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Systems biology models and simulation tools are critical components for bridging molecular biology with predictive medicine. We report a systematic comparison of popular simulation tools, including CellDesigner, COPASI and VirtualCell, to facilitate translational research in genomics, proteomics and systems biology. Different tools evaluating the same model may produce dissimilar results. This inconsistency...
Studies have implicated ceramide as a key molecular agent in regulating programmed cell death, or apoptosis. Consequently, there is significant potential in targeting intracellular ceramide as a cancer therapeutic agent. The cell's major ceramide source is the ceramide de novo synthesis pathway, which consists of a complex network of interdependent enzyme-catalyzed biochemical reactions. To understand...
In this paper, we report a focused case study to assess whether quantitative metrics are useful to evaluate molecular-level system biology models on cellular metabolism. Ideally, the bio-modeling community shall be able assess systems biology models based on objective and quantitative metrics. This is because metric-based model design not only can accelerate the validation process, but also can improve...
The goal of this work is to find optimal numerical solvers to study models of biological systems of interest. We report 2 simple rules to select the optimal numerical solver(s) for solving stiff, complex oscillatory systems. Numerical solvers currently used to solve mathematical models in systems biology can be ill-conditioned due to stiffness. As a case study, we choose the classic Belousov-Zhabotinskii...
The Emory-Georgia Tech Nanotechnology Center for Personalized and Predictive Oncology is one of the eight national centers funded by the National Cancer Institute (NCI). Its overall goal is to combine nanotechnology and biocomputing with clinical oncology for personalized detection, diagnosis and treatment of human cancer. Within this large-scale and multifaceted center, a key challenge is how to...
The Emory-Georgia Tech Nanotechnology Center for Personalized and Predictive Oncology is one of the eight national centers funded by the National Cancer Institute (NCI). Its overall goal is to combine nanotechnology and biocomputing with clinical oncology for personalized detection, diagnosis and treatment of human cancer. Within this large-scale and multifaceted center, a key challenge is how to...
The Emory-Georgia Tech Nanotechnology Center for Personalized and Predictive Oncology is one of the eight national centers funded by the National Cancer Institute (NCI). Its overall goal is to combine nanotechnology and biocomputing with clinical oncology for personalized detection, diagnosis and treatment of human cancer. Within this large-scale and multifaceted center, a key challenge is how to...
Technological advances increase the rate and quality of biomedical data collection. To exploit these advances to the fullest, laboratory information management systems (LIMS) have been developed to integrate laboratory equipment with software controls so as to achieve an automated and seamless workflow process. Ultimately, researchers and clinicians must collaborate closely to achieve a comprehensive...
In comparison to traditional "single-gene" study method such as reverse transcriptase-polymerase chain reaction (RT-PCR), microarray technology can produce high-throughout gene expression data simultaneously. The advancement of this technology also presents a big challenge. In cancer research, the issue is how to identify the signature genes, or biomarkers associated with particular cancer...
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