Title |
URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries
|
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Published in |
BMC Systems Biology, June 2012
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DOI | 10.1186/1752-0509-6-76 |
Pubmed ID | |
Authors |
Brian Drawert, Stefan Engblom, Andreas Hellander |
Abstract |
Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 1 | 100% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United States | 3 | 4% |
Switzerland | 2 | 3% |
Norway | 1 | 1% |
Japan | 1 | 1% |
Unknown | 73 | 91% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 26 | 33% |
Student > Ph. D. Student | 20 | 25% |
Student > Master | 9 | 11% |
Professor | 6 | 8% |
Student > Bachelor | 2 | 3% |
Other | 5 | 6% |
Unknown | 12 | 15% |
Readers by discipline | Count | As % |
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Computer Science | 15 | 19% |
Agricultural and Biological Sciences | 14 | 18% |
Mathematics | 8 | 10% |
Biochemistry, Genetics and Molecular Biology | 7 | 9% |
Physics and Astronomy | 4 | 5% |
Other | 20 | 25% |
Unknown | 12 | 15% |