{bio,medical} informatics
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The Scientist
A Flood in Genomics
[requires 'free' registration]
"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.
Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.
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News.Com
IBM computers picked for cancer research
"IBM will supply the University of Pennsylvania and four hospitals with computers that will link into a computing "grid" to check for breast cancer, the company will announce Wednesday.
The grid will be used to detect breast cancer in patients, store mammograms in digital form and identify populations that are particularly susceptible, the company said in a statement. The system can be used, for example, to compare a new mammogram to a previous year's image to detect changes.
IBM, along with rivals such as Sun Microsystems and Compaq Computer, have been backing grid computing, which joins computers and storage systems into a large pool of computing power.
redux [11.21.01]
"The US National Science Foundation has announced a $12 million programme - called the NSF Middleware Initiative (NMI) - to develop middleware: software that allows scientists to share applications, scientific instruments and data, and collaborate with their colleagues across high-performance networks.
The effort will build on the success of the Globus project in developing middleware tools for grid computing, and will integrate Globus and other emerging middleware components into a well-tested, comprehensive, commercial-quality, middleware distribution package that runs on multiple platforms. These middleware distributions will be disseminated to research labs and universities worldwide."
redux [11.12.01]
"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.
Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."
"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.
Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."
"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."
redux [11.06.01]
"Celera is utilizing a novel approach to bioinformatics to speed up its proteomics research.
The Rockville-based company is using Frontier, a proprietary technology, to harness computer power while the computers are shut down, in sleep mode, or being used for other applications."
" Through Frontier, Celera can tie together its employees' computers so that they all work on large-scale, proteomic sequencing. Frontier detects when a computer has idle capacity, and therefore room, to work on a research application. Such capacity could be available even when a person is using his or her computer during everyday tasks."
redux [04.04.01]
[requires 'free' registration]
"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."
""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""
redux [09.23.01]
"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.
IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.
"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."
redux [08.29.01]
"According to The Hitchhiker's Guide to the Galaxy, hyper-intelligent pan-dimensional beings (disguised as mice) are using us to compute The Ultimate Question of Life, The Universe, And Everything. Now earthling scientists have roped unsuspecting web servers into a similar - albeit slightly less ambitious - exercise in parasitic computing.
Using the Internet itself as a computer, Jay Brockman and colleagues at the University of Notre Dame, Indiana, have solved a mathematical problem with the unwitting assistance of machines in North America, Europe and Asia."
""The vast quantities of data involved in the genomic era of drug discovery are quickly outpacing advances in computing technology," said Robert North, Entropia CEO. "Distributed computing allows companies to cost-effectively access the massive computing power they'll need by using their existing PC networks. It's quite exciting that companies like Novartis are deploying our platform to demonstrate the potential of distributed computing as a valuable tool in drug discovery efforts.""
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."
"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
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Business Today
`Bioinformatics' grows: Biotech computing is boon to investors
The bioinformatics industry - broadly defined as using computers in drug discovery - generated revenue of $1.38 billion in 2000, analysts at Frost & Sullivan figure. That number will reach at least $6.9 billion by 2007, analysts predict.
Although computers have been used by biotechnology and drug companies for at least a decade, the bioinformatics segment has taken off only in the last three years. And most believe it isn't anywhere near its potential.
``It's an exciting area, but it's an area that will come into its own in the next three to five years,'' said Brad Peters, Frost & Sullivan senior industry analyst.
redux [11.20.01]
"A new Frost & Sullivan report augurs an explosion in the U.S. bioinformatics market from $1.38 billion in 2000 to $6.9 billion in 2007. The industry is full of players, and there's almost certain to be consolidation. The friendly capital markets of 1999 and 2000 allowed many to raise enough cash to hold out for the best bid."
redux [07.16.01]
"A year after the deciphering of the human genome boggled the world, investors are realizing that manipulating genes to fight disease is still in its infancy -- and far from profitable."
Nowhere is that more clear than in the industry for genetic information, or bioinformatics."
redux [03.14.01]
"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.
If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.
Wow! Rewrite that resumé to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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SiliconValley.Com
Computer scientists push to publish code powering genetic research
"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.
Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.
``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."
redux [08.18.01]
"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.
While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."
"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."
redux [11.05.01]
"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."
"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.
For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"
redux [08.23.01]
"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."
redux [07.27.00]
"Good software forms seamless connections; as George Orwell said of prose, the best is like a window pane: transparent. The obscurity of commercial binaries is an obstacle to good quality communication between systems. In healthcare, good communication is too important to remain proprietary. Software developers should remain confident that there will always be work for the future in discovering, providing, and adapting applications for organizations, and training people to use them. This, rather than the sharp-suited gouging of Bill Gates wannabees, should become the predominant business model for software in the British NHS. Software engineering will become a profession more like medicine and the law: in which practitioners earn a fair hourly reward for their experience at interpreting, evaluating and applying knowledge from a specialized domain to the benefit of their clients. Current models, which restrict the sharing and development of knowledge, are certainly counterproductive and arguably unethical. Open source is the future: all we have to do is built it."
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Bio.OReilly.Com
An Interview with Nat Torkington and Lorrie LeJeune
"Tim O'Reilly has always felt that one of the most important missions of O'Reilly books is to address "information pain." Information pain happens when people want to do something and they can't find the resources to help them. Bioinformatics, being an intersection point between two very different disciplines, is filled with information pain. Biologists are learning to program, programmers are struggling to understand genetics. We saw it as an opportunity to help both communities learn the critical skills of the other."
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Scientific Computing World
Scientific sharing across computer networks in USA
"The US National Science Foundation has announced a $12 million programme - called the NSF Middleware Initiative (NMI) - to develop middleware: software that allows scientists to share applications, scientific instruments and data, and collaborate with their colleagues across high-performance networks.
The effort will build on the success of the Globus project in developing middleware tools for grid computing, and will integrate Globus and other emerging middleware components into a well-tested, comprehensive, commercial-quality, middleware distribution package that runs on multiple platforms. These middleware distributions will be disseminated to research labs and universities worldwide."
redux [11.12.01]
"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.
Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."
"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.
Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."
"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."
redux [11.06.01]
"Celera is utilizing a novel approach to bioinformatics to speed up its proteomics research.
The Rockville-based company is using Frontier, a proprietary technology, to harness computer power while the computers are shut down, in sleep mode, or being used for other applications."
" Through Frontier, Celera can tie together its employees' computers so that they all work on large-scale, proteomic sequencing. Frontier detects when a computer has idle capacity, and therefore room, to work on a research application. Such capacity could be available even when a person is using his or her computer during everyday tasks."
redux [04.04.01]
[requires 'free' registration]
"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."
""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""
redux [09.23.01]
"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.
IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.
"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."
redux [08.29.01]
"According to The Hitchhiker's Guide to the Galaxy, hyper-intelligent pan-dimensional beings (disguised as mice) are using us to compute The Ultimate Question of Life, The Universe, And Everything. Now earthling scientists have roped unsuspecting web servers into a similar - albeit slightly less ambitious - exercise in parasitic computing.
Using the Internet itself as a computer, Jay Brockman and colleagues at the University of Notre Dame, Indiana, have solved a mathematical problem with the unwitting assistance of machines in North America, Europe and Asia."
""The vast quantities of data involved in the genomic era of drug discovery are quickly outpacing advances in computing technology," said Robert North, Entropia CEO. "Distributed computing allows companies to cost-effectively access the massive computing power they'll need by using their existing PC networks. It's quite exciting that companies like Novartis are deploying our platform to demonstrate the potential of distributed computing as a valuable tool in drug discovery efforts.""
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."
"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
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The New York Times
Exelixis in Deal for Genomica
[requires 'free' registration]
"Exelixis said yesterday that it would acquire Genomica, a maker of software for genetic analysis, for about $110 million in stock in a sign of further consolidation in the genomics business.
The price is roughly equivalent to the amount of cash and long-term investments held by Genomica, indicating that Exelixis is picking up Genomica's software essentially for nothing.
"Exelixis CEO George Scangos said although his company intends to use Genomica's software for its internal drug development activities, he stressed that he does not plan to continue commercial sales of the firm's products and said that he is more interested in Genomica's assets, which as of Sept. 30 comprised $110.8 million in cash, cash equivalents, and investments.
"We do not intend to get into the software business," said Scangos in a conference call to discuss the acquisition. "We believe that Genomica's substantial cash and investments will significantly enhance our ability to move our drug-discovery programs forward, and that their software will be an important tool to manage human data during the clinical development of our compounds.""
"A new Frost & Sullivan report augurs an explosion in the U.S. bioinformatics market from $1.38 billion in 2000 to $6.9 billion in 2007. The industry is full of players, and there's almost certain to be consolidation. The friendly capital markets of 1999 and 2000 allowed many to raise enough cash to hold out for the best bid."
redux [10.17.01]
""We're an information-based industry, but we've been a bit behind in the extent to which we've been using computer-based tools," Dinerstein says. "They've had better computer models for oil drilling than we've had for drug discovery."
While executives in this closely guarded industry won't say how much they're investing in research and development informatics, they are definitely hopping on board. Merck & Co. in Whitehouse Station, N.J., recently paid $620 million to acquire Rosetta Inpharmatics, a genomics and technology company based in Kirkland, Wash. And New York City-based Pfizer says it recently spent more than $100 million to create an "integrated system of high-speed discovery technologies." Pradip Banderjee, a senior partner with Accenture Consulting, conservatively estimates that drugmakers as a whole spend more than $4 billion a year on that kind of technology, not including the cost of hardware."
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Perl.Com
Parsing Protein Domains with Perl
"The Perl programming language is popular with biologists because of its practicality. In my book, Beginning Perl for Bioinformatics, I demonstrate how many of the things biologists want to write programs for are readily--even enjoyably--accomplished with Perl.
My book teaches biologists how to program in Perl, even if they have never programmed before. This article will use Perl at the level found in the middle-to-late chapters in my book, after some of the basics have been learned. However, this article can be read by biologists who do not (yet) know any programming. They should be able to skim the program code in this article, only reading the comments, to get a general feel for how Perl is used in practical applications, using real biological data."
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KDNuggets
New Book: Statistical Methods in Bioinformatics: An Introduction
"This book grew out of the need to teach bioinformatics to graduate students. At the same time however, it is organized to appeal to a wider audience. It should appeal to any biologist or computer scientist who wants to know more about the statistical methods of the field, as well as to a trained statistician who wishes to become involved in bioinformatics. Only a basic understanding of biological concepts is assumed, and all concepts are explained when used or can be understood from the context. This book also describes some of the main statistical applications in the field, including BLAST, gene finding, and evolutionary inference, much of which has not yet been summarized in an introductory textbook."
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GenomeWeb
Genome Database Head Ousted in Dispute Over Commercializing Data
"The principal investigator and director of the GDB Human Genome Database in Canada has been ousted by the hospital that hosted the database, GenomeWeb has learned.
A. Jamie Cuticchia, who has worked with the GDB since 1992, said that he was fired by the Toronto-based Hospital for Sick Children on Nov. 2, and that the hospital had “seized” data from the GDB three weeks earlier in a dispute over efforts to commercialize the database."
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Stanford Medical Informatics Preprint Archive
Automating Data Acquisition into Ontologies from Pharmacogenetics Relational Data Sources Using Declarative Object Definitions and XML
"Ontologies are desirable for building knowledge bases that can perform inference over the breadth of genetic and clinical knowledge in domains such as pharmacogenomics. But because ontologies change and evolve, it is time consuming to maintain stable connections with external data sources that are in relational format. A method for interfacing ontology models with data acquisition from external relational data sources is proposed. This method uses a declarative interface between the ontology and the data source, modeled in the ontology and implemented using XML schema. Data is imported from the relational source into the ontology using XML that is validated using an XML schema. We have implemented this approach in PharmGKB (http://www.pharmgkb.org/), a pharmacogenetics knowledge base we are developing. Our goals were to (1) import genetic sequence data, collected in relational format, into the pharmacogenetics ontology, and (2) automate the process of updating the links between the ontology and data acquisition when the ontology changes. We tested our approach by linking PharmGKB with data acquisition from a relational model of genetic sequence data. The ontology subsequently evolved, and we were able to rapidly update our interface with the external data and continue acquiring the data. Similar approaches may be helpful for integrating other heterogeneous information sources in order make the diversity of pharmacogenetics data amenable to computational analysis."
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GenomeWeb
Venter Greets Geeks, Geeks Greet Venter
"Celera Genomics president Craig Venter has asked the high-performance computing community for its help in solving the coming data challenges of life sciences research.
"All existing database structures are totally inadequate" for the next generation of biology, said Venter in his opening keynote address to SC2001, the annual supercomputing conference that began in Denver on Tuesday."
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ZDNet News
New boost for open-source supercomputing
"Platform Computing, a company that tries to harness the collective computing power on computer networks, has signed a deal to commercialize an open-source supercomputing project.
Platform is working with the Globus Project to commercialize the Globus Toolkit for governing the use of computers and storage systems joined into a large computing "grid," Platform said Wednesday."
"Grid computing, though, often uses higher-powered computers than mere desktop PCs, and has attracted the interest of IBM, which thinks corporate customers as well as academics will use grid methods. IBM is working with Globus to boost this expansion.
Grid computing has long held potential for some types of computing tasks--typically those that don't require as much communication between one computing task and another. For this reason, they don't replace single mammoth supercomputers such as those from Cray. However, grid computing is popular among pharmaceutical companies and others."
"Computational Grids are emerging as a popular paradigm for solving large-scale compute and data intensive problems in science, engineering, and commerce. However, application composition, resource management and scheduling in these environments is a complex undertaking. In this paper, we illustrate the creation of a virtual laboratory environment by leveraging existing Grid technologies to enable molecular modeling for drug design on distributed resources. It involves screening millions of molecules of chemical compounds against a protein target, chemical database (CDB) to identify those with potential use for drug design. We have grid-enabled the molecular docking process by composing it as a parameter sweep application using the Nimrod-G tools. We then developed new tools for remote access to molecules in CDB small molecule database. The Nimrod-G resource broker along with molecule CDB data broker is used for scheduling and on-demand processing of jobs on distributed grid resources. The results demonstrate the ease of use and suitability of the Nimrod-G and virtual laboratory tools."
redux [11.06.01]
"Celera is utilizing a novel approach to bioinformatics to speed up its proteomics research.
The Rockville-based company is using Frontier, a proprietary technology, to harness computer power while the computers are shut down, in sleep mode, or being used for other applications."
" Through Frontier, Celera can tie together its employees' computers so that they all work on large-scale, proteomic sequencing. Frontier detects when a computer has idle capacity, and therefore room, to work on a research application. Such capacity could be available even when a person is using his or her computer during everyday tasks."
redux [04.04.01]
[requires 'free' registration]
"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."
""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""
redux [09.23.01]
"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.
IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.
"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."
redux [08.29.01]
"According to The Hitchhiker's Guide to the Galaxy, hyper-intelligent pan-dimensional beings (disguised as mice) are using us to compute The Ultimate Question of Life, The Universe, And Everything. Now earthling scientists have roped unsuspecting web servers into a similar - albeit slightly less ambitious - exercise in parasitic computing.
Using the Internet itself as a computer, Jay Brockman and colleagues at the University of Notre Dame, Indiana, have solved a mathematical problem with the unwitting assistance of machines in North America, Europe and Asia."
""The vast quantities of data involved in the genomic era of drug discovery are quickly outpacing advances in computing technology," said Robert North, Entropia CEO. "Distributed computing allows companies to cost-effectively access the massive computing power they'll need by using their existing PC networks. It's quite exciting that companies like Novartis are deploying our platform to demonstrate the potential of distributed computing as a valuable tool in drug discovery efforts.""
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years."
"The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
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National Post Online
Compaq Canada reaches deal to distribute genome database
"Celera Genomics, the first company to successfully sequence the human genome, announced a deal with Compaq Canada Corp. yesterday that will give Canadian non-profit researchers access to its genomic database."
""This is the first time we've entered into an agreement where the computing environment and the data will go hand in hand," said Dr. Craig Venter, president of Celera and one of world's foremost genome researchers. "There's been interest in giving Canada access to this information for some time, it just hasn't been possible to get it together.""
"Academic research contracts for access to this system have been priced around $15,000, said Lewis, but under the new arrangement the price will fall to around $8,000. He estimated that Celera, based in Rockville, Md., holds fewer than 25 contracts with Canadian academic organizations.
“It allows smaller universities to access our products without a lot of hassles,” Lewis added in an interview. “There’s been some really good work in the Maritime provinces, for example, but they are small universities. This will make it as easy for them as it is for large universities.”"
redux [06.26.01]
"In 1998, biotech upstart Celera Genomics needed a supercomputer to help it map the human genome. It didn't turn to IBM , which built 204 of the 500 fastest supercomputers. Both Celera and its academic competition, the Human Genome Project, used machines built by Compaq Computer. Two years later, Compaq is the leading seller of supercomputers to biological researchers.
But IBM noticed that biologists now need microprocessors as much as microscopes. A year ago, it used $100 million to start a division that sells computers, software and services to biotechnology and drug companies. This life sciences division has had some success; pulling into second place behind Compaq, it must do better."
redux [08.14.01]
"For years, technologists have dreamed that information technology and biotechnology would someday converge into one seamless superscience that could crack the molecular code of disease and yield a gold mine of new treatments and cures. It always seemed so logical, even if it never quite seemed to happen. Some very big names in tech -- Bill Gates ( MSFT ), Paul Allen, and Jim Clark, among others -- for years have been placing bets on so-called convergence companies that promised to exploit the merging of computing and biotech. Allen alone has investments in more than 50 of them, mostly obscure companies that use words like "genomics," "bioinformatics," and "proteomics" to describe what they do. This industry is so new it hasn't settled on a single name yet."
"Now, like a middle-age actor who has just been discovered, convergence has hit the big time. Corporate giants such as IBM ( IBM ) and Compaq ( CPQ ) are pouring $100 million dollops of cash into "life science" projects that mesh computers and biotech."
[ rhetoric ]
“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”
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