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Application of system theory in biology has led to development of computer languages for mathematical modeling which are in open source and apply common standards for model trans-platform exchangeability and integration with extensive model banks, databases, numerical and statistical methods and graphical tools. Standardization has led to systems biology Markup language (SBML) based on XML format, while open source policy enables integration of computer resources and provides synergistic integration of scientific results and methodologies from various scientific fields. Different software projects have been initiated resulting in software such as: SB Toolbox, J Designer, SB Workbench (SBW), and Cell Designer. The main use of the systems biology software is to investigate biochemical networks, gene regulatory networks, signal transduction, cell communication, dynamical complex behavior, and most importantly to lead to understanding of life regulation. In this work is presented use of systems biology markup language and modeling tools applied for analysis of signal transduction in T-cell as apart of a human immune system.