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Article in Science Daily on 22 January 2005 at http://www.sciencedaily.com/releases/2005/01/050121101919.htm
Date: 2005-01-22 'Rosetta' Software To Unlock Secrets Of Many Human Proteins University of Washington TechTransfer recently licensed software that will give scientists a huge advantage in the fight against disease. The software, known as Rosetta, predicts how proteins fold, information that is highly valuable to biological and biomedical researchers. UW Tech Transfer's Digital Ventures licensed Rosetta software without charge to the Institute for Systems Biology (ISB), a non-profit research organization. The institute has partnered with IBM and United Devices, an Austin-based company, to create the Human Proteome Folding Project, a global effort to determine the structures of the approximately 60 percent of human proteins with no known function. "How proteins fold determines how they are structured," said Lars Malmstroem of the UW laboratory that developed the program, "And how they are structured is related to their function in the body." Because there is an astronomical number of possible conformations for a given protein, collecting the data would take many thousands of lifetimes to complete with conventional computers, said Dr. Richard Bonneau, one of the researchers. But by summoning the computing power of millions of volunteers around the world, he said, the task will be completed in less than a year. IBM's World Community Grid, which was built using grid technology developed by United Devices, will enable millions of people to volunteer their personal computers to run Rosetta during periods of computer downtime. The information will be entered into a publicly accessible database, which scientists can then use to conduct research into new drugs and treatments. Rosetta works by virtually folding protein sequences into thousands of possible shapes, based on certain protein folding "rules" known by scientists. These rules are summarized in the program and are termed the "Rosetta score." The program tries a great many conformations and returns those with the lowest Rosetta scores; these conformations come closest to the actual shape of the protein. Rosetta was developed in the laboratory of UW Professor David Baker by a large team of scientists and students. Former post-doctoral fellow Richard Bonneau, who is now with the ISB, is the technical lead for the project. Rosetta software is available for licensing at: http://depts.washington.edu/ventures/UW_Technology/Licensing/. Editor's Note: The original news release can be found at http://www.uwnews.org/article.asp?articleID=7605 This story has been adapted from a news release issued by University Of Washington. |
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article in Grid Today dated 22 November 2004 at http://www.gridtoday.com/04/1122/104297.html
Special Section -- World Community Grid LEAD SCIENTIST ON PROTEOME PROJECT ON WORKING WITH BIG BLUE By Derrick Harris, Editor GRIDtoday spoke with Dr. Rich Bonneau from the Institute for Systems Biology, lead scientist on on the Human Proteome Folding Project, about how Grid computing will help his cause, and what it was like working with United Devices and industry bigshot IBM. GRIDtoday: How did IBM go about choosing the Human Proteome Folding Project as the first project on the World Community Grid? Was there a selection process? RICH BONNEAU: United Devices approached ISB and together ISB and UD approached IBM and other potential cooperate sponsors. IBM was by far the most open-minded and the ball started rolling (this was spring of 2003). Gt: How familiar with were you with Grid computing before the project came into being? How familiar are you now? BONNEAU: In graduate school we were familiar with SETI@home and dreamed that we would one day use such a strategy. But we're scientists, not programmers, so we focused mostly on developing the algorithm. A few years ago, when we realized that we (myself, Charlie Strauss, David Baker, etc. ) needed to scale up the Rosetta-annotation if we were going to annotate genomes. We've also always known that our algorithm is "embarrassingly parallel" and potentially perfect for distributed computing. When UD and IBM agreed to take on the project, that was the last step in a very long development process leading from showing we can fold small proteins to folding the human proteome. Gt: How much time do you estimate will be saved by using Grid technology versus predicting the shapes of proteins using the conventional method? BONNEAU: The method, Rosetta, is the same on the Grid or on our in-house cluster. What is different is that it would take 10-100,000 years to fold all the proteins we want to fold on our in-house cluster. On the Grid, we can do it in three-six months, without the Grid we can't think about it with current hardware and even a lavish budget. Gt: How is the Human Proteome Folding Project related to the Human Genome Project? BONNEAU: It is a logical next step: (A) The human genome project gave us the genome sequence; (B) lots of people worked hard to annotate the human genome and find the genes; (C) several proteins in the genome remain unannotated (they have no know function or structure); and (D) we try to fold those mystery proteins to get clues about their function in the cell. Gt: What kind of results can we expect to see as the process moves along? What cures could possibly emerge from this research, and what is the timeline for producing real, tangible results? BONNEAU: There is no silver bullet in biomedical research. What we want to do is take the 30-50 percent of protein domains that are of unknown function and begin the process of figuring out what roles they play in the human animal. Lots of these proteins are involved in disease, so we expect to facilitate large numbers (thousands) of functional insights into human proteins that play roles in disease. This will take the form of a large database that biologists can navigate to find information about the proteins they are interested in. Another important point is that biologists use lots of different kinds of information and we'll be integrating the data from this project with several other sources of bioinfo. Gt: Do you believe that being involved with such a high-profile project will result in further funding or other benefits for ISB? BONNEAU: This project is great for all parties involved. ISB has the problem and IBM and UD are showing that they can enable biotech research in big ways with their IT infrastructure know-how. I was a little afraid of working with Big Blue at first, but they've been great. In fact I want to thank Bill Bovermann, Viktors Berstis and Rick Alther of IBM. They are the guys that took Rosetta from us and put it up on the Grid. This process is called "boarding" an application and is made much faster by United Devices Software. Gt: What other research is ISB conducting right now? How do you foresee ISB using Grid computing (either public or private) on future research endeavors? BONNEAU: ISB is a big place, intellectually speaking, and is at the forefront of lots of stuff. Leroy Hood has more medals and prizes than you could fit in a Toyota van and was the inventor of the first DNA sequencer. There is cutting edge research going on in fields such as Cancer Biology, Alzheimer's, Biotechnology development, computational Biology, immunology, etc. ISB also has affiliations with lots of other places. http://www.systemsbiology.org will give you our party line, which is that we're working to get from current medicine (you go to the doctor and say "ahhhh") to quantitative, predictive, preventative, systems-wide medicine. So don't look at one part of the system, look at the whole thing (all 30,000-plus parts screaming around inside us). You can imagine that it is easier said than done, but we're making progress and it is an exciting time in biotech. |
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Article in the February 2005 issue of Technology Review at http://www.technologyreview.com/articles/05/02/wo/wo_hoffman020105.asp?p=1
Graham has already posted this in the 'Start Here' forum, but I am consolidating it with the other articles in this thread. The Protein Grid By Karen Epper Hoffman February 1, 2005 The Human Genome Project gave researchers an important initial roadmap to the human gene sequence, but it's a map that might prove tough to navigate, given that the function and structure of most of the proteins that do the work for those genes remains a mystery. That's why the Human Proteome Folding Project -- a recent collaboration between IBM, United Devices, the Institute for Systems Biology and the University of Washington -- is picking up where the Human Genome Project left off. Understanding the form and function of these proteins, which are at the core of many diseases and the natural target for many treatment drugs, will ultimately put researchers that much closer to understanding why certain diseases happen and how to treat and cure them. "The Human Genome Project is the foundation on which this project sits," say Dr. Rich Bonneau, senior scientist for the Institute for Systems Biology, the Seattle, Washington non-profit research institute that is spearheading the biology research effort for the Human Proteome Folding Project. But running the computations necessary to create such a catalogue could take literally a million years on a state-of-the-art PC -- 50 years if you used a substantially more powerful commercial 1,000-node cluster computer. But by 'borrowing' unused computing cycles from volunteers who download a program to their PCs -- a la SETI@Home -- researchers believe they can get at least a rough sketch of more than 100,000 proteins before the end of this year. Tens of thousands of people have already downloaded the program through IBM's and United Devices' grids, both of which are being used for this program, and that number is hoped to quickly reach into the millions. The Beginning of a Beautiful Friendship The Institute for Systems Biology (ISB) was approached about 18 months ago by United Devices, an Austin technology firm that makes software for grid computing. The software company had a vested interest in life science-related projects as it counts five of the world's six biggest pharmaceutical companies as customers, and has been running its own distributed community grid since April 2001. As with the well-known SETI@Home project, computer users can go online to United Devices' site at www.grid.org, and download a client that runs computations on their computer's unused cycles. Using the huge computational power of its own grid, United Devices has run previous projects looking into anti-viral leads for smallpox, and screening molecules to find treatments for anthrax. When United Devices approached the Institute for Systems Biology, says Ed Hubbard, the software company's president and founder, he was looking for "problems that they might solve" by harnessing the grid's computing strength. And, as it turned out, mapping human protein structures was a good fit. Researchers at the Institute were already using Rosetta, a software package developed at the University of Washington to predict the structure of proteins. But while Rosetta offers a good forecast for what these proteins might look like, its predictions are not infallible. Researchers still need to run countless computations to determine the accuracy of a protein's three-dimensional structure. That's where the grid comes in handily. "I had the idea for some time that Rosetta would be the ideal application for the grid," Bonneau says. The United Devices grid, with more than three million participants, already runs about a petaflop of computing power -- that means that the system can run 1,000 trillion calculations per second, making the grid about as powerful as all the supercomputers in the world combined. Indeed, Bonneau has already had an early insight into how much the grid could speed up the Institute's work: He says his team had been working with Rosetta for two years to get half-way through predicting the structure of a yeast genome -- a project they were able to finish up on the grid in two weeks. Two Grids, No Waiting Together, the ISB and United Devices brought in IBM -- with whom United Devices had worked on its previous grid-based smallpox project. IBM was in the process of setting up its own World Community Grid, which it officially launched in November 2004. The Human Proteome Folding Project became its first effort -- and indeed the first time grid computing has been used for a biology-related project. Since its launch, Stan Litow, president of IBM's International Foundation, which helps oversee the World Community Grid, says about 70,000 people have downloaded the software and he expects to have at least one million participants by year end. "It was so clear that the repetitive calculations [of the protein project] needed the grid," Litow says. "And this was not a narrow project…it has ramifications across a variety of research areas." With two grids at work, Bonneau says that within six months he hopes to have the database populated with upwards of 100,000 protein "domain" structures -- a "low-resolution" shot of what the protein looks like at the architecture or fold level. Biologists and medical researchers can, in turn, use that data to get a better (if still not exact) idea of what proteins look like and how they interact. Bonneau expressed hope that success in the Human Proteome Folding Project will lead to a second phase, where the grid is used to model a few key proteins to a higher level of detail. Modelling protein structures down to their atomic detail would give researchers more to work with, but would also be even more computationally intense. But for now, the Human Protein Folding Project is a necessary next step to better understanding why our bodies do what they do. "I really like the idea that this project will have usable, practical results," Bonneau says. "A lot of distributed computing projects don't produce results that people can relate to." |
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Here is a 26 November 2004 article from Protein Feed at http://feed.proteinos.com/item/2368
Protein Feed 5.1 Protein Powered Posted 26.11.04 By will If the Human Genome Project gave biologists the equivalent of a parts list for a car, then the latest biology mega-project will be like the instructions that show how the parts combine to make an operating fuel injector. That's one way to describe the aim of a partnership announced yesterday between IBM, the Seattle-based Institute for Systems Biology, the University of Washington and United Devices, an Austin, Texas, software company. The actual goal will be to put together a database of human proteins, the three-dimensional substances that carry out the functions of genes. This collaboration on the Human Proteome Folding Project will be performed on IBM's World Community Grid, which can tap into the computational power of millions of idle computers around the world. The off-hours computer capacity, which can be donated by businesses and individuals, will run calculations to predict the shape of 50,000 to 100,000 proteins that scientists know little about. Once the results are in, they will be available on a public database. Scientists may someday use it to better understand how bodily proteins go bad in diseases like cancer, Alzheimer's and AIDS. Understanding how a protein fold helps researchers know what the protein will or will not do, and how it connects to other proteins. For example, muscle proteins of a certain shape connect to form a muscle fiber. The grid computing technique has been used to sift through data from space for signs of extraterrestrial life, but the protein project will be applied for the first time to biology. When it is complete, the database is expected to hold 400 terabytes of data, which some believe may top the amount now on the Internet. Richard Bonneau, a scientist leading the project at the Institute for Systems Biology, said if enough computer users volunteer from around the world, the millions of calculations to predict protein folding could be done in three to six months. At the current speed of the institute's own supercomputers, it would take 100,000 years, Bonneau said. "The computational resources are priceless," Bonneau said. Bonneau is a former graduate student at the University of Washington who developed mathematical formulas there to predict protein folding. He said his methods are accurate about half the time, significantly better odds than most who have tried. He will collaborate on the folding project with his former professor at the UW, Dr. David Baker. Bonneau said there will be challenges in storing the data, checking for accuracy and integrating the results with other databases. Then the task is to figure out how to make other biologists use it. "In biology there are no silver bullets, and this is clearly not a silver bullet, but we hope to shine a light on the functioning of 100,000 proteins," Bonneau said. In the words of institute co-founder Leroy Hood, "This project will take an enormous step toward defining the dark universe of proteins." Jennifer Van Brunt, editor of Signals, an online biotech industry magazine, said the project could be very useful for academic and industry scientists. She said companies often struggle to make folded proteins into drugs that bind tightly and properly with cells. But with a deeper knowledge of how proteins configure, she said, scientists could think of ways around the problems. "Ultimately, it will be very useful if you could use it to design proteins from scratch," she said. Source: The Seattle Times |
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From the February 2005 issue of Primeur Monthly, the monthly news service for the European HPCN community at http://www.hoise.com/primeur/05/articles/monthly/AE-PR-02-05-60.html
'Rosetta' software to unlock secrets of many human proteins Seattle 22 January 2005 University of Washington (UW) TechTransfer recently licensed software that will give scientists a huge advantage in the fight against disease. The software, known as Rosetta, predicts how proteins fold, information that is highly valuable to biological and biomedical researchers. UW Tech Transfer's Digital Ventures licensed Rosetta software without charge to the Institute for Systems Biology (ISB), a non-profit research organisation. The institute has partnered with IBM and United Devices, an Austin-based company, to create the Human Proteome Folding Project, a global effort to determine the structures of the approximately 60 percent of human proteins with no known function. "How proteins fold determines how they are structured", stated Lars Malmstroem of the UW laboratory that developed the programme, "and how they are structured is related to their function in the body." Because there is an astronomical number of possible conformations for a given protein, collecting the data would take many thousands of lifetimes to complete with conventional computers, according to Dr. Richard Bonneau, one of the researchers. But by summoning the computing power of millions of volunteers around the world, he said, the task will be completed in less than a year. IBM's World Community Grid, which was built using Grid technology developed by United Devices, will enable millions of people to volunteer their personal computers to run Rosetta during periods of computer downtime. The information will be entered into a publicly accessible database, which scientists can then use to conduct research into new drugs and treatments. Rosetta works by virtually folding protein sequences into thousands of possible shapes, based on certain protein folding "rules" known by scientists. These rules are summarized in the programme and are termed the "Rosetta score". The programme tries a great many conformations and returns those with the lowest Rosetta scores; these conformations come closest to the actual shape of the protein. Rosetta was developed in the laboratory of UW Professor David Baker by a large team of scientists and students. Former post-doctoral fellow Richard Bonneau, who is now with the ISB, is the technical lead for the project. Rosetta software is available for licensing at http://depts.washington.edu/ventures/UW_Technology/Licensing/". |
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Abstract of 13 January 2005 seminar at University of British Columbia at http://www.michaelsmith.ubc.ca/BioEvents/event.php?ID=43&Date=2005-01-13
UBiC Seminar Thursday January 13th, 2005 Time: 10:00 AM - 11:00 AM Contact: Francis Ouellette Phone: 604 875-38036 Email: admin@bioinformatics.ubc.ca Web: http://bioinformatics.ubc.ca Location: MSL Auditorium 2185 East Mall, Vancouver, BC BC V6T 1Z4 Information: UBC Bioinformatics Centre presents a seminar by Dr. Richard Bonneau, Senior Scientist, Institute for Systems Biology Title: The Human Proteome Folding Project and the Inferelator: two examples of computational biology in a systems biology context Abstract: I will survey two major computational efforts currently underway to 1) determine the structure of a large fraction of all proteins of unknown function using Rosetta structure prediction on the World Community Grid and 2) infer the regulatory networks of several organisms de novo from systems-biology data. Human Proteome Folding Project: Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of genome-wide changes in mRNA and protein expression, protein-protein and protein-DNA interactions. I have previously shown that Rosettade novostructure prediction can be used to predict three-dimensional structures for proteins of unknown function and that those predicted structures can be used in a systems biology context to glean biological insight into protein function. Rosetta de novo structure prediction is quite computationally intensive and we have implemented a distributed computing strategy that currently employs over 3 million devices globally in collaboration with United Devices and IBM. We have begun folding on the grid, using Rosetta, all relevant protein domains in all fully sequenced genomes (including the Human genome and the genomes of all sequenced major Human pathogens). The results from this effort will be publicly available. http://www.systemsbiology.org/Default.aspx?pagename=humanproteome Regulatory Network Inference: I will describe a transparent modular method for the inference of gene regulatory influences on a genome-wide scale. At the core of this statistical learning framework are two methods that work in tandem to infer regulatory networks, simultaneously cluster genes and experimental conditions (bicluster), and detect cis-acting regulatory motifs. I will describe our results from our initial application of this method to the Halobacterium NRC-1 and H. pylori. The first part of the procedure (biclustering) detects groupings of genes that are coherent across subsets of conditions (based on microarray data and upstream sequence) resulting in sets of gene/condition groupings and regulatory motifs for a given organism. The biclustering procedure uses motif detection and function information in the form of predicted association networks to guide an iterative search for coherent gene/condition groupings, effectively integrating three major biological data-types (co-expression, co-occurrence of transcription factor binding motifs, and previously known or predicted functional networks). The second phase of the regulatory network inference procedure, the Inferelator, then determines the network of regulatory influence that control the expression of each bicluster (based on microarray data, chip-chip data, and the results of the Biclusterer). |
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Here is a wire report that David Autumns found at
----------------------------------------http://home.businesswire.com/portal/site/goog...425006124&newsLang=en Note the time on the wire report is just before the scheduled time for the presentation at the ISB Symposium. Added: Now it is listed in the ISB press release archive at: http://www.systemsbiology.net/extra/PressRelease_042505.html April 25, 2005 04:53 PM US Eastern Timezone Institute for Systems Biology Symposium Addresses Need for Better Computational Tools; World Community Grid Touted as Novel Approach to Untangling Complexities of Protein Function BIOWIRE2K SEATTLE--(BUSINESS WIRE)--April 25, 2005--The Institute for Systems Biology announced today at its 2005 international symposium on Computational Challenges in Systems Biology that ISB's Human Proteome Folding Project launched on IBM's World Community Grid in November 2004 has already predicted 50,000 protein structures. "This project showcases the enormous power of collaborations," stated Dr. Richard Bonneau, senior scientist at the Institute for Systems Biology. "Through a partnership with IBM we are utilizing World Community Grid which is enabling us to complete a project in less than a year that would have taken us approximately 100,000 years to complete with the current computational power at ISB. We have already predicted 50,000 protein structures and are well on our way to reaching the goal of between 100,000-150,000 structures." The project, funded by IBM and tapping into the unused computational power of idle computers is helping predict the shape of human proteins and helping make new scientific and medical breakthroughs come at an ever faster pace -- certainly more rapidly than in any new field of biology in the 20th Century. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of genome-wide changes in mRNA and protein expression, protein-protein and protein-DNA interactions. World Community Grid is enabling ISB researchers to predict three dimensional structures, which are more highly conserved than one dimensional structures. Understanding three dimensional structures allow researchers to identify the presumptive function of proteins. These functions can then be assigned to appropriate networks. Researchers expect that approximately 2/3 of the folded proteins will result in correct topologies and that approximately 1/3 of the predicted structures will match previous folds now stored in the protein data bank/PDB. Folded proteins explain many biological functions -- just as the parts in a car determine the role they play in the car's function, three dimensional protein structures of protein determine the roles they play in living organisms. Once completed, the Human Proteome Folding Project will enable ISB to provide a new proteomics tool that can be widely used by the academic community in an open source environment. Speakers at this year's symposium included Rich Bonneau, ISB senior scientist and Viktors Berstis, Senior Software Engineer at IBM Global Services, outlining current efforts to run Rosetta de novo structure prediction on World Community Grid, and applications of this new dataset to the reannotation of proteins of unknown function in over 60 complete genomes via de novo structure prediction. Other presenters included keynote speaker Dr. Nathan Myhrvold, Founder of Intellectual Ventures, LLC and former chief technologist at Microsoft Corporation who founded Microsoft Research, and world leaders in the area of computational biology. About the Institute for Systems Biology The Institute for Systems Biology (ISB) is an internationally renowned non-profit research institute dedicated to the study and application of systems biology. ISB's goal is to unravel the mysteries of human biology and identify strategies for predicting and preventing diseases such as cancer, diabetes and AIDS. The driving force behind the innovative "systems" approach is the integration of biology, computation, and technology. This approach allows scientists to analyze all of the elements in a system rather than one gene or protein at a time. Located in Seattle, Washington, the Institute has grown to 11 faculty and more than 170 staff members; an annual budget of more than $25 million; and an extensive network of academic and industrial partners. For more information about the ISB visit: http://www.systemsbiology.org About World Community Grid To date, more than 100,000 computers are participating in World Community Grid but more are needed to continue this important work. Individuals can volunteer their computer's idle computing time by joining at http://www.worldcommunitygrid.org. World Community Grid is powered by IBM technology, which includes IBM eServer p630 and x345 systems and IBM's Shark Enterprise Storage Server running IBM DB2 database software and the AIX and Linux operating systems. IBM DB2 software will supports millions of SQL queries a day as it manages all aspects of the data provided by potentially millions of computers working in concert. World Community Grid will harnesses computing time donated by potentially millions of PCs and laptops around the world for humanitarian research. For more information about the Human Proteome Folding Project, visit http://www.worldcommunitygrid.org Contacts Institute for Systems Biology Gretchen Sorensen, 206-732-1239 gsorensen@systemsbiology.org [Edit 1 times, last edit by Former Member at Apr 26, 2005 7:00:24 PM] |
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Here is a report about our partner, Marist College, that David Autumns found at http://www.midhudsonnews.com/News/WWG-25Apr05.htm
Monday, April 25, 2005 World Community Grid powered by 100,000 devices World Community Grid enlisted its 100,000th computer and its first university partner, Marist College in Poughkeepsie, in the humanitarian effort to find answers to the world's most daunting scientific problems through unparalleled computational research provided by IBM. World Community Grid ( http://www.worldcommunitygrid.org ) is harnessing the unused computer power of the world's computers and directing it to humanitarian efforts. In less than five months, more than 64,000 individuals have signed up their personal and business computers and have donated more than 8,250 years of run time. By joining World Community Grid, Marist has the potential to contribute more than 7,000 PCs and laptops to this humanitarian effort. The Human Proteome Folding Project, World Community Grid's first project, is identifying the proteins that make up the Human Proteome so that scientists can better identify causes and potential cures for diseases like malaria and tuberculosis. In this project, World Community Grid has completed more than six million work units in five months, which might have taken a large supercomputer five years to accomplish. "World Community Grid has tremendous appeal and in a few months already has enabled individuals concerned about important causes like fighting cancer to get involved in the solution," said Stanley Litow, vice president, IBM Corporate Community Relations, and president, IBM International Foundation. "We are very excited to welcome Marist College as World Community Grid's first university partner. We applaud Marist's leadership as the first of many universities we expect to join this effort." "Joining World Community Grid was a natural for us," said Marist College President Dennis Murray. "With our emphasis on technology and our commitment to serving others, we saw this opportunity as a great way to get our students directly involved in a very innovative project first hand. By joining World Community Grid, they are learning about the power of grid computing while at the same time giving back to society, which is in keeping with the Marist mission." |
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