{bio,medical} informatics
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Information Week
IBM Joins In Genome Work"IBM is pushing hard against the boundaries of data processing andintegration in a way that ultimately could affect everyone'shealth and well-being.
Through a technology license with Incyte Genomics Inc., IBM is applying its DiscoveryLink technology to the challenge of sifting mountains of genetic data to better identify the causes of diseases and aid in developing cures. DiscoveryLink's data- integration technology will be integrated with Incyte's Genomic Knowledge Platform."
"IBM says it has earmarked $100 million to develop advanced research technology for biotechnology, genomic, E-health, pharmaceutical, and agri-science industries."
"Genomica Corp., a maker of software for the pharmaceutical and biotechnology industries, rose 2.3 percent on its first day of trading.
Shares of Genomica rose 44 cents to $19.44 in trading on the Nasdaq Stock Market. The Boulder-based company sold 6.44 million shares in an initial public offering at $19 a piece, raising $122 million.
Genomica develops software to help drugmakers manage and process large volumes of genetic information."
"Compaq Computer said it plans to invest $100 million in early-stage companies that focus on genomics, tapping into a growing market of biotech start-ups involved in gene discovery, analysis, and information.
The company said its goal is to help promote development of biotech companies through a combination of financial support and access to its AlphaServers and StorageWork computing systems for use in gene sequencing, gene discovery, and other related activities.
Compaq said it would make its first investment in the Applied Genomics Technology Capital Fund, a Cambridge, Mass.-based venture capital fund that invests in companies specializing in genomics and bioinformatics, a new field that develops systems for analyzing, processing, and storing genetic information."
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Slashdot
Distribute Stuff: Cosm Project's CS-SDK"Duncan3 writes: "After almost 3 months of public testing the Mithral Client-Server Software Development Kit is now officially out. The Mithral CS-SDK is a part of the Cosm Project which longtime slashdot readers will remember, and is fully buzzword-compliant with "distributed computing", "peer-to-peer", "file-sharing", and "cycle-sharing" - meaning you can easily build any of those types of applications in a weekend. So I expect to see slashdot readers put out at least 20 projects by next Thursday. The Folding@home project based at Stanford has been running for a couple months now doing protein folding and uses the CS-SDK. You can visit them at and download their client software or OpenGL screensaver for Linux x86/Alpha, Tru64, and Win32." Interesting to see how mainstream distributed computing has become even in just the past 12 or so months. Fold proteins, find aliens, break crypto ... what else?"
"The Mithral Client Server Software Development Kit allows developers to quickly and easily write large scale client-server applications including "distributed computing" and peer-to-peer types. Examples of what this will allow you to build with this technology are distributed.net, SETI@Home, Napster, Gnutella, and hundreds of other applications. The example code is an instance of an application that hands out work for the clients to do, then collects the results.
One primary use for the CS-SDK is for a company or research lab who has large amounts of computation to do. This allows you to network the systems you have behind your firewall to get real work done quickly and securely.
The kit should allow a first-year programmer to take an application and make it into a client-server application in a weekend."
"Understanding how proteins self-assemble ("protein folding") is a holy grail of modern molecular biophysics. What makes it such a great challenge is its complexity, which renders simulations of folding extremely computationally demanding and difficult to understand. (See Scientific Background for more details about what are proteins, why do they fold, why this is so difficult, and why do we care).
Our group has developed a new way to simulate protein folding ("distributed dynamics") which should remove the previous barriers to simulating protein folding. However, this method is extremely computationally demanding and we need your help (see below). We have already demonstrated that our distributed dynamics technique can fold small protein fragments and protein-like synthetic polymers. The next step is to apply these methods to larger, considerably more important and complicated proteins. Unfortunately, larger proteins fold slower and thus we need more computers to simulate their folding. While the alpha helix folds in 100 nanoseconds, proteins just a little larger fold 100x slower (10 microseconds). Thus, while 10-100 processors were enough to simulate the helix, we will need many more to simulate these larger, more interesting proteins."
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Individual.Com
Geneticists discuss Estonia's ambitious gene
bank plan"Leading geneticists scrutinized plans for a national gene bank Thursday, with advocates saying it could dramatically improve understanding of diseases and critics saying it's a waste of money in a country still struggling with basic health needs.
The government in this former Soviet republic recently OK'd the dlrs 200 million proposal to digitally store the genetic codes of at least two-thirds of the 1.4 million population and sent it to parliament, where it's expected to win easy approval."
""Estonia can be a follower of knowledge in the world or it can a leader,'' said Jaanus Pikani, chairman of the Genome Foundation, which drafted the project. "I want it to be one of the leaders.''"
"KUCHING: The Chemistry Department will complete building the DNA (deoxyribonucleic acid) database for the Iban, Bidayuh and Melanau communities in Sarawak by December or early next year, said Science, Technology and Environment Minister Datuk Law Hieng Ding.
He said a similar database for Sarawak's other minority sub-groups, like the Penans, Kayans and Bisaya, would be established next year.
The department relies on hospitals for the supply of blood from the various ethnic groups to build up the DNA database.”
"Law said the first to be established were the DNA database for the Malay, Chinese and Indian communities in the peninsula, which could also be used for Sabah and Sarawak.
Taib said the state government would set up a research council next year to coordinate research actitivities in the state."
redux [08.30.00]
[requires 'free' registration]
"The Icelandic Medical Association and deCODE, the company set to run a national database of health information in Iceland, are unable to reach a compromise over whether the "anonymized" data should automatically include all patients' health records without consent. The company is playing down the problem, but most Icelandic doctors are opposed to "presumed consent." The CEO of deCODE says that the database still will be useful without needing to represent 100% of the population.
Reference: Abbott, A. 2000. Iceland's doctors rebuffed in health data row. Nature 406(6798):819."redux [06.15.00]
[requires 'free' registration]
"Should genetic material be collected from individuals for the purpose of studying human disease in specific populations? The native genome of Iceland offers a powerful and rare resource in genomic research -- a relatively homogeneous population. In this setting, the proposed Icelandic Healthcare Database, which would integrate medical information with genealogy and molecular genetic data, has driven a number of issues -- both ethical and scientific -- to the fore."
"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."
Science When an Entire Country Is a Cohort
[summary - can be viewed for free once registered]
"Denmark has gathered more data on its citizens than any other country. Now scientists are pushing to make this vast array of statistics even more useful by easing restrictions on the use of data coded by personal identification numbers. But government officials are reluctant to do so, citing privacy concerns."
redux [02.25.00]
[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.”
redux [02.13.00]
"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."
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Wired News
Brother, Can You Spare a DNA?"A genetics company is beginning its first studies less than two months after launching an effort to recruit volunteers via the Internet to donate their DNA for experiments.
DNA Sciences has persuaded 4,500 people to give up a little of their genetic code for the greater good of science, which gives them enough samples to begin to search for the genetic causes of asthma, breast cancer and colon cancer."
"The researchers at DNA Sciences hope to help herald the much-hyped "age of personalized medicine." By studying variations in individuals' genes called "single nucleotide polymorphisms," or SNPs (pronounced snips), scientists say they will be able to determine who might be more susceptible to disease, and how people will react to certain drugs."
redux [09.02.00]
"Robert talks with Barry Eisenstein M.D., Vice President of Science and Technology for Beth Israel Deaconess Medical Center, and Professor of Medicine at Harvard Medical School, about his hospital's participation in creating an international tissue bank. They will be asking patients for permission to sell tissue left over from surgery. The tissue will be used by scientists worldwide for genetic research.”
redux [05.15.00]
[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. "
redux [08.24.00]
"The company also announced that Scott is forming a new online health company that will use the genetic information supplied by Incyte's technology and databases for public, procedural and research applications.
The company will link individuals to genomic information regarding their disease in order to reach understanding of a particular condition and enable individual participation in the search for remedy."
redux [08.01.00]
[requires 'free' registration]
"Wanted: your genes.
A California start-up called DNA Sciences is introducing a Web site today that will recruit people to donate their DNA to help find genes that cause disease. The company, which has James D. Watson, a discoverer of the DNA double helix, as a director and James H. Clark, Netscape's founder, as an investor, hopes to get 50,000 to 100,000 people to contribute to its "gene trust" by appealing to their altruism."
"Under DNA Sciences' program, volunteers answer on-line questionnaires about their medical history, and their family's. The company will then send someone to their homes or offices to collect blood samples. Healtheon/WebMD, the medical Web site, owns a stake in DNA Sciences and will be used to help recruit patients.
Donors will not be paid, as is true with the other companies as well."
redux [08.14.00]
"LAST WEEK DNA Sciences announced plans to become a major force in the genomics sector by establishing a facility that will eventually identify one million genotypes a day. The company, which is backed by such industry icons and financiers as James Watson, Jim Clark, and George Soros, plans to use the information it generates from the 50,000 to 100,000 DNA donors it hopes to enlist to create better diagnostic methodologies.
But the Mountain View, Calif., upstart won’t be doing any of this with prepackaged bioinformatics tools. Instead, DNA Sciences will store, manage, and mine SNP data using software the company has developed in-house.
“You cannot buy off-the-shelf software that solves these problems and I think every company that does genetics has built their own software,” said DNA Sciences’ CEO Hugh Rienhoff."
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LinuxMedNews
Innovation, Open Source and Lessig"Wayne Wilson on the openhealth-list has a profoundly interesting summary (reprinted here with permission) of a lecture given by Lawrence Lessig, Professor for Entrepreneurial Legal Studies at Harvard. His bio and a collection of his thoughtful articles can be found here. Wilson writes: 'Lessig is a legal scholar and it is not immediately obvious that legal arguments would be appealing to us, but I think they are.' "
"The Openhealth mailing list is a place for IT professionals and members of the public who are interested in health care and open source software to gather and discuss the issues of this field. This list is provided as a public service by Minoru Development Corporation. While Minoru staff are participants of the list, they do not direct list content. Areas of discussion include:- Deployment storiesredux [07.27.00]
- Discussion of open source projects and products
- Question and answer
- Open source licences and their applicability to health care
- Authentication and privacy issues for data over the Internet
- Obstacles for open source software in health care ”
"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."
"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]
"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]
"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]
"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]
""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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kuro5hin
Why not parallel (agent frameworks)?"Several months ago I was given a task of writing a very fast genetic sequence alignment software. For people that dont know, this software takes two gene sequences of arbitrary lenght and produces all of their possible alignments (see chapter four of this tutorial)..."
"The real problem arises in lab use where a scientist has to compare a new gene sequence to an existing database of hundreds of thousands of sequences. There are already a lot of web sites to do this but this particular piece of software was supposed to be "ours" (sigh). At first I didnt know much about the whole subject so I decided to conduct an experiment using a dynamic programming algorithm. To be fast, C was the programming language choice. The sequential version of the algorithm worked smoothly, however wasnt nearly as fast for what we wanted to do. So I decided to try and parallelize the algorithm. Writing threaded applications that work under different platforms can be a pain, no matter how much standardization people have thrown in it. Soon, my parallelized version worked on a two-cpu Alpha machine and I was pleased (it was faster too). However, when compiled under Linux or Solaris or FreeBSD it trashed the memory and then the painful task of debugging a multi-threaded application started. Due to lack of time and proper tools(my finals were coming) I abandoned the code.
"For now, I am stuck to solving matters on a single machine and telling it to do exactly what it has to, no matter what the complexity of the problem attacked is. Many people observe that Open Source usually produces tools and methods that are (better) copies of commercial originals. Perhaps an Open Source tool such as the above proposed would be a good thing to do. Give people the power, for free."
"We often mention distributed computing models: JavaSpaces, Sash, BizTalk, WebL, and so on. Our lead column in August gave particular attention to the technical prospects for Microsoft's .NET initiative. Piper is an alternative to those models, and .NET in particular, on both engineering and business levels.
Microsoft, for example, has specific business motivations with .NET that involve licensing issues and how the company is paid for its products. Crudely, Microsoft wants to use .NET capabilities to ensure it receives payment every time its software is used. Piper, in contrast, is a free software project to make "anything and everything buildable by linking small components," even across a network, according to J.W. Bizzaro, director of Bioinformatics.org. "
"Moreover, Piper's connections are considerably richer than Unix's pipes. Rather than just a one-way, unstructured datafeed, Piper "[l]inks can depict protocol-independent data flow, procedural steps, and relationships," according to one Piper document. Moreover, those links "can merge or split streams."
Most compelling of all, perhaps, is the opportunity to escape the confines of a single desktop and access resources throughout a rich network. Piper knows how to do that, too." [via bioinformatics.org]
"Piper is a system for managing multi-protocol connections between Internet-distributed objects. Networks, programs, files, widgets, and so on, are all treated as objects and represented in a graphical user interface (GUI) as the nodes of a flow chart (with the Pied/Piper user interface). The user can join nodes via lines that depict links for data flow, procedural steps, relationships, and so forth.
The Internet-distributed nature of Piper lets the user work in a unique way: Only the graphical representation of an object resides on a local workstation. Compute-intensive programs and large data sets can reside remotely on high-performance, high-capacity computers.
Joining nodes across the Internet can also be used to form world-wide collaboratives (such as The Loci Project) and provide an almost limitless collection of objects for the user. "
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Tools:
BioWurld"BioWurld is a semi-automated index of resources in the fields of bioinformatics and molecular biology. We are in the process of populating the database: a continuing process. You are kindly invited to add a resource yourself too if you miss a certain favourite bioinformatics or molecular biology link. Just browse to the category where you deem the link is best placed, then click the 'Submit a url to this category' hyperlink and fill in the details. Besides categorised resources BioWurld also contains other resources that were found while traversing bioinformatics related websites. These resources can be found by searching on keywords or phrases."
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BioMedCentral
Freedom of Information Conference: The impact of open access on biomedical research"How should biomedical research be communicated? How should research be assessed and validated?"
"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.
We have also commissioned editorial articles from several speakers and delagates at the meeting.
All thoughts, comments, and suggestions are welcome on our email discussion list"
"What if you could wave a wand, in this very Harry Potter decade, and make libraries - at least digital libraries - more open, more easy to manage, cheaper, and even more eclectic and democratic? What if content contributors could submit, catalog, index, manage, rate and rank materials in large collections themselves? I believe that, thanks to the innovations from the Open Source community and perhaps more importantly the Free Software community, that we can have a contributor-run library at this very moment.
In fact, there are several very successful examples from which we can draw not only best practices, but also - that grail of the programmer - working code. But better still, these projects are also examples of vibrant, lively, noisy, democratic communities. "
"Librarians are increasingly called upon not only to collect information in electronic form but also to organize it into digital libraries. The materials may be created and held locally, or they may be created and accessed in a distributed fashion as a virtual library. Digital libraries can provide material on a variety of topics, from children's games to high-energy physics. Their scope may be local, national, or even international; the audience may be a small group with specialized interests or the broader public. Essential to the successful implementation and use of any digital library is the organization of that library, either directly or indirectly, by one or more knowledge organization systems (KOS).
The term knowledge organization systems is intended to encompass all types of schemes for organizing information and promoting knowledge management. Knowledge organization systems include classification and categorization schemes that organize materials at a general level, subject headings that provide more detailed access, and authority files that control variant versions of key information such as geographic names and personal names. Knowledge organization systems also include highly structured vocabularies, such as thesauri, and less traditional schemes, such as semantic networks and ontologies. Because knowledge organization systems are mechanisms for organizing information, they are at the heart of every library, museum, and archive. "
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SFGate
Enjoying the Best of Both Worlds Molecular biology, programming is gold Programming skills, molecular
biology can pay big dividends"If job searching were a poker game, Alan Williams would be sitting pretty with a full house.
Fresh out of graduate school, he happens to have a rare combination of skills that drives employers to offer hefty salaries, stock options and bonuses. And it's not even a dot-com job.
Williams has a combination of computer programming and molecular biology know- how. His job is to use computers to mine the vast store of data in the human genome model."
redux [09.01.00]
[requires paid registration]
"Since Next Wave last covered bioinformatics, in our July 1996 Profiles of Bioinformaticians and February 1997 Bioinformatics Skills features, the prominence of the bioinformatician's role in modern biology has only increased. This month, Next Wave provides a comprehensive picture of the current state of bioinformatics, from the funding situation in Europe and the U.S. to the new bioinformatics degree programs and the immediate hiring needs of industrial and academic labs around the world.”
redux [07.25.00]
"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]
"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]
"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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Financial Times
Human genome copied to CD"The entire human genome - the genetic instructions to make a man or woman - has been squeezed on to a compact disc. The CD will be available in newsagents later this week, stuck on the front cover of Prospect, a monthly political and intellectual magazine."
"Dr Hubbard, who is head of human sequence analysis at the Wellcome Trust's Sanger Centre near Cambridge, said: "This may be a bit of a gimmick but I had been thinking about how to fit the genome on a CD, so when Prospect contacted me I was keen to make it happen."
He used compression technology to squeeze the genome's working draft on to a standard CD without losing data. The CD contains a programme that enables anyone with an up-to-date computer to view the entire DNA sequence as a series of chemical letters, examine any of the 23 human chromosomes, or look at the 10,000 or so genes that scientists have identified."
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Individual.Com
Gene Expression Markup Language (GEML(TM)) - a Data format to Facilitate the Interchange of Gene Expression Data
from Multiple Technologies - NOW AVAILABLE"Rosetta Inpharmatics, Inc. (Nasdaq: RSTA) announced today the availability of a new file format, called Gene Expression Markup Language (GEML), to facilitate the interchange of data from DNA chip and other gene expression technologies into a consistent format for more efficient and extensive data analysis."
"GEML is an extensible markup language (XML-based) data file format that operates independently of any specific database schema. GEML supports data from various gene expression platforms including Affymetrix, Agilent, Incyte, Molecular Dynamics, 1-color or 2-color fluorescent labeling and scanning, nylon filters, and other data formats. GEML also tracks which data format was used, and with this knowledge enables normalization, integration, and comparison of data across technologies."
"As part of Rosetta's efforts to encourage this potential industry standard for gene expression data, Rosetta intends to offer users of GEML additional tools for viewing and analysis of genomic data in GEML format."
"This data standard is designed to separate data reporting and collection from methodology used. The profile_type attribute enables keeping track, in the data file, of which methodology was used, enabling normalization across methodologies and thus comparison of data which was collected by a variety of methodologies.
Expression analysis data is generated by a variety of sources and is usually stored in the form of disk files. Industry-wide standards for the formats of such files do not exist, so there are now many different formats, with different representations of data and different types of information stored. For example, some data file formats for chip scans reference a specific pattern, while others do not. Similarly, some data file formats for chip scans can contain the raw image data or can reference one or more image files, while others cannot.
"GEML is a free, public-domain, open-standard XML DTD. GEML was created and is licensed in order to define a single, distinct GEML format and avoid proliferation of incompatible variations.
You may freely use, publish, and redistribute the GEML DTDs, subject to the restrictions in these Terms of Use; write and sell applications which create, load, or write GEML-compliant files; or distribute or sell your own GEML-compliant files. You may transmit verbatim copies of the GEML DTD to any person if the entire original DTD file is transmitted and the recipient accepts the terms and conditions of this GEML Terms of Use.
You may not modify, lease, loan, sell, distribute, charge for, or create derivative works of the GEML DTDs, without written permission from Rosetta Inpharmatics."
"With XML has come a proliferation of consortia from every industry imagineable to populate structured material with standard terms (see Appendix B). By one estimate, a new industry consortium is founded every week, perhaps one in four of which can collect serious membership dues. Rising in concert are intermediary groups to provide a consistent dictionary in cyberspace, in which each consortium's words are registered and catalogued.
Having come so far with a syntactic standard, XML, will E-commerce and knowledge organization stall out in semantic confusion?"
"How are semantic standards to come about?"
"There is an increasing demand for formalized knowledge on the Web. Several communities (e.g. in bioinformatics and educational media) are getting ready to offer semiformal or formal Web content. XML-based markup languages provide a 'universal' storage and interchange format for such Web-distributed knowledge representation. This tutorial introduces techniques for knowledge markup: we show how to map AI representations (e.g., logics and frames) to XML (incl. RDF and RDF Schema), discuss how to specify XML DTDs and RDF (Schema) descriptions for various representations, survey existing XML extensions for knowledge bases/ontologies, deal with the acquisition and processing of such representations, and detail selected applications. After the tutorial, participants will have absorbed the theoretical foundation and practical use of knowledge markup and will be able to assess XML applications and extensions for AI. Besides bringing to bear existing AI techniques for a Web-based knowledge markup scenario, the tutorial will identify new AI research directions for further developing this scenario."
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Christian Science Monitor
Controlling the flood of genetic information"With the completion of a "rough draft" of the entire human genome in June, government and corporate scientists have assembled enough genetic code to fill 2,000 computer diskettes.
Now, the scientific footrace shifts from spelling out the seemingly endless string of "A's," "C's," "T's," and "G's" that make up our DNA, to actually understanding what it means.
That's where a new field of "bioinformatics" comes in."
"Researchers at the University of Idaho are building their own "super" computer using parts from 40 to 100 desktop PCs. The hardware will cost only about $44,000, but with the proper connections, the system will be sophisticated enough to run experiments on "jumping genes," bits of genetic material that migrate along the DNA double helix like microscopic hitchhikers.
James Foster, the computer scientist at the University of Idaho directing the project, said that building better programs called algorithms is more important to understanding biological data than just building bigger computers.
"Nature can always defeat brute-force approaches," says James Limpan, director of the National Center for Biotechnology Information in Rockville, Md.
"We need the most clever ways of measuring things and not more CPU power," he says."
"Despite the existence now of a rough draft of the human genome, the story it tells is still full of holes. Just one of them: the mystery of how human proteins get molded into the functional building blocks of life. What's stood in the way of researchers unraveling this puzzle has been the enormous complexity of the chemistry, and inadequate computing power to decipher those intricate workings. That may all change in five years when IBM (NYSE: IBM) researchers enlist the company's newest water-cooled silicon circuits to model the way in which a human protein folds into a specific shape, thus determining its biological function. Called Blue Gene, the supercomputer project will cost $100 million and will be 1,000 times more powerful than Deep Blue, which defeated legendary chess master Garry Kasparov three years ago. It will need all the extra circuitry it can muster, because simulating the behavior of a sinuous strand of protein is no simple task. It involves applying basic principles of physics and chemistry to instruct Blue Gene to calculate the atomic forces at work along a single strand of the human protein. Paul Horn, senior vice president of IBM Research, says this unlocking of protein folding is a milestone in the future of medicine and health care.
Blue Gene is so powerful that even the terminology used to describe its processing abilities is beyond today's computing lexicon. Researchers say it will be able to harness a petaflop of processing power, which is 5 million times faster than a PC. IBM's researchers say the best way to envision that is by imagining a picture one inch tall (representing a single PC processor's capability), while Blue Gene's processing prowess would stretch 30 miles into the sky."
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ABCNews
Mapping Tiny Differences"Celera Genomics Inc., the Maryland-based company that is working to map every single human gene, said today it had found 2.8 million of the little changes that make one person different from another."
"The announcement means Celera has outstripped the rival public project to map the human genome, Craig Venter, president of Celera, said in a telephone interview.
“It is a far greater number of SNPs than there are in the public databases,” Venter said. Earlier this month, the publicly funded Human Genome Project and the public-private SNP consortium, which includes 10 major pharmaceutical companies, announced that they had found 800,000 different SNPs (pronounced “snips”).
Venter said Celera had duplicated 400,000 of these in its 2.8 million. But the public project has 400,000 unique SNPs, which means 3.2 million NPs are now known."
redux [06.29.00]
"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.''"redux [02.18.00]
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
Science SNP Mappers Confront Reality and Find It Daunting
[summary - can be viewed for free once registered]
"The genetic markers called SNPs have been widely touted as the key to personalized medicine, with drugs tailored to an individual's genotype and simple tests to determine one's risk of specific diseases. But a closed meeting held last week, sponsored by the SNP Consortium and the U.S. National Human Genome Research Institute, concluded that those promises may be harder to achieve than expected, and that more SNPs may be required to track down a particular disease gene than previously estimated.”
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Wired
Genome Map Heralds Cheap Drugs"Top genomics researchers from around the world are gathering in Miami this week to explore ways of using the mountains of information created by the Human Genome Project.
The main thrust of this research is to discover new drugs faster and cheaper. To do that, scientists need to find innovative ways to combine biology with information technology, a field dubbed bioinformatics."
"Researchers predict that the time and cost it takes to develop drugs will be significantly reduced by biology-based approaches. It now takes about 12 years and $500 million to bring a drug to market.
"We think we can reduce this by about six years," said William Haseltine, CEO of Human Genome Sciences (HGSI), a genomics company in Rockville, Maryland. "By both increasing the success rates and shortening the trial period, we think we can dramatically improve cost efficiency in drug discovery."
redux [05.26.00]
""The data suggest that the biotechnology industry used to be more productive than Big Pharma, but not any longer," said Rebecca Henderson, a professor at MIT's Sloan School of Management whose been studying the question for six years. "The public biotechs have declining productivity… and look as if they are running into the same problems as Big Pharma."On every metric that Henderson has studied---number of scientific papers and patents per R&D dollar, cost per new drug--she found that biotech and Pharma productivity were quickly converging, and both were getting worse. After spending six years of studying the question, Henderson says she has found "no systematic evidence that small firms are more productive.""
"First came germ theory with antibiotics. Then came replacement theory with insulin and growth factors. Now the paradigm for drug development has shifted once again: We have entered the era of genomics-based medicine.
In less than a decade a new genomics industry has taken hold. Gemomics companies now ferret through miles of genetic code to identify the genetic causes of disease, select potential target genes, and help big pharma find the next blockbuster.
But the face of genomics—or at least its role in drug discovery—is about to change, due largely to its own success. “We’re knee deep in potential targets,” says Nicholas Dracopoli, executive director of pharmacogenomics with Bristol-Myers Squibb. “Prioritising the targets is the rate limiting step.”"
"Leaders in the genomics field, as in any other industry, will be companies that offer a value-added service. Large pharmaceutical companies agree on what that service should be: integration of all the genomics information available. With more information readily accessible, companies can easily decide on whether to continue investigating potential targets.
So the future of genomics companies may rest in their IT and software capabilities, a view held by Celera Genomics, a newcomer to genomics. “We are entering an era of ‘cyberpharmaceutical’ drug development,” says Samual Broder, executive VP and chief medical officer. “Pharmaceutical corporations will use genomic databases, and other relational databases involving gene expression, proteomics etc. as the foundation of their drug discovery pipelines. One of the immediate goals... is to produce appropriate databases and software to link biologic and genomic information.” "
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The New York Times
After Deciphering the Map, the Next Task Is a Guidebook for the Human Genome[requires 'free' registration]
"Labor Day has come and gone, and I am chagrined to find that I haven't made it through my summer reading. My list comprised only a single book, but a rather unusual one: the text is three billion years old, has six billion copies in print, runs three billion letters long (about one million pages), and is written entirely in four characters (A, T, C, G) with no spaces or punctuation. The book, of course, is a great classic, The Sequence of the Human Genome."
redux [06.24.00]
"For insiders in genome research, the name Eric Lander evokes a palpable image of the trends sweeping biology—automation, computers, entrepreneurialism, big science and big ideas.
A mathematician turned Harvard Business School professor turned gene scientist, the 42-year-old Lander is director of the Whitehead Institute for Biomedical Research/MIT Center for Genome Research. Lander has built the lab into the world’s most productive academic gene sequencing facility and the flagship of the international Human Genome Project. "
"TR Senior Associate Editor Antonio Regalado managed to catch up with Lander by phone early on a recent Sunday morning."
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Bioinform
Lincoln Stein Makes Annotation Easy"Hanging out at the University of California, San Diego watering hole one evening during the Bioinformatics Open Source Conference, a young researcher from the Berkeley Drosophila Genome Project turned to his colleague and whispered with the kind of reverence generally reserved for rock stars, “Hey, that’s Lincoln Stein.”
Although Stein isn’t known for playing in a rock ‘n roll band, he has achieved celebrity status among bioinformaticists. The revolutionary CGI.pm Perl module he created for the Common Gateway Interface is considered one of the most widely used programs for creating Web applications.
These days Stein is working on a new project at the Cold Spring Harbor Laboratory that he said will enable researchers increased access to and understanding of genomic annotations."
redux [08.09.00]
"A natural complement to distributed file-sharing capabilities is distributed computation. The idea behind distributed computation is that a really big problem gets split into discrete, independent chunks, which are then parceled out to individual computers whose owners have volunteered their idle processor time to the cause. In aggregate, the users' computers form a sort of distributed supercomputer. The concept was first popularized by U.C. Berkeley's SETI@Home project, a 1999 PC Magazine Technical Excellence finalist that's now been downloaded by more than 2 million users. Though SETI@Home is a single-purpose tool designed solely to scour radio-telescope signals for signs of extraterrestrial transmissions, you can expect to see general-purpose mechanisms for distributing all kinds of massive computations. United Devices, for example, is a company that will use distributed computing for projects in areas such as bioinformatics research, drug design, and climate studies."
redux [07.22.00]
"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]
"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.""
"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."
"* 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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LA Times
IBM, Incyte to Blend Genome Software"IBM Corp. and Incyte Genomics Inc. have agreed to combine their specialized software into a product companies can use to analyze the human genetic code for drug research.
"Terms weren't disclosed. Palo Alto, Calif.-based Incyte, a software and services company for the pharmaceutical and biotechnology industries, will incorporate IBM's DiscoveryLink data-management software into its own related products."
redux [07.31.00]
"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."