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{bio,medical} informatics

Sunday, January 14, 2001

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find related articles. powered by google. Feed Living Language
"EVERYTHING'S COMING up roses! Or more precisely, Arabidopsis thaliana, a somewhat nondescript white flower selected by biologists as the model in the plant kingdom for genetic research. Related to broccoli and cauliflower, A. thaliana is the most studied plant in human history; every week new papers are published about its properties. In an astounding leap forward, the journal Nature just announced that the entire genome for A. thaliana has been sequenced -- a first for the vegetal world. As plants go, it was a relatively easy task; the complete genome runs to 120 megabytes of information, compared to 1.6 gigabytes for wheat and a hefty 3 gigabytes for humanity. What makes this discovery just a bit different from the ever-increasing flow of genetic revelations is that, in another first, Nature has announced that all genomic information presented in its pages -- and on its Web site -- will be published in GEML, or Gene Expression Markup Language, a lingua franca defining a common standard for the bits of life."
redux [12.22.00]
find related articles. powered by google. GenomeWeb Nature Clarifies Role in GEML Community; Denies it 'Endorses' Standard
"While the Nature Publishing Group has joined Rosetta Inpharmatics's Gene Expression Markup Language Community, the journal " is not taking sides or picking any standard over another," a Nature spokesman said Friday."

"This clarification of Nature's role in the GEML community came in response to Rosetta's recent public relations campaign, which claimed the journal " officially endorses" the GEML standard.

The announcement prompted the Microarray Gene Expression Database Group to send a letter to the journal stating that the Microarray Markup Language, which the MGED supports, has wider support in academia and industry."

redux [12.12.00]
find related articles. powered by google. Wired News Genomics Gets a New Code: GEML
"The Internet uses HTML, and soon perhaps genomics will use GEML.

At least that's what Rosetta Inpharmatics (RSTA), the creators of Genetic Expression Markup Language, or GEML, is hoping. The prestigious science journal Nature adopted the language on Monday, which should give a significant boost to its acceptance in the scientific community."

"According to Metcalfe's law, penned by 3Com founder Robert Metcalfe, the more people who use any system, the more valuable it becomes. And since researchers will now be required to submit papers using GEML, the value of the language should increase exponentially."

redux [10.30.00]
find related articles. powered by google. BioresearchOnline Universal gene expression software is being offered as freeware
"Version 1.0 of Rosetta Inpharmatics’ Gene Expression Markup Language (GEML) Conductor tools is now available for downloading from the company website ( This suite of applications, which employs an open-standard XML file format, enables researchers to visualize and exchange data between different gene expression databases and analysis systems.

The company refers to its GEML Conductor tool as a universal solution for visualizing and exchanging gene expression information produced by different technology platforms. It allows users to convert any well-formatted gene expression data file into a common, flexible data format.

Rosetta GEML Conductor tools' features include:

  • File Conversion. Users can convert any gene expression data file, including Affymetrix GeneChip and BioDiscovery AutoGen, into the GEML format.
  • Plot Viewer. Users can visualize and share data by turning any GEML profile into a plot. The Plot Viewer includes a Zoom feature, which allows magnification into or out of particular sections of a plot.
  • Magic Lasso. Users can select specific plot areas for closer viewing.
  • Intensity Plot Viewer. Users can measure the intensity of one channel of data against the intensity of another channel of data.
  • Customizable Visualization. Users can customize groups, colors, and labels according to viewer preferences.
  • InstaLink. Users can access built-in hotlinks to popular databases and information centers on the World Wide Web.
  • Table Viewer. Users can convert GEML data into customizable tables with resizable and reorderable columns.
"The inability to analyze gene expression data from multiple technology platforms has long been hampered by software compatibility issues," stated Mark Boguski, senior vice president of research and development for Rosetta Inpharmatics. "By translating diverse data formats into a single common format, the Rosetta GEML Conductor tools enable users to share and visualize information across platforms, thus maximizing the value of gene expression data."

redux [09.15.00]
find related articles. powered by google. Rosetta Inpharmatics The Gene Expression Markup Language (GEML)
"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."

[ 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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