This Article Full Text Full Text (PDF) Supplemental Research Data Erratum (v14,p197) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Efroni, S. Articles by Cohen, I. R. Search for Related Content PubMed PubMed Citation Articles by Efroni, S. Articles by Cohen, I. R. Social Bookmarking                   What's this?

Resources

Toward Rigorous Comprehension of Biological Complexity: Modeling, Execution, and Visualization of Thymic T-Cell Maturation

¹ Computer Science Department, Weizmann Institute of Science, Rehovot, Israel ² Department of Immunology, Weizmann Institute of Science, Rehovot, Israel

One of the problems biologists face is a data set too large to comprehend in full. Experimenters generate data at an ever-growing pace, each from their own niche of interest. Current theories are each able, at best, to capture and model only a small part of the data. We aim to develop a general approach to modeling that will help broaden biological understanding. T-cell maturation in the thymus is a telling example of the accumulation of experimental data into a large disconnected data set. The thymus is responsible for the maturation of stem cells into mature T cells, and its complexity divides research into different fields, for example, cell migration, cell differentiation, histology, electron microscopy, biochemistry, molecular biology, and more. Each field forms its own viewpoint and its own set of data. In this study we present the results of a comprehensive integration of large parts of this data set. The integration is performed in a two-tiered visual manner. First, we use the visual language of Statecharts, which makes specification precise, legible, and executable on computers. We then set up a moving graphical interface that dynamically animates the cells, their receptors, the different gradients, and the interactions that constitute thymic maturation. This interface also provides a means for interacting with the simulation.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1215303.

[Supplemental material is available online at www.genome.org and at www.wisdom.weizmann.ac.il/sol/sysbio2002/.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				J. Fisher, N. Piterman, E. J. A. Hubbard, M. J. Stern, and D. Harel Computational insights into Caenorhabditis elegans vulval development PNAS, February 8, 2005; 102(6): 1951 - 1956. [Abstract] [Full Text] [PDF]

				P. Lecca, C. Priami, P. Quaglia, B. Rossi, C. Laudanna, and G. Constantin A Stochastic Process Algebra Approach to Simulation of Autoreactive Lymphocyte Recruitment SIMULATION, June 1, 2004; 80(6): 273 - 288. [Abstract] [PDF]