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<citation key="gillespie_exact_1977"> | ||
<article_title>Exact stochastic simulation of coupled | ||
chemical reactions</article_title> | ||
<author>Gillespie</author> | ||
<journal_title>The Journal of Physical | ||
Chemistry</journal_title> | ||
<issue>25</issue> | ||
<volume>81</volume> | ||
<doi>10.1021/j100540a008</doi> | ||
<issn>0022-3654</issn> | ||
<cYear>1977</cYear> | ||
<unstructured_citation>Gillespie, D. T. (1977). Exact | ||
stochastic simulation of coupled chemical reactions. The Journal of | ||
Physical Chemistry, 81(25), 2340–2361. | ||
https://doi.org/10.1021/j100540a008</unstructured_citation> | ||
</citation> | ||
<citation key="bernstein_simulating_2005"> | ||
<article_title>Simulating mesoscopic reaction-diffusion | ||
systems using the Gillespie algorithm</article_title> | ||
<author>Bernstein</author> | ||
<journal_title>Physical review. E, Statistical, nonlinear, | ||
and soft matter physics</journal_title> | ||
<volume>71</volume> | ||
<doi>10.1103/PhysRevE.71.041103</doi> | ||
<cYear>2005</cYear> | ||
<unstructured_citation>Bernstein, D. (2005). Simulating | ||
mesoscopic reaction-diffusion systems using the Gillespie algorithm. | ||
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, 71, | ||
041103. | ||
https://doi.org/10.1103/PhysRevE.71.041103</unstructured_citation> | ||
</citation> | ||
<citation key="gillespie_approximate_2001"> | ||
<article_title>Approximate Accelerated Stochastic Simulation | ||
of Chemically Reacting Systems</article_title> | ||
<author>Gillespie</author> | ||
<journal_title>Journal of Chemical Physics</journal_title> | ||
<volume>115</volume> | ||
<doi>10.1063/1.1378322</doi> | ||
<cYear>2001</cYear> | ||
<unstructured_citation>Gillespie, D. (2001). Approximate | ||
Accelerated Stochastic Simulation of Chemically Reacting Systems. | ||
Journal of Chemical Physics, 115, 1716–1733. | ||
https://doi.org/10.1063/1.1378322</unstructured_citation> | ||
</citation> | ||
<citation key="hoffmann2019readdy"> | ||
<article_title>ReaDDy 2: Fast and flexible software | ||
framework for interacting-particle reaction dynamics</article_title> | ||
<author>Hoffmann</author> | ||
<journal_title>PLoS computational biology</journal_title> | ||
<issue>2</issue> | ||
<volume>15</volume> | ||
<doi>10.1371/journal.pcbi.1006830</doi> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Hoffmann, M., Fröhner, C., & Noé, | ||
F. (2019). ReaDDy 2: Fast and flexible software framework for | ||
interacting-particle reaction dynamics. PLoS Computational Biology, | ||
15(2), e1006830. | ||
https://doi.org/10.1371/journal.pcbi.1006830</unstructured_citation> | ||
</citation> | ||
<citation key="10.1093/bioinformatics/bti431"> | ||
<article_title>Stochastic reaction-diffusion simulation with | ||
MesoRD</article_title> | ||
<author>Hattne</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>12</issue> | ||
<volume>21</volume> | ||
<doi>10.1093/bioinformatics/bti431</doi> | ||
<issn>1367-4803</issn> | ||
<cYear>2005</cYear> | ||
<unstructured_citation>Hattne, J., Fange, D., & Elf, J. | ||
(2005). Stochastic reaction-diffusion simulation with MesoRD. | ||
Bioinformatics, 21(12), 2923–2924. | ||
https://doi.org/10.1093/bioinformatics/bti431</unstructured_citation> | ||
</citation> | ||
<citation key="Elf2004"> | ||
<article_title>Spontaneous separation of bi-stable | ||
biochemical systems into spatial domains of opposite | ||
phases</article_title> | ||
<author>Elf</author> | ||
<journal_title>Syst Biol (Stevenage)</journal_title> | ||
<issue>2</issue> | ||
<volume>1</volume> | ||
<doi>10.1049/sb:20045021</doi> | ||
<unstructured_citation>Elf, J., & Ehrenberg, M. (2004 | ||
December). Spontaneous separation of bi-stable biochemical systems into | ||
spatial domains of opposite phases. Syst Biol (Stevenage), 1(2), | ||
230–236. https://doi.org/10.1049/sb:20045021</unstructured_citation> | ||
</citation> | ||
<citation key="10.1093/bioinformatics/btw469"> | ||
<article_title>BioNetGen 2.2: advances in rule-based | ||
modeling</article_title> | ||
<author>Harris</author> | ||
<journal_title>Bioinformatics</journal_title> | ||
<issue>21</issue> | ||
<volume>32</volume> | ||
<doi>10.1093/bioinformatics/btw469</doi> | ||
<issn>1367-4803</issn> | ||
<cYear>2016</cYear> | ||
<unstructured_citation>Harris, L. A., Hogg, J. S., Tapia, | ||
J.-J., Sekar, J. A. P., Gupta, S., Korsunsky, I., Arora, A., Barua, D., | ||
Sheehan, R. P., & Faeder, J. R. (2016). BioNetGen 2.2: advances in | ||
rule-based modeling. Bioinformatics, 32(21), 3366–3368. | ||
https://doi.org/10.1093/bioinformatics/btw469</unstructured_citation> | ||
</citation> | ||
<citation key="10.3389/neuro.11.015.2009"> | ||
<article_title>STEPS: Modeling and simulating complex | ||
reaction-diffusion systems with python</article_title> | ||
<author>Wils</author> | ||
<journal_title>Frontiers in Neuroinformatics</journal_title> | ||
<volume>3</volume> | ||
<doi>10.3389/neuro.11.015.2009</doi> | ||
<issn>1662-5196</issn> | ||
<cYear>2009</cYear> | ||
<unstructured_citation>Wils, S., & De Schutter, E. | ||
(2009). STEPS: Modeling and simulating complex reaction-diffusion | ||
systems with python. Frontiers in Neuroinformatics, 3. | ||
https://doi.org/10.3389/neuro.11.015.2009</unstructured_citation> | ||
</citation> | ||
<citation key="harris_numpy_2020"> | ||
<article_title>Array programming with NumPy</article_title> | ||
<author>Harris</author> | ||
<journal_title>Nature</journal_title> | ||
<issue>7825</issue> | ||
<volume>585</volume> | ||
<doi>10.1038/s41586-020-2649-2</doi> | ||
<issn>1476-4687</issn> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Harris, C. R., Millman, K. J., Walt, | ||
S. J. van der, Gommers, R., Virtanen, P., Cournapeau, D., Wieser, E., | ||
Taylor, J., Berg, S., Smith, N. J., Kern, R., Picus, M., Hoyer, S., | ||
Kerkwijk, M. H. van, Brett, M., Haldane, A., Río, J. F. del, Wiebe, M., | ||
Peterson, P., … Oliphant, T. E. (2020). Array programming with NumPy. | ||
Nature, 585(7825), 357–362. | ||
https://doi.org/10.1038/s41586-020-2649-2</unstructured_citation> | ||
</citation> | ||
<citation key="hunter_matplotlib_2007"> | ||
<article_title>Matplotlib: A 2D graphics | ||
environment</article_title> | ||
<author>Hunter</author> | ||
<journal_title>Computing in Science & | ||
Engineering</journal_title> | ||
<issue>3</issue> | ||
<volume>9</volume> | ||
<doi>10.1109/MCSE.2007.55</doi> | ||
<cYear>2007</cYear> | ||
<unstructured_citation>Hunter, J. D. (2007). Matplotlib: A | ||
2D graphics environment. Computing in Science & Engineering, 9(3), | ||
90–95. https://doi.org/10.1109/MCSE.2007.55</unstructured_citation> | ||
</citation> | ||
<citation key="Milo2015"> | ||
<volume_title>Cell biology by the numbers</volume_title> | ||
<author>Milo</author> | ||
<doi>10.1201/9780429258770</doi> | ||
<isbn>9780815345374</isbn> | ||
<cYear>2015</cYear> | ||
<unstructured_citation>Milo, R., & Phillips, R. (2015). | ||
Cell biology by the numbers (1st ed., p. 213). Garland Science, Taylor | ||
& Francis Group. | ||
https://doi.org/10.1201/9780429258770</unstructured_citation> | ||
</citation> | ||
<citation key="Fujiwara2016"> | ||
<article_title>Confined diffusion of transmembrane proteins | ||
and lipids induced by the same actin meshwork lining the plasma | ||
membrane</article_title> | ||
<author>Fujiwara</author> | ||
<journal_title>Molecular Biology of the Cell</journal_title> | ||
<issue>7</issue> | ||
<volume>27</volume> | ||
<doi>10.1091/mbc.E15-04-0186</doi> | ||
<cYear>2016</cYear> | ||
<unstructured_citation>Fujiwara, T. K., Iwasawa, K., Kalay, | ||
Z., Tsunoyama, T. A., Watanabe, Y., Umemura, Y. M., Murakoshi, H., | ||
Suzuki, K. G. N., Nemoto, Y. L., Morone, N., & Kusumi, A. (2016). | ||
Confined diffusion of transmembrane proteins and lipids induced by the | ||
same actin meshwork lining the plasma membrane. Molecular Biology of the | ||
Cell, 27(7), 1101–1119. | ||
https://doi.org/10.1091/mbc.E15-04-0186</unstructured_citation> | ||
</citation> | ||
<citation key="Strengths_doc"> | ||
<article_title>Building and simulating a reaction-diffusion | ||
system. Documentation for strengths</article_title> | ||
<author>Fillion</author> | ||
<cYear>2024</cYear> | ||
<unstructured_citation>Fillion, T., & Piazza, F. (2024). | ||
Building and simulating a reaction-diffusion system. Documentation for | ||
strengths. | ||
https://strengths.readthedocs.io/en/latest/building_and_simulating_rds.html</unstructured_citation> | ||
</citation> | ||
<citation key="McGough2004"> | ||
<article_title>Pattern formation in the Gray–Scott | ||
model</article_title> | ||
<author>McGough</author> | ||
<journal_title>Nonlinear Analysis: Real World | ||
Applications</journal_title> | ||
<issue>1</issue> | ||
<volume>5</volume> | ||
<doi>10.1016/S1468-1218(03)00020-8</doi> | ||
<issn>1468-1218</issn> | ||
<cYear>2004</cYear> | ||
<unstructured_citation>McGough, J. S., & Riley, K. | ||
(2004). Pattern formation in the Gray–Scott model. Nonlinear Analysis: | ||
Real World Applications, 5(1), 105–121. | ||
https://doi.org/10.1016/S1468-1218(03)00020-8</unstructured_citation> | ||
</citation> | ||
<citation key="Ruijgrok1997"> | ||
<article_title>A reaction-diffusion equation for a cyclic | ||
system with three components</article_title> | ||
<author>Ruijgrok</author> | ||
<journal_title>Journal of Statistical | ||
Physics</journal_title> | ||
<volume>87</volume> | ||
<doi>10.1007/BF02181277</doi> | ||
<cYear>1997</cYear> | ||
<unstructured_citation>Ruijgrok, T., & Ruijgrok, M. | ||
(1997). A reaction-diffusion equation for a cyclic system with three | ||
components. Journal of Statistical Physics, 87, 1145–1164. | ||
https://doi.org/10.1007/BF02181277</unstructured_citation> | ||
</citation> | ||
<citation key="refpytest"> | ||
<article_title>pytest 8.2.1</article_title> | ||
<author>Krekel</author> | ||
<cYear>2004</cYear> | ||
<unstructured_citation>Krekel, H., Oliveira, B., | ||
Pfannschmidt, R., Bruynooghe, F., Laugher, B., & Bruhin, F. (2004). | ||
pytest 8.2.1. | ||
https://github.com/pytest-dev/pytest</unstructured_citation> | ||
</citation> | ||
</citation_list> | ||
</journal_article> | ||
</journal> | ||
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