackle. The expectations are that, by combining a high-throughput screening application with the substantial power provided by grid computing, the project will shave years off the time required to develop a commercial drug.

    Creating a Grid Solution Using Off-The-Shelf Components
    This project uses the Accelrys docking and scoring application LigandFit to analyze, measure and rank each candidate molecule's interaction with smallpox-related proteins. As strong candidates are identified, the likelihood increases that a cure, potentially successful in laboratory experiments and clinical trials, will be found.

    Powering the project is a 2-million device public grid running MetaProcessor software from United Devices. This software is available for deployment inside corporate enterprises, as a hosted pay-per-use service, or (as in this case) on a global grid.

    A project of this scale requires a solid hardware and data infrastructure. Filling this need are IBM eServer p690s running DB2 database software on AIX and Linux operating systems.

    Project Data Statement for the Smallpox Research Grid Project

    The Smallpox Research Grid Project ("Project") will attempt to analyze approximately 35 million molecules against a series of protein targets related to smallpox. This Project is made possible through the support of several Partner Organizations who have made various contributions to this effort. The Partner Organizations include: Accelrys, Evotec OAI, IBM, Oxford University, United Devices, and numerous scientific researchers led by Dr. Grant McFadden and Dr. Stewart Shuman.

    Accelrys will contribute the LigandFit virtual screening software;
    Evotec will provide the modeling expertise;
    Oxford University, assisted by researchers at Essex University, will prepare the proteins for use with LigandFit and has contributed the large molecular library;
    United Devices will provide the grid computing software called the MetaProcessor and has coordinated all aspects of the Project. It has contracted with PC owners for the use of their idle computing time; and
    IBM Corporation is providing the infrastructure technology (high-performance computing and data management software) that will be used for the Project, as well as funding and marketing support to assist in the Project's launch.

    The hope is that a combination of the above efforts will help identify the most promising drug-like molecular candidates that could be effective in combating smallpox.

    The resulting data ("Results Data"), produced as a result of the Project will consist of a list of "hits" and their relative score. When a molecule docks successfully with a protein, it registers as a hit and is scored or ranked for strength of interaction. By binding to the particular site the drug candidate would disable the virus. The ranked list of hits will be provided to the U.S. Department of Defense, who has contracted with United Devices for this Project through the U.S. Army Medical Research Institute of Infectious Diseases and potentially other allied governments (e.g., UK government, Canadian government) as directed by the US government, so that they also can take the "hits" and further process and develop them to help combat the use of smallpox as a bioterrorist threat or military weapon. It is essential that in blocking the action of smallpox the related human enzyme is not affected so the binding to that human target will also be tested.

    Each Partner Organization has separately agreed that it has no rights to the Results Data.
  15. The PatriotGrid:

    A global effort to combat bioterrorism
    The threat of bioterrorism affects people worldwide. From distant continents to the house next door we're all susceptible to the potential impact of a bioterrorist attack, where the enemy is an unseen biological agent with no known cure.
    That's why United Devices established the PatriotGrid: A family of research projects designed specifically to identify new leads for cures to diseases that are known to be potential weapons of bioterrorism.

    The threat
    Terrorists select agents designed to infect humans with debilitating diseases such as anthrax and smallpox for which cures do not exist. Because many of these deadly agents are available on a growing scale, creating a defense by identifying new leads for cures is a global priority. Unfortunately, with conventional computational screening methods, drug leads take years to discover and develop into viable treatments.

    The proven technology behind the PatriotGrid
    By using the Global MetaProcessor @ grid.org, research groups can speed their lead-finding processes dramatically — shaving years off the timeline for developing new treatments. The Global MetaProcessor has been utilized in drug discovery projects of similar scope including the groundbreaking Cancer Research Project (with Intel & the National Foundation for Cancer Research) and the Anthrax Research Project (with Intel, Microsoft and the University of Oxford).


    Anthrax Research Project

    On the road to curing Anthrax
    On January 22, United Devices announced the launch of the Anthrax Research Project.

    United Devices is excited to announce that as of February 14, 2002, the screening phase of the Anthrax Research Project has been completed.

    Prompted by recent events and a heightened concern around the threat of anthrax, this project's goal was to accelerate what is usually a time-consuming step in the lengthy drug discovery process. The project entailed presenting a key protein component of anthrax into the general rotation of the United Devices Member Community's current virtual screening project, which works with the MetaProcessor platform over the Internet. This allowed UD Members to lend their computers in the screening of 3.57 billion molecules for suitability as a treatment for advanced-stage Anthrax.

    Screening is only one step in a long drug discovery process that ultimately must move from the computational realm into the actual laboratory. The project used a 5-time redundancy rate for each molecule to ensure a high level of accuracy and quality. With the invaluable help of the UD Member Community, NFCR Centre for Computational Drug Design in the Department of Chemistry at the University of Oxford, and corporate sponsors Intel and Microsoft, the project was completed in a stunning 24 days.

    Dr. Graham Richards, Chairman of the Chemistry Department at Oxford and the Director of the Centre for Computational Drug Design, called the results "unprecedented," commenting, "Had we done this using traditional methods, it would have taken years instead of less than 4 weeks."

    Preliminary indications are that we have narrowed the original pool of 3.57 billion molecules down considerably, having identified over 300,000 crude unique hits in the course of the project. This significantly reduces the next phase of the discovery process, in which the ranked hits will be further refined and analyzed, accelerating the overall time to availability of a treatment.

    Some Members of the UD Community continued processing results over the weekend while initial results were verified.

    Genetic research with HMMER

    Improving genetic research
    Knowing how DNA works is crucial to finding new treatments and cures for disease. If scientists can find out exactly which parts of DNA control eye functions, they may be able to help cure certain eye diseases.

    Since all biological functions can eventually be traced back to DNA, successful genetic research could provide mankind with a tremendous supply of disease fighting knowledge.

    Ever since Watson and Crick discovered the double-helix structure of DNA in 1953, genetics has been a quickly developing and closely watched field. The very blueprint for living things, DNA has intrigued biologists, philosophers, and politicians alike. Recently there has been a flurry of media attention surrounding the completion of an effort to map out human DNA. The first stage of this project is now complete—the entire sequence of human DNA is spelled out. However, a virtually endless string of A's, T's, G's, and C's (representing the four nucleic acids that make up DNA) is not useful unless the roles of the underlying sequences are discovered.

    The quest to understand this vast new body of information has brought about an entirely new field of study called bioinformatics. Bioinformatics encompasses mathematics, computer science, and engineering, and life sciences. While genetic research is commonly associated with white coats, test tubes, and laboratories, it is sophisticated statistical modeling and massive supercomputers that are the critical bioinformatic tools that move genetic research forward. United Devices' first project uses a bioinformatics software program created at Washington University in St. Louis, under the leadership of Sean Eddy, Assistant Professor in the Department of Genetics, to analyze DNA and other proteins. This software is called HMMER (pronounced "hammer").

    How HMMER works
    HMMER's name comes from the technique it uses, called Hidden Markov Modeling (HMM). HMM was originally used in speech recognition. HMM tracked patterns in the English language, finding that certain sounds are more likely to come before or after other sounds. Because DNA also has sequence patterns in its structure, HMM has easily been adapted to genetic research.

    HMMER's task of finding matching patterns between two potentially related genetic sequences is comparable to searching for a particular phrase within a body of literature. This may be a relatively simple concept, but as a task, it would take a fair amount of effort to execute. An illustration could be a search for the phrase "To be, or not to be, that is the question" and its shorter subphrases such as "that is" within the collected works of Shakespeare. What makes HMMER special is that it would not only search for all occurrences of the phrase and its subphrases, but it would also attempt to answer the question, "In each instance of the subphrases, did Shakespeare intend to convey the same idea?" Another approach might be to take the collected works of Shakespeare and to use HMMER to test them against a newly discovered, old literary work to determine whether Shakespeare was the author.

    Scientists can use HMMER for different purposes. For example, a scientist might seek to establish a relationship between a disease and repeating genetic patterns in multiple people who have that disease. Another scientist might seek to establish relationships between humans and other animals by identifying similar patterns of genetic subsequences within the two species. Theoretically, this would allow a scientist to translate understanding about a disease or a birth defect found in mice into an understanding of the same condition in humans.

    Unraveling the mysteries of human genetics and human disease will undoubtedly be a challenge for some time to come. However, by choosing HMMER as our first application to run on the MetaProcessor platform, United Devices hopes to make a significant contribution to improving the diagnosis and treatment of disease.
  16. sorry about the 20,000 words but hey - you asked...

    Alembic eight string: 128 - .105 - .080 - .065 - .045 - .030 - .020 - .013
  17. john turner

    john turner You don't want to do that. Trust me. Staff Member

    Mar 14, 2000
    atlanta ga
    wow, cool stuff rockandroller. thanks for the heads up. :)

Share This Page