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{bio,medical} informatics

Monday, July 17, 2000

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Yahoo! News Physiome Sciences Raises $50 Million in Private Placement; Adds Major Institutional Investors to its Shareholder Base
"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."
"...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.”

[ 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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