CellLine, a stochastic cell lineage simulator
نویسندگان
چکیده
منابع مشابه
CellLine, a stochastic cell lineage simulator
UNLABELLED We present CellLine, a simulator of the dynamics of gene regulatory networks (GRN) in the cells of a lineage. From user-defined reactions and initial substance quantities, it generates cell lineages, i.e. genealogic pedigrees of cells related through mitotic division. Each cell's dynamics is driven by a delayed stochastic simulation algorithm (delayed SSA), allowing multiple time del...
متن کاملCellLine, a stochastic cell lineage simulator: Applications
Here we present a complete description of the example models that we tested and the results we obtained using CellLine. We also provide all reactions files (see Availability section). To demonstrate the use of CellLine, we first simulate a model of the P53-Mdm2 feedback loop, where transcription and translation are modelled by multiple time delayed reactions [5]. This model is a modified versio...
متن کاملStochastic Timed Automata Simulator
In the paper the idea of timed automata simulator is introduced. The proposed simulator is an extension of the UPPAAL tool simulator. Instead of choosing transition to be performed randomly or manually, the simulator calculates transition times according to transition guard and state invariant for each transition. A probability density function, which is needed for such calculation, is formally...
متن کاملEvaluation of Cell Growth Inhibition of Bifidobacterium Bifidum Cell-free Supernatant Extract on 4T1Tumor Cell Lineage
Background: Cancer is amongst the leading reasons of death in all parts of the world. Breast cancer is also responsible for the largest number of deaths among women population. Several studies confirmed that Bifidobacterium bifidum as a probiotic meaningfully inhibited breast cancer development. The present study aimed to investigate the effect of B. bifidum supernatant on the cell growth inhib...
متن کاملA stochastic particle-based biological system simulator
The simulation and visualization of biological systems is expected to enhance our understanding of biological processes towards the development of effective therapeutic treatments. Biological systems are inherently stochastic at the molecular level, exhibit modified behavior under crowded conditions and may be affected by spatial locality. Common simulation approaches fail to account for these ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2007
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btm491