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{bio,medical} informatics

Monday, April 07, 2003

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find related articles. powered by google. Bio-IT World Data Sharing Is Key to Understanding the Genome

"For informatics, I've been a big proponent of standardized tools and interchange formats. For sequence data, it is sort of essential to have these. If I had to choose between a fancy sequencing technology and these basic things, I'd have to choose the latter.

It would be nice if we could agree on standard formats. There is a lot of data out there already, and it is a bit of a pain converting one person's data model into another. It slows things down, but doesn't make things impossible. The most important thing is for the data to be made available though, not how it's made available."

redux [01.31.02]
find related articles. powered by google. The O'Reilly Network Lincoln Stein's Keynote: Building a Bioinformatics Nation

"Lincoln then summarized efforts to unify the bioinformatics data services. These efforts started 12 years ago with the Meetings of the Molecular Biology Databases (MMBD), which essentially ended in argument. Every member thought his or her way of doing things was the best way. Next came the federated models like Gaea and Kleisli , and then the data warehouses of Ensembl, UCSC, and others. This brings us to the ad hoc Web services that are currently in place. These allow programmatic access to data, as in the GenBank/EMBL example. To truly unify the services of bioinformatics data providers we need to move beyond this to a more formal Web services model.

In this Web services model, the data providers would register their services in a formalized service registry, and researchers' scripts would no longer need to be concerned with the interface details of the different databases. This model represents the unification that Lincoln, and judging by the response, apparently everyone in the audience, hopes to see in bioinformatics."

redux [09.27.01]
find related articles. powered by google. XEMBL Project What is the XEMBL Project?

"As you might be aware of, flat-files have severe limitations, and we have been asked various times if we are going to distribute the EMBL data in different formats as well, XML being the one most prominently mentioned. In short, the XEMBL project will bring to the user several alternative formats of EMBL data."

"We have XEMBL running as a web service using SOAP (Simple Object Access Protocol) and WSDL (Web Service Definition Language)."

find related articles. powered by google. XML.Com Web Services: It's So Crazy, It Just Might Not Work

"Web Services can't create a framework in which any two arbitrary applications can interact because XML doesn't provide shared languages, merely shared alphabets. The Web Services stack pushes this shared semantics problem into higher and higher layers without solving it. Humans often cannot create perfectly transparent descriptions even when they are trying to, and they simply won't try when there's an economic incentive to stretch the truth."

redux [11.06.00]
find related articles. powered by google. IBM developerWorks The Tao of e-business services

"The semantics of services -- what they do and what data elements they manipulate mean -- is the key issue. Business value results from B2B collaborations that do the right thing. If they do something else, the damage may be dramatic. How, then, do we trust that a service does the right thing before it is used? And how do we make that determination at Internet speeds?

In small-scale OO systems, interface compatibility usually implies semantic compatibility. That is, an object that implements the right set of messages with the right types of arguments probably does "the right thing." This is true, in part, because small-scale systems tend to be built by a small team of programmers with shared understanding of how the system operates and, in part, because small systems offer little opportunity for ambiguity. However, in large-scale OO systems, the semantics provided by a given class cannot be reliably deduced from the message interface alone. Clearly, in an Internet populated with many thousands of services offered by thousands of different companies with very different agendas, compliance with some specified message set will not be sufficient to deduce the semantics of the service."

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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