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The model was constructed using local (e.g., protein–protein interaction) information from the primary literature. In other words, during the construction phase of the model, there was no attempt to determine the local interactions based on any other larger phenotypes or phenomena. However, after the model was completed, verification of the accuracy of the model involved testing it for the ability to reproduce complex input–output phenomena that have been observed in the laboratory. To do this, the T-cell model was simulated under a multitude of cellular conditions and analyzed in terms of input–output dose–response curves to determine whether the model behaves as expected, including various downstream effects as a result of activation of the TCR, G-protein-coupled receptor, cytokine, and integrin pathways.<ref>Conroy BD, Herek TA, Shew TD, Latner M, Larson JJ, Allen L, et al. Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4 T-lymphocytes. Front Immunol. 2014;5: 599 doi: 10.3389/fimmu.2014.00599</ref>
The E-Cell Project<ref>http://www.e-cell.org/</ref> aims "to make precise whole cell simulation at the molecular level possible".<ref>{{Cite web |url=http://www.e-cell.org/ecell/ |title={title} |access-date=2010-11-09 |archive-url=https://web.archive.org/web/20101029020449/http://www.e-cell.org/ecell |archive-date=2010-10-29 |dead-url=yes |df= }}</ref>
[[CytoSolve]] - developed by [[Shiva Ayyadurai|V. A. Shiva Ayyadurai]] and C. Forbes Dewey Jr. of Department of Biological Engineering at the [[Massachusetts Institute of Technology]] - provided a method to model the whole cell by dynamically integrating multiple molecular pathway models. ."<ref>{{cite journal |last1=Al-Lazikani |first1=Bissan|last2=Banerji |first2=Udai | last3=Workman |first3=Paul |year=2012 |title= Combinatorial drug therapy for cancer in the post-genomic era|journal=Nature Biotechnology |volume=30 |issue= 7|pages=679–692 |publisher=Nature |doi= 10.1038/nbt.2284|url= |pmid=22781697}}<!--|accessdate=14 February 2013 --></ref><ref>{{Cite journal| last1=Ayyadurai| first1=VA Shiva|first2=C. Forbes|last2=Dewey|journal=Cell Mol Bioeng.|date=March 2011|volume=4|issue=1|pages=28–45|doi=10.1007/s12195-010-0143-x|title=CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models|publisher=Springer|pmid=21423324|pmc=3032229}}</ref>
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