{bio,medical} informatics
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"IBM HAS announced plans to invest $100 million in its new life sciences unit, marking a major step in the company’s efforts to bridge the divide between biology and computational science.
“We see this as an important emerging growth market,” Caroline Kovac, vice president of IBM’s Life Science Solutions Software Group, said. “Over the next two and a half years we are going to put $100 million in business development in life sciences.”"
"IBM’s life science unit, which currently employs 40 people, will focus on four main areas: supercomputing, databases, knowledge management, and e-business for the life sciences. In 2000 at least, the unit expects to dedicate the lion’s share of its resources to bioinformatics."
redux [06.03.00]
Washinton Post IBM to Put Genetics on Fast Track
"Here is the plan: IBM scientists intend to spend five years building the fastest computer in the world, 500 times faster than anything in existence today. It will suck down every spare watt of electricity and throw off so much heat that engineers have bought a gas turbine the size of a jet engine to cool it.
The machine, dubbed Blue Gene, will be turned loose on a single problem. The computer will try to model the way a human protein folds into a particular shape that gives it unique biological properties. Obscure as it may sound, that kind of puzzle is at the heart of mankind's efforts to understand the nature of consciousness, the origins of sex, the causes of disease and many other mysteries."
redux [06.05.00]
BusinessWeek The Genome Gold Rush
"But for all the drama behind the unveiling of humanity's genetic code, the race marks a beginning, not an end. In fact, the pharmaceutical and biotech industries are already drowning in a flood of genetic information, says Mihael Polymeropolous, vice-president for pharmacogenetics at Novartis. ''That's why this race for me is a little silly,'' he says. ''The real race is who will develop the tools to analyze the genome first.''"
"Another consequence of this flood of information is that the computer has become one of the most important tools in biology. Consider these experiments. You want to measure how each of tens of thousands of drugs affects every one of humanity's 34,000 to 120,000 genes and its 1 million proteins. Or you want to compare the sequences of thousands of unknown proteins with the 3 billion bits of DNA in the human genome. In each case, the amount of data to analyze is mind-boggling. ''We have reached a point where processing information is one of the major bottlenecks,'' says Sharon L. Nunes, senior researcher at the computational biology center at IBM's T.J. Watson Research Center.
Once the information problem has been solved, scientists will be left with a wealth of possibilities. Having the full human genome sequence and all these new tools ''will keep researchers busy for a long time,'' says Vincent Dauciunas, head of strategic planning in the chemical analysis group at toolmaker Agilent. ''I call it the Full-Employment Act for the millennium.''"
redux [02.07.00]
IBM.com IBM Joins Group to Create Library of Genetic Markers
"IBM has pledged to contribute about $3 million to the SNP Consortium, a group dedicated to creating a public database of single nucleotide polymorphisms (SNPs) patterns, which can indicate whether individuals are predisposed to certain diseases. IBM will also develop software, computers, and services to be sold to pharmaceutical companies engaged in the study of SNP patterns."
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"A new mathematical model shows that competition for food among a small group of animals can lead to “synergistic epistasis.” This is a genetic interaction in which the negative effects of a deleterious mutation are more pronounced in a genome that has other harmful mutations. The authors note that similar models could demonstrate synergy stemming from competition for other resources besides food. Territory is one example. Furthermore, the approach might be applied to other sources of fitness variation aside from mutations.
Reference: Peck, J.R. and Waxman, D. 2000. Mutation and sex in a competitive world. Nature 406(6794):399-404."
redux [04.25.00]
UniSci Selfish Gene Theory Of Evolution Called Fatally Flawed
"In the current issue of Advances in Complex Systems (February-April), Dr. Yaneer Bar-Yam, president of the New England Complex Systems Institute and an expert on the application of mathematical analysis to complex systems, contends that the selfish-gene theory of evolution is fatally flawed.
If his mathematical proof gains general acceptance, it will shut the door on controversial "gene-centered" views of evolution.
Bar-Yam, in the upcoming article, proves that the "selfish gene" approach is not valid in the general case. He demonstrates that the gene-centered view, expressed in mathematical form, is only an approximation of the dynamics actually at work."
"The key to Bar-Yam's analysis lies in recognizing three levels of structure in nature: the gene, the organism and the group (or network) of organisms."
redux [04.05.00]
HMS Beagle Are Computers Evolving in Biology?
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
redux [02.24.00]
Science Revealing Uncertainties in Computer Models
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”
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"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."
The Washington Monthly Reboot! How Linux and open-source development could change the way we get things done
"Imagine a scale with all the advantages of a proprietary model on the left and all the advantages of an open-source model on the right. Pretend everybody who wants to solve a problem or build a project has a scale like this. If it tips to the left, the proprietary model is chosen; if it tips to the right, the open model is chosen. Now, as connectivity increases with the Internet, and computer power increases exponentially, more and more weight accumulates on the right. Every time computer power increases, another household gets wired, or a new simulator is built online, a little more weight is added to the right. Having the example of Linux to learn from adds some more weight to the right; the next successful open-source project will add even more.
"Perhaps the next boom in open source will come from the law; perhaps from drug X; perhaps it will be something entirely different. Although it's difficult to tell, it is quite likely that the scale is going to tip for some projects and that there will be serious efforts at open-source development in the next decade. Moreover, it's quite likely some of these projects will work."
redux [06.08.00]
GeneLetter Managed care needs to prepare for biotech revolution
"Unless they begin preparing now, health plan executives and medical directors could be blindsided by the revolution in medicine that will come with the mapping of the human genome, members of a managed care conference keynote panel warned on Monday."
"You think the genetic revolution is still 3-to-5 years off for your health plans," said Dr. Billings, who also serves as deputy director and chief medical officer of the Heart of Texas Veterans Health Care System. "I have to tell you, you better wake up. The tsunami is on the horizon," he warned.
For example, Schering-Plough's Dr. Haverty predicted that gene-based information could lead to the identification of many different types of asthma. As a result, health plans will need to develop many new codes and to upgrade their information systems, he said."
redux [06.17.00]
Stanford Medical Informatics Preprint Archive Bioinformatics in Support of Molecular Medicine
"Basic biological science has always had an impact on clinical medicine (and clinical medical information systems), and is creating a new generation of epidemiologic, diagnostic, prognostic, and treatment modalities. Bioinformatics efforts that appear to be wholly geared towards basic science are likely to become relevant to clinical informatics in the coming decade. For example, DNA sequence information and sequence annotations will appear in the medical chart with increasing frequency. The algorithms developed for research in bioinformatics will soon become part of clinical information systems. In this paper, I briefly review the intellectual roots of bioinformatics and how the field has evolved in the last few years. Fortunately, a core set of scientific paradigms have provided a focus to the field. Even in this short period, however, there has been a change in the nature of the questions being asked and the types of experiments being attempted. These changes are consistently leading bioinformatics towards problems of clinical relevance. Some molecular biology information systems already have important clinical implications. I will discuss the differences in the culture and approach to science of clinical informatics and bioinformatics, but will argue that the two disciplines share important intellectual challenges which make them very closely allied fields (despite the cultural differences). Finally, I will identify a few areas common to both disciplines where developments in one field may help catalyze faster progress in the other. For example, useful database integration technologies have (arguably) matured more rapidly within bioinformatics than in clinical informatics. At the same time, clinical informatics embraced the idea of controlled terminologies relatively early, and offers lessons to those in bioinformatics attempting similar tasks."
redux [04.28.00]
Nature Open-source work even more vital to genome project than to software
"We note with dismay and alarm the controversy concerning access, distribution and patenting of the human genome sequence (Nature 404, 317; 2000 & Nature 404, 324; 2000). We wish to point out some analogies between the human genome sequencing efforts and 'open-source' software development, which have implications for the data-release policy of the public sequencing effort.""The reasons why the Linux project could succeed against commercial wisdom have been analysed by Eric S. Raymond in his book The Cathedral and the Bazaar (O'Reilly, 1999). Most of these findings are of relevance to academic and commercial benefits arising from human genome sequencing." [via bioinformatics.org]
LinuxMedNews LinuxMedNews Open Source Medical Project List
""An army of LinuxMedNews correspondents (me and my Chihuahua Cindy) combed the Internet to form an alphabetized, comprehensive list of medical open source medical projects resulting in 17(!) such projects and many other interesting sites. If your project or site isn't listed, please e-mail. We have opened a new section on medical software companies that support Linux.""
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"Are you a hacker? Do you yearn for something more important to work on than yet-another-gnome-applet? Are you annoyed that you can't find a problem that is fun to code and stretches your brain in new ways... bioinformatics might be the answer."
"The amount of data is growing faster than anyone expected and only a handful of people can both remain with academic ideals and coding potential. We need hackers to join any number of projects out there. And there are a host to join. If you just liking hacking perl or you prefer compiler technology, there is something to suit you. "
redux [06.27.00]
The Boston Globe Bioinformatics : In the spotlight
"A fast-growing field known as bioinformatics uses computing to analyze the vast amount of biological, genomic, and related research to make sense of things too complex for the human brain to fathom.
But bioinformatics is also a bottleneck for many drug and biotech companies that can't find enough talented software engineers who combine sophisticated analysis tools with an understanding of genomics.
''We resolve the bioinformatics issue [by hiring] two people: one who understands computer science and the biologist or researcher,'' said Kenneth Fasman, vice president and global head of informatics of AstraZeneca LLC in Waltham."
"...according to Dr. Donald Johnson, a pathologist at the Nebraska University Medical Center. He estimated there are about 60,000 jobs available to scientists and managers versed in bioinformatics."
redux [05.10.00]
Alfred P. Sloan Foundation Hiring Patterns Experienced by Students Enrolled in Bioinformatics/Computational Biology Programs
"As expected, salaries for the most part climb as the level of training rises, starting in the $40,000-$50,000 range for BAs and reaching over $100,000 for one post doc. But there are exceptions. For example, two of the three undergraduates who were placed received salaries between $50,0000 to $60,000. This is higher than that earned by seven of the masters students, although ten of the nineteen masters students for whom we have salary information earn more than $60,000. One masters student received a starting salary of over $100,000. Reported salaries for five hires at the doctorate level are over $70,000. One is between $80,000 to $90,000; another is over $100,000; yet another is between $60,000 to $70,000. Three post docs received placements with a salary between $80,000 to $90,000. One post doc was placed at a salary of over $100,000. One institution reported that one or more masters student(s) received a signing bonus.""The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs—who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised."
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"To translate the billions of sequenced bases of the human genome into meaningful information, investigators in the private and public sectors continue to use computer prediction to automatically annotate the human genome--to attach biological footnotes about genes, the proteins they encode, and the ailments to which they may be linked. But as with any translation, there's potential for multiple interpretations. Annotation projects could present geneticists with significantly different genome schematics.
"I think that for the moment scientists are going to have to revel in the variety," maintains Robert Waterston, director of the genome sequencing center at Washington University in St. Louis. A joint effort in the United Kingdom from the European Bioinformatics Institute (EBI) and the Sanger Centre, U.S. efforts at the National Center for Biotechnology Information (NCBI) and Oak Ridge National Laboratory (ORNL), and commercial efforts will present different annotations based on the data available, algorithms employed, and weight given to different data points. "
redux [06.23.00]
Guardian Unlimited Genome project recruits the world
"Bioinformatics is the science of life as a software problem. An international co-operation called the Human Genome Project is about to finish putting the human DNA blueprint on the internet.
And a team working closely with them is about to distribute a software package that will turn the world of biology into a co-operative research laboratory. The exploration of the human software will become a kind of global interactive game, with a new tool called Ensembl."Tools The Ensembl Projectredux [04.24.00]
"Ensembl provides complete and consistent annotation across the human genome. It will soon also process mouse, (in conjunction with other projects, hopefully people like the Jackson Lab). To understand how Ensembl fits into the human genome project, please read EnsemblHGP"
"A central element of the Ensembl project is openness: all data is freely available; all code is freely available. You can read about the EnsemblSoftwareDesign and about how to DownloadEnsembl software and data and how to go about InstallingEnsembl on your own site in our developers area. You can follow Ensembl announcements, user discussion or development issues via a number of mailing lists as well as view previous emails here."
Eurekalert! Genome annotation experts take standardized test
"Now that the age of the genome is upon us, scientists must find a way to spin mountains of DNA code into biological gold. To do it, they are building their own Rumpelstiltskins: powerful computer programs that automatically scrutinize the code and decipher its genetic elements. The April issue of Genome Research reports a new enterprise to test the state of the art in computer "genome annotation." Organized by a team from University of California, Berkeley, 12 international groups compared the power of their computer programs to predict gene elements within a 3 million base pair stretch of Drosophila DNA.The groups compared the results of their programs against each other and against the results of an exhaustive experimental and computational effort to locate all the genes in this region (not available to the participants during the test).
When the results were in, many programs had detected the genes in the region with 95% accuracy compared to the experimental effort. Furthermore, the programs made predictions of genes that had not been found in that effort, which researchers are now investigating. However, the programs were less accurate in defining the exact boundaries of the genes within the code, and groups that attempted to find elements controlling gene activity (e.g., promoters) made a large number of false predictions."
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"Once the world had a single language and not too many words, but then clarity deteriorated into clamor. Today in the small but prolific world of bioinformatics, another Tower of Babel is rising up, with the miscommunication due as much to the rapid expansion of information as to basic changes in how it is processed. "Horrible problems" crop up as more information is computed on instead of read by a human researcher, according to Ewan Birney, a group leader in the Ensembl genome annotation project at the European Bioinformatics Institute (EBI) in Cambridge, England.
In the early days of bioinformatics, human-readable data exchange formats such as ASN.1, the format adopted for GenBank by the National Center for Biotechnology Information (NCBI) 10 years ago, were the norm. Easily editable with a text utility, ASN.1's syntactic looseness makes it congenial to the human user, but not to the machine, which likes its inputs defined with dictatorial rigidity."
redux [05.10.00]
The XML Cover Pages XML and Semantic Transparency
"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis-à-vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless.
Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."
redux [06.22.00]
Conference : Third Annual Bio-Ontologies Meeting
"We would like to invite you to the Third Annual Bio-Ontologies Meeting (Bio-Ontologies 2000), on August 24th in La Jolla, California, USA. This is immediately after ISMB-00 August 20-23 in La Jolla.
The goal of this consortium is the identification and promotion of a practical set of technologies that will aid in the knowledge management and exchange of concepts and representations in the life sciences. The first meeting took place in Montreal in 1998, and made clear the general interest and support people had for ontologies in the life sciences. The following year in Heidelberg we discussed ontology exchange and presented ontologies currently under development.
Many in the group have been active since our last meeting. The community now has considerable experience in the development and deployment of ontologies in the life sciences, so it is appropriate for us to take stock and reflect. So the theme for this year's meeting is Sharing Experiences and Spreading Best Practice. The idea is that we share not only the results of our labours but how we got there, and what we wished we had known while we did it."redux [05.01.00]
Stanford Medical Informatics Preprint Archive Ontology-Oriented Design and Programming
"In the construction of both conventional software and intelligent systems, developers continue to seek higher level abstractions that both can aid in conceptual modeling and can assist in implementation and maintenance. In recent years, the artificial intelligence community has placed considerable attention on the notion of explicit ontologies -- shared conceptualizations of application areas that define the salient concepts and relationships among concepts. Such ontologies, when joined with well defined problem-solving methods, provide convenient formalisms for modeling and for implementing solutions to application tasks. This chapter reviews the motivation for seeking such high-level abstractions, and summarizes recent successes in building systems from reusable domain ontologies and problem-solving methods. As the environment for software execution moves from individual workstations to the Internet at large, casting new software applications in terms of these high-level abstractions may make complex systems both easier to build and easier to maintain. "Gene Ontology Consortium
"This is the home of the Gene Ontology Consortium. The goal of the Gene Ontology consortium is to produce a dynamic controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.""The three organising principles of GO are molecular function, biological process and cellular component. A gene product has one or more molecular functions and is used in one or more biological processes; it may be, or may be associated with, one or more cellular components."
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"To dissect out the influence of genes on behavior, scientists often compare results in different strains of rodents. A new study provides a good reason to take extra care in designing such experiments. It seems that past experience can alter behavior in some strains of mice. In particular, scientists found that past feeding experience can dramatically affect the response of one strain of mice to amphetamines. The researchers suggest that “strain differences in behavior appear highly dependent on environmental experiences.”
Reference: Cabib, S., Orsini, C., Le Moal, M., et al. 2000. Abolition and reversal of strain differences in behavioral responses to drugs of abuse after a brief experience. Science 289(5478):463-465."
redux [07.13.00]
The New York Times Genes May Cause 25% of 3 Major Cancers
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"Genes may cause more than one-quarter of three major types of cancer, more than previously thought, a group of researchers says.
Scandinavian researchers concluded that genes account for 42 percent of the risk for prostate cancer, 35 percent for colorectal cancer and 27 percent for breast cancer.
The rest of the cases are caused by what people do, such as smoking and diet, or what happens to them, such as on-the-job hazards or viral infections, the researchers said."
"...the conclusion runs contrary to the widespread belief that scientists "will find solutions or cures to all diseases in the genes," Dr. Lichtenstein said. "That won't be the case."redux [05.26.00]redux [04.25.00]
British Medical Journal Genetic epidemiology
"Research in disease aetiology has shifted towards investigating genetic causes, powered by the human genome project. Successful identification of genes for monogenic disease has led to interest in investigating the genetic component of diseases that are often termed complex, that is, they are known to aggregate in families but do not segregate in a mendelian fashion. Genetic epidemiology has permitted identification of genes affecting people's susceptibility to disease, although progress has been much slower than many people expected. While the role of genetic factors in diseases such as hypertension, asthma, and depression is being intensively studied, family studies and the large geographical and temporal variation in the occurrence of many diseases indicate a major role of the environment. Thus, it is necessary to consider findings about susceptibility genes in the context of a population and evaluate the role of genetic factors in relation to other aetiological factors. This article discusses some approaches used to resolve the genetic architecture of disease and to study the relation of genes to environmental factors in the population. "
UniSci Selfish Gene Theory Of Evolution Called Fatally Flawed
"In the current issue of Advances in Complex Systems (February-April), Dr. Yaneer Bar-Yam, president of the New England Complex Systems Institute and an expert on the application of mathematical analysis to complex systems, contends that the selfish-gene theory of evolution is fatally flawed.
If his mathematical proof gains general acceptance, it will shut the door on controversial "gene-centered" views of evolution.
Bar-Yam, in the upcoming article, proves that the "selfish gene" approach is not valid in the general case. He demonstrates that the gene-centered view, expressed in mathematical form, is only an approximation of the dynamics actually at work."
"The key to Bar-Yam's analysis lies in recognizing three levels of structure in nature: the gene, the organism and the group (or network) of organisms."
redux [07.11.00]
Biospace.Com Big Picture Biology
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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"Genomics can best be defined as the branch of science devoted to the investigation and understanding of genomes. This might sound straightforward enough, but in practice there is no small amount of misuse and misunderstanding of this term. Genomics is not the analysis of individual genes, an endeavor firmly established in the pre-genomics era by the time-honored disciplines of genetics and molecular biology. Rather, genomics treats the genome in its entirety as the unit of investigation. Thus, a genomics scientist who wishes to analyze the consequences for a cell of a mutation, or a change in growth conditions, cannot restrict himself/herself to looking at a selection of the cell’s genes, but must consider all the changes resulting from the introduction to the cell of the perturbagen under investigation. Whilst the desirability of such an approach is clear, allowing for the integration of data from the vast array of cellular pathways into a unified understanding of the cell, the feasibility of such an approach was, until very recently, unconscionable. Remarkably, a series of breathtaking technological advances in the past few years have made genomic approaches a reality, opening up the way towards a new level of understanding of the cell, and also towards a revolution in the biotechnology and pharmaceutical industries."
Biospace Genomics Primer
"With the announcement of the completion of the Human Genome Project, comes the end of the sequencing stage of the genomic revolution and the start of the post-genomic era. The 3 billion letters of DNA coding the human genome have been fully sequenced, well before the initial target date of 2005. This is an important milestone in the efforts to translate this knowledge into practical uses to benefit humankind. For all of its importance, however, the sequencing of the genome is but a humble first step into the Genomic Era. It provides the letters of a new alphabet and a tantalizing glimpse of the future, but the ultimate payoff will be the successful application of genomics to improve human health and quality of life. Knowledge of the sequence of the human genome is virtually useless in and of itself, much as pages in a foreign script are of little value without a way to decipher the meaning and the intelligence to evaluate that meaning. There exists a tremendous opportunity for companies to intercede at multiple levels in this process with technologies and information that will catalyze the realization of the genomics promise in its ultimate incarnation: novel approaches to improving human health."
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"Much as Cisco Systems did with the Internet, PE Biosystems -- which is changing its name back to Applied Biosystems -- has emerged as by far the leading supplier of equipment to the exploding genomics industry."
""There used to be a saying in the computer business that no one ever got fired for buying I.B.M.," said Lawrence S. Schmid, president of Strategic Directions International, a market research company in Los Angeles that tracks the analytical instrument industry. "The same is true with PE."
"The real game is not more sequencing," said Michael McKenna, vice president for operations at the CuraGen Corporation, a genomics-based drug development company. "The real game is seeing which genes are drug targets. It's a completely different set of tools.""
"And technology is evolving rapidly: start-up companies have developed chips as small as postage stamps that can analyze thousands of genes at a time or perform complex chemical analyses. Such chips could undermine PE's bigger instruments, just as personal computers undermined I.B.M.'s mainframes and the Internet threatens Microsoft's dominance."
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"Recently, an organization called "The Human Genome Project"--which, incredibly, turns out NOT to be rock band--announced that it had deciphered the human genetic code. Scientists reacted by holding a celebration so joyous that many of them woke up the next day with undershorts stains that they believe could take years to fully analyze.
Clearly, then, cracking the genetic code is a big deal for the scientific community. But what does it mean to you, the non-scientist who still secretly believes that radio works by magic?"
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"Entropia, Inc., the company creating the world's largest Internet computing service, today named Dr. Larry Smarr chairman of its Scientific Advisory Board.
Smarr is the founding director of both the National Center for Supercomputing Applications (NCSA) and the National Computational Science Alliance."
""Entropia will enable a profound change in the nature of computing and the Internet,'' said Dr. Smarr. "We are at a major discontinuity in the evolution of high-performance computing. Currently, the largest scale computing systems have thousands of processors. Entropia's approach will create megacomputer systems with millions of processors. Entropia's Internet computing model will accelerate the rate of academic scientific progress and enable the private sector to become more competitive.''"
Entropia Welcome to Entropia
"For the first time in history, your computer can collectively join with millions of others to:
- help research new treatments and cures for cancer, AIDS and other diseasesThe Standard Distributed Computing Goes Commercial
- explore new horizons in human knowledge and make actual discoveries
- deepen the ability to predict climate change protect the environment for future generations
- help create safer products
- accomplish new wonders in record time "
"The distributed-computing model could be one of those rare cases where capitalism and pure scientific research mesh. Not every lab can afford to pay $200,000 for an eight-processor Origin 2000 SGI supercomputer, much less $1 million for a 40-processor machine, says David Fenstermacher, director of scientific computing for the medical school at the University of North Carolina at Chapel Hill. (Fenstermacher is also acting director of the campus' Center for Bioinformatics and a United Devices adviser.) And even the most powerful supercomputers need time to process data.
A project that would take several months on a supercomputer – creating a 3D model of a protein's linear be accomplished in much less time using thousands of distributed computers"
redux [04.05.00]
Wired Researcher Borrows from Napster
"A researcher working on the Human Genome Project is using Napster technology, and he's not looking for T3 connections to download Moby.
Dr. Lincoln Stein, an associate professor of bioinformatics at the Cold Spring Harbor Lab in New York, is investigating ways to use Napster-type technology to allow scientists to share their discoveries of the genome.
"I was very interested when I saw Napster," Stein said. "It has a similar architecture (to what we use now), but it allows for 'peer-to-peer' data exchange and it dawned on me that it would be marvelous for our annotation system.""
Stein Laboratory Distributed Sequence Annotation System (DAS)
"The pace of human genomic sequencing has outstripped the ability of sequencing centers to annotate and understand the sequence prior to submitting it to the archival databases. Multiple third-party groups have stepped into the breach and are currently annotating the human sequence with a combination of computational and experimental methods. Their analytic tools, data models, and visualization methods are diverse, and it is self-evident that this diversity enhances, rather than diminishes, the value of their work."
"The solution that we advocate allows sequence annotation to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. A single server is designated the "reference server." It serves essential structural information about the genome: the physical map which relates one entry to another (where an "entry" is an arbitrary segment of the sequence, such as a sequenced BAC or a contig), the DNA sequence for each entry, and the standard authorship information. Multiple sites then act as third-party "annotation servers." Using a web browser-like application, researchers can interrogate one or more annotation servers to retrieve features in a region of interest. The servers return the results using a standard data format, allowing the sequence browser to integrate the annotations and display them in graphical or tabular form. No attempt is made to automatically resolve contradictions between different third-party annotations. Indeed, it is the ability to facilitate comparison among different centers' annotations that distinguish this proposal. We currently have a working prototype of this system based on ACeDB servers and CGI scripts, and are now generalizing this architecture to support other client and server combinations."
egroups : Decentralization Description
"* Is decentralization ever a good idea? If so, when? Is there non-anecdotal evidence on costs and benefits?
* What protocol issues are there? Can we begin assembling a good protocol for decentralized messaging? To what degree do the protocols for Freenet, Gnutella or WorldOS meet the need? Do we need an application protocol or something lower level? Can HTTP do the job? Can we implement peer routing as an add-on to existing protocols? Is there a call to develop an IETF working group?
* Given that authoring and versioning are critical but hard in a decentralized environment, how can we approach the job? Is it possible to integrate WebDAV with peer networking?
* What are the business issues? Who are the players? Who else stands to win or lose, and why?
At present many people and groups are working on the issues in isolation, some for competitive reasons and some for lack of an alternative. My belief is that a communal approach will be more productive."
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[requires 'free' registration]
"Harvard University's recent conference Internet & Society 2000: Changing Our Lives (IS2K), held May 31 - June 2, 2000, included an exciting breakout session called "Genes on the Web." A panel of experts discussed how the Internet accelerates discoveries related to the human genome and spreads the information to researchers. In the introduction, Josh Lerner of the Harvard Business School called the current state of genomics research the "marriage of information technology with biotechnology and bioinformatics.""
"George Church of the Harvard Medical School sees the Human Genome Project as part of the Internet revolution. Church believes that the project to sequence the human genome displays a "community spirit of cooperation unprecedented in human genetics." In the past, labs hoarded their genetic data. Now, there's a 24-hour standard for posting genomic data on the Web, and input from research labs and biopharmaceutical and genomics companies soon follows."
redux [06.30.00]
Wired Biotech: The Internet, With Soul
"The flood of knowledge that will follow the human genome map will answer many questions, but experts pointed out that some questions just can't be answered, even by unraveling each of the 3.2 billion chemical letters that make us human."
"Nonetheless, [Incyte's CEO Randy] Scott said answers in medicine will come fast. Both Moore's Law and Metcalfe's Law will accelerate the speed of progress in the biotech industry, replicating the growth of the computer and Internet industries.
"The effect of Moore's Law is pretty straightforward," Scott said. Moore's Law, conceived by Gordon Moore, the founder of Intel, maintains that computer power doubles every 18 months. In biology, DNA sequencing rates are doubling every year.
"While you may recognize that the Human Genome Project has been going on for the past ten years, you may not realize that all of the sequencing for the human genome has happened in the last year, and over 50 percent of that just within the last four months," said Scott."
"Metcalfe's Law, Scott said, will help researchers waste less and make discoveries faster. Conceived by Robert Metcalfe who invented the ethernet, the law states that the power of a network increases exponentially with the number of computers connected to it."
Right now up to 80 percent of research is wasted, because graduate students and postdocs repeat past experiments as part of their training, and scientists refuse to share their research until it's published, which can be up to two years after the results are compiled.
"Metcalfe's Law is going to do to biology what the Internet has done to e-commerce," he said. "It's going to connect vast groups of people who previously didn't talk."
"Instead of putzing around in the lab for weeks or months, scientists will search Web-based databases to quickly narrow their ideas and devise experiments that they know they are unique and relevant."
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"Celera Genomics, which last month announced sequencing the human genetic blueprint, is interested in possibly developing antibody-based drugs to fight cancer and other diseases, Celera president Craig Venter told Reuters Thursday.
"We are thinking about developing cancer vaccines down the road. We haven't decided whether to do our own clinical trials," Venter said."
"If it chooses to develop drugs, Venter said Celera could conceivably do it alone -- without having to partner with existing drug makers."
redux [07.17.00]
BBC News Celera plans next step
"Craig Venter, head of Celera Genomics which last month completed the map of the human genome, has outlined his next goal.
Speaking at a conference he said his new task was to map the proteins which drive all chemical reactions in the body."
""A big part of the business is the straightforward providing of information, but I'm not complacent just to do that," Venter said."Wired Gene War Heating Up Again
"Academic researchers and private companies are continuing their tug of war over the human genome map. This time the fight centers around who has the best system for delivering cloned genes for research.
""The Human Genome Project provides information, but it's only terabytes of information in computers, not the physical DNA," said Joshua LaBaer, an instructor of medicine and director of the Harvard Institute for Proteomics. "You can't do an experiment on it. All you can do is look up information."
Harvard researchers and several private companies have begun competing to build the best gene clone warehouses.
Celera, the company that last month announced it had completed a map of the human genome, said Wednesday it has joined with Life Technologies, a biotechnology tool company, to create its own bank of cloned genes and their complete chemical sequences."
"Whether the projects will succeed comes down to money for both Celera and Harvard. Celera needs to make it. Harvard needs to acquire it in the form of funding, which it hopes to get partly from the National Institutes of Health.
But McPherson doubts it can be a big moneymaker.
"Celera's current business plan seems to be to produce resources similar to those that are freely available," he said. "I don't see how they can do that profitably.""
redux [06.29.00]
Yahoo! News Celera to Shift Focus to Patentable Discoveries
"A day after Monday's announcement that it had sequenced the entire human genome, Celera Genomics said on Tuesday that it will turn its attention to other, potentially more profitable, endeavors.
"Speaking to investors during a conference call, Tony L. White, chairman of the PE Corporation, Celera's parent company, said that "all of the energy'' of the genomics unit will be directed toward discovery efforts "that are subject to intellectual property protection.''"
"The move toward discovery efforts represents "a shift from what we've been doing,'' White acknowledged. "Our focus from the formation of the company 2 years ago was to build a significant bioinformatics presence,'' he said, "but we have the money to pursue a much more grandiose strategy now and we intend to do that.''"
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"Thank you for your interest in the Database Mining in the Human Genome Initiative white paper.
This paper is presented in the spirit of Open Source software. The concept of Open Source software is quite simple - when people on the Internet read, redistribute and update software, it evolves. This white paper will become a living document that will transcend its original boundaries with the addition of your updates, postings and comments.
With your help, this evolving document will define and shape the future of Database Mining in the Human Genome Initiative.
To send your comments or updates, please click here info@biodatabases.com"
redux [04.28.00]
Nature Open-source work even more vital to genome project than to software
"We note with dismay and alarm the controversy concerning access, distribution and patenting of the human genome sequence (Nature 404, 317; 2000 & Nature 404, 324; 2000). We wish to point out some analogies between the human genome sequencing efforts and 'open-source' software development, which have implications for the data-release policy of the public sequencing effort.""The reasons why the Linux project could succeed against commercial wisdom have been analysed by Eric S. Raymond in his book The Cathedral and the Bazaar (O'Reilly, 1999). Most of these findings are of relevance to academic and commercial benefits arising from human genome sequencing." [via bioinformatics.org]
redux [04.24.00]
Conference Bioinformatics Open Source Conference
"The Bioinformatics Open Source Conference (BOSC) is the successor to the successful bioperl-99 conference. Like bioperl-99, BOSC is a satellite conference of ISMB, allowing people who are making the trip to San Diego to extend it for a couple of days and talk real code.BOSC is designed to be open to all the open source efforts in bioinformatics, including Perl, Java, Python, C and C++ - even Fortran would be fun. We don't expect all attendees to be participating in a particular open source project (like, say, biojava), but we do expect that a lot of the people involved in the open source projects in bioinformatics will attend."
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"Clark is the only person in history to have guided three companies from inception to becoming public companies with more than one billion in market cap each. In addition to privately held Shutterfly and Mycfo.com, Jim is currently hard at work on his sixth startup: DNA Sciences."
"DNA Sciences is focused on exploiting the genome information and specifically finding the genotypes variations in genes that give rise to the genes that are associated with certain diseases. The variations in those genes that give rise to variance of that disease and treatment for that disease so the company is heavily focused on gene applications in the genome area."
"Healtheon was driven four or five years ago when I started the company in attempt to try to bring the internet to what I thought was the most inefficient industry in the world, the U.S. Healthcare system. I am still positive and bullish about the company's future. In the case of DNA Sciences it was more because I think it is more immediate. It has a tremendous potential. I put the two companies together and WebMD has a lot of disease affinity groups, if you will. People with breast cancer, prostate cancer, hepatitis, a variety of ailments and we can collect blood samples from people in the groups and identify genes and put them in a specific category to see what the best treatment is."
Bloomberg DeCode Genetics Shares Surge on First Trading Day on Nasdaq
"DeCode Genetics Inc., which is mapping the genes of Iceland's population, saw its shares surge as much as 75 percent in their first day of trading in the U.S. "
"DeCode is taking advantage of Iceland's homogenous population and careful record-keeping to find genes linked to illness."
"Iceland is considered an ideal venue for this type of research because there's little variation in the population's genetic makeup. Settlers who came to the country more than 11 centuries ago remained largely cut off from the rest of the world until World War II.
What's more, Iceland's health-care system, centralized in 1915, has kept careful records, and Icelanders' penchant for genealogy means that family trees can be reconstructed with ease and accuracy. DeCode works with the records and blood samples to build its genetic database."
redux [06.17.00]
Stanford Medical Informatics Preprint Archive Bioinformatics in Support of Molecular Medicine
"Basic biological science has always had an impact on clinical medicine (and clinical medical information systems), and is creating a new generation of epidemiologic, diagnostic, prognostic, and treatment modalities. Bioinformatics efforts that appear to be wholly geared towards basic science are likely to become relevant to clinical informatics in the coming decade. For example, DNA sequence information and sequence annotations will appear in the medical chart with increasing frequency. The algorithms developed for research in bioinformatics will soon become part of clinical information systems. In this paper, I briefly review the intellectual roots of bioinformatics and how the field has evolved in the last few years. Fortunately, a core set of scientific paradigms have provided a focus to the field. Even in this short period, however, there has been a change in the nature of the questions being asked and the types of experiments being attempted. These changes are consistently leading bioinformatics towards problems of clinical relevance. Some molecular biology information systems already have important clinical implications. I will discuss the differences in the culture and approach to science of clinical informatics and bioinformatics, but will argue that the two disciplines share important intellectual challenges which make them very closely allied fields (despite the cultural differences). Finally, I will identify a few areas common to both disciplines where developments in one field may help catalyze faster progress in the other. For example, useful database integration technologies have (arguably) matured more rapidly within bioinformatics than in clinical informatics. At the same time, clinical informatics embraced the idea of controlled terminologies relatively early, and offers lessons to those in bioinformatics attempting similar tasks."
redux [05.15.00]
The New York Times Who Owns Your Genes?
[requires 'free' registration]
""I just wanted to do something good," Mr. Fuchs said. "But once money came into the picture, why not have it be shared with me?"These days more and more patients are asking the same question. Laboratories offer tests for more than 700 human genes, with more being discovered almost daily. And, for almost every gene, some medical institution or some company owns a patent on its use.
"The value of patients' tissues has potentially gone up enormously," said Dr. Barry Eisenstein, the vice president for science and technology at the Beth Israel Deaconess Medical Center in Boston. But, Dr. Eisenstein said, patients whose cells provided the genes that have been patented are almost never compensated. "
HMS Beagle Caught in secret tests
[requires 'free' registration]
"Lawrence Berkeley National Laboratory in California has settled a class-action suit over genetic and medical testing for more than $2 million. The suit was brought by employees who charged that they were discriminated against and that their privacy was invaded when they were tested for pregnancy, syphilis, and genetic traits without their knowledge. Each of the plaintiffs will get $25,000, and other employees may get $2,000 each. The settlement also covers legal fees estimated at $440,000.Reference: Lehrman, S. 2000. Medical tests cost Lawrence Berkeley $2.2 million. Nature 405(6783):110."
redux [02.25.00]
Science U.K. Plans Major Medical DNA Database
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”
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"In the wake of breakthroughs in genetic research, Internetcentric business opportunities will explode in tandem with re search and development challenges and opportunities in biotechnology, industry executives said.
"Companies such as Affymetrix (www.affymetrix.com), diaDexus (www.diadexus.com), DNA Sciences (www. kivagen.com) and Orchid BioSciences (www.orchid.com) are using the Net to deliver information relating the genome sequence to specific parts of the DNA that have mysterious tendencies to mutate, said Howard Goldstein, chief executive of eBioinformatics (www. ebioinformatics.com), which provides researchers with databases and software tools online. And high-tech heavy weights, recognizing the need for sophisticated systems to gather, store, manipulate and disseminate genome information, have also undertaken initiatives in the field. AGTC Fund's Stone cited IBM, Microsoft, Motorola, Oracle and Sun Microsystems.
""If you're dealing with a distributed applications race that's data- and computation-intensive, the Internet will clearly be a key tool in tackling that problem," Stone said. "It'll allow communication between people working in different geographic locations. It will allow access to databases that are too large to go to the software store to buy. It will allow access in an applications service provider model to the computing power necessary to manipulate those databases. In that sense, the Internet will play as big a role in genomics applications as it is already playing in other information-intensive businesses."
redux [06.06.00]
Bioinform eBioinformatics Will Put $10 Million Toward Efforts to Reach Customers
"To be sure, many industry insiders are skeptical of the bioinformatics internet portal business model. Even among vendors of the 220-plus software products available at the BioNavigator site, some told BioInform they wondered how companies such as eBioinformatics and DoubleTwist will make money. A product manager at one of eBioinformatics’ partner com-panies said, “I don’t see how either company will make the sort of money necessary to cover these costs. Scientists are used to free stuff. I’m not sure they will pay money for the not-free stuff.”"
redux [05.23.00]
The Standard DNA Detectives
"For all the "brave new world" rhetoric surrounding the recent rapid advances in genetics, scientists are only on the threshold of understanding how genes work and their role in health and disease.So too are the DNA dot-coms in their search for success. By combining strains of Wall Street's two favorite industries of the moment – biotech and the Internet – online genomics companies have reaped valuations last seen by Net companies circa 1999. "You take the two great buzzwords, 'genome' and 'Internet,' put them together and someone will throw money at them..."
"But the rush to go public has made the DNA dot-coms vulnerable to the volatility that seems to strike biotech and Net startups particularly hard. "
Chemical & Engineering News Bioinformatics for the Masses
"As computing and biology have converged, software tools for data capture, management, analysis, mining, and dissemination have emerged. More than 40 companies, most of them small, are trying to capitalize on the development and marketing of new bioinformatics tools. Whereas the market for generated data or "content" is very lucrative, bioinformatics sales are expected to reach about $160 million this year, according to market research firm Frost & Sullivan""Who I really want as customers are the scientists themselves," says John Couch, chief executive officer of DoubleTwist , Oakland, Calif. "We're challenged in this field to deliver something to the scientists so that they can do their science."
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"Privacy advocates, still reeling from last year's passage of legislation that allows banks and insurance companies to share personal information, are bracing against a new threat to the confidentiality of medical and financial information: The Human Genome Project.
"Latanya Sweeney, professor of computer science and public policy at Carnegie Mellon University, said currently more than 40 US states have laws requiring hospitals to make available to insurance companies and researchers certain information about each visit they receive, including the diagnosis, birth date, ethnicity, gender and Zip code of all patients discharged.
While state regulations say such categories are sufficiently anonymous to conceal the identity of patients, Sweeney said companies can and do match such information with personally identifiable data, using just a few publicly available resources."
""It may surprise some to know that 87 percent of the US population is uniquely identifiable today by just their birthday, gender and zip code," Sweeney said."
"Sweeney said the stakes become much higher when genetic information comes into play. For instance, she said, gender can usually be identified using just the base of a person's DNA sequence. Using a larger chunk of DNA information, researchers can infer particular diseases by catalogued and known sequence patterns. Link those sequences to publicly available hospital data, and you have an undeniably complete picture of an individual's most private information, Sweeney said."
redux [06.08.00]
GeneLetter Managed care needs to prepare for biotech revolution
"Unless they begin preparing now, health plan executives and medical directors could be blindsided by the revolution in medicine that will come with the mapping of the human genome, members of a managed care conference keynote panel warned on Monday."
"You think the genetic revolution is still 3-to-5 years off for your health plans," said Dr. Billings, who also serves as deputy director and chief medical officer of the Heart of Texas Veterans Health Care System. "I have to tell you, you better wake up. The tsunami is on the horizon," he warned.
For example, Schering-Plough's Dr. Haverty predicted that gene-based information could lead to the identification of many different types of asthma. As a result, health plans will need to develop many new codes and to upgrade their information systems, he said."redux [03.30.00]redux [02.13.00]
JAMIA Integration and Beyond: Panel Discussion
"I think one of the toughest things we all have to deal with is updating our dictionaries. In the simplest cases, the name of an organism is changed and we just have to do the maintenance. It is tougher, when, as with Citrobacter, they do genetic studies and say, "Oh, it's really six different organisms, not one." We have the human genome project coming very quickly. Even that is just the tip of the iceberg. We're not only going to see all the genes; we're then going to see clinical tests based on gene expression. Essentially, you'll be able to look at something on the order of 180,000 gene products and whether they're up or down regulated. How are we going to integrate such an incredible amount of data at a time when we're going to also be changing how we think about these processes? Classification and simple mapping are not going to work, because the lumpers and splitters are going to be arguing furiously on a daily basis."
The Daily Davos Beyond the Genome
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.
The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.
Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."
redux [06.15.00]
New England Journal Of Medicine Rules for Research on Human Genetic Variation -- Lessons from Iceland
"DNA molecules are entirely separate from medical records. In the future, however, the DNA molecule and the medical record are likely to merge into one when it becomes possible to sequence a person's entire genome and put that information on a computer chip or disk. This is not deCODE's current project, but we should not wait until this step is taken to explore its implications. The most important questions would then be who has the authority to make such a disk in the first place; who owns the disk; who controls the use of the disk; and whether the disk containing the genome should be treated as specially protected medical information, as is the case for psychiatric and drug-dependency records? In clinical settings, it seems reasonable to treat such a disk as containing particularly private and sensitive medical information. It also seems reasonable to permit patients to agree to have their entire genome scanned without detailing the tens of thousands of tests that would be run. This is akin to consent to a battery of tests during an annual physical examination.
On the other hand, in a research setting, or when a specific genetic disorder is suspected, the creation and use of an individual patient's genome disk should be subject to the informed consent of the patient. And since they can be both separated from the medical record and readily recreated, research subjects should retain the right to have the files containing their genetic information destroyed at any time.
Iceland's experience with deCODE provides a useful catalyst for formulating fair and ethical rules for research on genetic variation. The Icelandic experience demonstrates that people are concerned about how genetic research is done, that medical-records research and DNA-based research are not the same, that community consultation is necessary but not sufficient to justify DNA-based research ethically, that the probable benefits of such research should be spelled out as clearly as possible, and that international standards for consent to and withdrawal from research should apply directly to research on human genetic variation. Rules for such research will retain their relevance even after it becomes possible to transfer all the genetic-sequence information in a DNA molecule to a computer disk."
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"Physiome Sciences, Inc. has completed a $50 million private placement, one of the largest private rounds of the year.
""Physiome is poised to make an enormous impact on the challenge of how to convert the fruits of human genome research into medicines for the benefit of humanity,'' commented Daniel Green of Dresdner Kleinwort Benson. "We co-led this financing because we believe that Physiome fills the critical step between connecting gene sequence to function and drug discovery. The company's powerful and seasoned management team is exceptionally well-qualified to drive the business forward.''
"It is now critical that researchers gain a full understanding of how genes and proteins function at the level of the cell and organ. We believe that computer-based biological models provide the most effective means of organizing and interpreting these data,'' commented Dr. Thomas J. Colatsky, Physiome's Executive Vice President and Chief Scientific Officer. "We have enabled these efforts by creating a common mark-up language for describing and exchanging biological models, and an integrated technology platform that permits users to build new models rapidly and effectively on multiple computer platforms. The models generated by our technology will aid researchers in designing and validating new drugs within a cost-effective virtual setting.''
Physiome Sciences' goal is to become the pre-eminent provider of tools to simulate living cells, tissues and organs. These tools are used to create the basis of virtual drug discovery programs in pharmaceuticals and ultimately could become the basis to build the virtual human."
Physiome.Com PHYSIOME SCIENCES GIVES BIOLOGICAL COMPUTER MODELS A SINGLE NEW LANGUAGE
"...the new Cell Markup Language, or CellML, will enhance and facilitate the exchange and validation of information among laboratories with a speed and accuracy not previously possible. CellML is an Extensible Markup Language (XML) application that provides a single means of integrating biological models, experimental data and text documents in a platform-independent and web-accessible way.“
We are organizing a global network of academic centers to aid us in this important effort,” said Tom Colatsky PhD, Executive Vice President and Chief Scientific Officer. “Computer-based models are an important means of integrating gene and protein data to understand cell and organ function. Having a common language to describe these data will speed model development and enable researchers to access the massive amounts of information pouring out of biomedical laboratories world wide.”
Physiome Sciences, Inc., will develop and maintain a website as the primary source of information about CellML and its development. The website will also provide access to cell models in the public domain that can be downloaded, run, modified and updated. Researchers will be invited to learn about CellML and to use a wide range of computer models in their research."
redux [05.10.00]
The XML Cover Pages XML and Semantic Transparency
"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis-à-vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless.
Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."
redux [02.24.00]
HMS Beagle Virtual Cures
[requires 'free' registration]
"For a brief period, supplying the data was enough. More genes meant more potential drug targets. But now the victims of the data flood are crying for help. Companies like Entelos, Inc. (Menlo Park, California) are coming to the rescue by building models that integrate all those data into a single, homeostatic, interconnected whole. The models allow researchers to run virtual drug trials to determine the best drug targets, treatment regimens, and patient populations."
Modelers feel that their time has come. "Leaders in the genomics field are all coming to this realization that model building is becoming the rate-limiting step," says Palsson. "There's a major shift taking place in the biological sciences." Math is back, he says, and "biology is going to become quantitative."Biospace Virtual Drug Development: Start-ups Put Biology in Motion
"One way of animating our growing store of static information is through computer simulation. It is an area that is beginning to emerge slowly in the life sciences, with only a handful of academic and commercial players active in the area. But for a fledging discipline, there is a great variety in the scope of work being undertaken. While academic labs try to create accurate simulations of red blood cells and simple bacteria, the private companies are taking on bolder projects--simulating human organs and even human diseases in their entirety."
Science Revealing Uncertainties in Computer Models
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”
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"Craig Venter, head of Celera Genomics which last month completed the map of the human genome, has outlined his next goal.
Speaking at a conference he said his new task was to map the proteins which drive all chemical reactions in the body."
""A big part of the business is the straightforward providing of information, but I'm not complacent just to do that," Venter said."
Wired Gene War Heating Up Again
"Academic researchers and private companies are continuing their tug of war over the human genome map. This time the fight centers around who has the best system for delivering cloned genes for research.
""The Human Genome Project provides information, but it's only terabytes of information in computers, not the physical DNA," said Joshua LaBaer, an instructor of medicine and director of the Harvard Institute for Proteomics. "You can't do an experiment on it. All you can do is look up information."
Harvard researchers and several private companies have begun competing to build the best gene clone warehouses.
Celera, the company that last month announced it had completed a map of the human genome, said Wednesday it has joined with Life Technologies, a biotechnology tool company, to create its own bank of cloned genes and their complete chemical sequences."
"Whether the projects will succeed comes down to money for both Celera and Harvard. Celera needs to make it. Harvard needs to acquire it in the form of funding, which it hopes to get partly from the National Institutes of Health.
But McPherson doubts it can be a big moneymaker.
"Celera's current business plan seems to be to produce resources similar to those that are freely available," he said. "I don't see how they can do that profitably.""
redux [06.29.00]
Yahoo! News Celera to Shift Focus to Patentable Discoveries
"A day after Monday's announcement that it had sequenced the entire human genome, Celera Genomics said on Tuesday that it will turn its attention to other, potentially more profitable, endeavors.
"Speaking to investors during a conference call, Tony L. White, chairman of the PE Corporation, Celera's parent company, said that "all of the energy'' of the genomics unit will be directed toward discovery efforts "that are subject to intellectual property p