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News

Bringing quality control to systems biology modeling

Virginia Polytechnic Institute And State University : 01 September, 2006  (Technical Article)
An international group of scientists from 14 different organizations around the world are proposing a new quality standard for biochemical models. The background for this effort is the pressing need for a minimum standard of information that will allow scientists to build and use effective models of biological systems. If biological models are incompletely described, it causes major obstacles for scientists wishing to apply these models to their research efforts. By introducing a framework for quality control, the scientists hope to make it easier for researchers to reuse, modify, and combine computer models of biological processes.
An international group of scientists from 14 different organizations around the world are proposing a new quality standard for biochemical models. The background for this effort is the pressing need for a minimum standard of information that will allow scientists to build and use effective models of biological systems. If biological models are incompletely described, it causes major obstacles for scientists wishing to apply these models to their research efforts. By introducing a framework for quality control, the scientists hope to make it easier for researchers to reuse, modify, and combine computer models of biological processes.

The new recommendations, which have been developed through the combined effort of different international research groups, were outlined in the publication Nature Biotechnology.1 Pedro Mendes, research associate professor at the Virginia Bioinformatics Institute, and one of the co-signatories of the recommendations, remarked: “Problems of this type are not new to the field of biology. Over the years, incomplete information and data sets have hampered the growth of other repositories of biological data, whether they are nucleotide or protein sequences, macromolecular structures, or results acquired from microarray systems.”

He added: “Those involved in the biological modeling community are acutely aware of the need for quality control of the building blocks of biological models. If the guidelines put forward were to be adopted by the scientific community, this would go a long way towards ensuring that systems biology achieves its undeniable potential in the years ahead.”

MIRIAM, which stands for Minimum Information Requested in the Annotation of Biochemical Models, has two main parts. The first is a set of checks that matches the model to its description, which in many cases would be a publication in a peer-reviewed scientific publication. The second part is a set of annotations or labeling schemes that show who created the model, whether it has been changed (history of modifications), as well as a link to a full description of the model. If these steps are implemented, the work of a scientist using a particular model is greatly simplified since this minimum standard ensures that scientists are able to search a particular model on the basis of its components. If difficulties were to be encountered, a reference point or contact person is available to resolve potential restrictions.

The authors hope that these standards are adopted by publishers in the life sciences since this will go a long way towards achieving the successful adoption of the recommendations by the global scientific community.

Virginia Bioinformatics Institute at Virginia Tech has a research platform centered on understanding the “disease triangle” of host-pathogen-environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today’s key challenges in the biomedical, environmental and plant sciences.
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