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<li>The inducer, without any binding sites or states</li> | <li>The inducer, without any binding sites or states</li> | ||
</ul> | </ul> | ||
− | <div id="Figure_1"><img src="https://static.igem.org/mediawiki/2017/6/67/T--TU-Eindhoven--iGEM_general.png" width="60" height="60" alt="Figure_1_of_model_part" /></div> | + | <div id="Figure_1"><img src="https://static.igem.org/mediawiki/2017/6/67/T--TU-Eindhoven--iGEM_general.png" width="60" height="60" alt="Figure_1_of_model_part" /></div><br/> |
The next step is the definition of the <i>species</i>, which means that you can define the initial amount of the already defined molecule types. It is not sufficient to only mention the molecule type, as you also need to define the state of the pockets. We choose to start with only empty pockets of the Scaffold Construct.<br/> | The next step is the definition of the <i>species</i>, which means that you can define the initial amount of the already defined molecule types. It is not sufficient to only mention the molecule type, as you also need to define the state of the pockets. We choose to start with only empty pockets of the Scaffold Construct.<br/> | ||
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<li>The binding of a Binding Partner with a pocket of the Scaffold Construct, of which the pocket already needs to have an inducer bound to it. (Three different reaction rules)</li> | <li>The binding of a Binding Partner with a pocket of the Scaffold Construct, of which the pocket already needs to have an inducer bound to it. (Three different reaction rules)</li> | ||
<li>And for each of the above also the reverse reaction, as the system is dynamic. (4 + 3 + 3 different reaction rules)</li> | <li>And for each of the above also the reverse reaction, as the system is dynamic. (4 + 3 + 3 different reaction rules)</li> | ||
− | </ul> | + | </ul><br/> |
The BNGL-file ends with defining the simulation (with its end-time and number of steps) that has to be executed. Additionally, by adding one extra line, you can let the program generate a xml-file, which is useful for running the simulation in another way. This gives the option to generate even more output-files. The last two lines of the BNGL-file can look like: | The BNGL-file ends with defining the simulation (with its end-time and number of steps) that has to be executed. Additionally, by adding one extra line, you can let the program generate a xml-file, which is useful for running the simulation in another way. This gives the option to generate even more output-files. The last two lines of the BNGL-file can look like: | ||
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<li>simulate_nf({suffix=>nf,t_end=>…,n_steps=>…,get_final_state=>1});</li> | <li>simulate_nf({suffix=>nf,t_end=>…,n_steps=>…,get_final_state=>1});</li> | ||
<li>writeXML();</li> | <li>writeXML();</li> | ||
− | </ul> | + | </ul><br/> |
+ | |||
The output generated of the final state is a .species-file and shows all the molecules in their final state. This can be, in the case of a very large network, a very long name for one molecule, as there are many bonds that connect the different molecules with each other, leading to one large molecule definition.<br/> | The output generated of the final state is a .species-file and shows all the molecules in their final state. This can be, in the case of a very large network, a very long name for one molecule, as there are many bonds that connect the different molecules with each other, leading to one large molecule definition.<br/> | ||
Other output files that are generated are an additional xml-file and one file containing the data (.gdat) of the observables.<br/> | Other output files that are generated are an additional xml-file and one file containing the data (.gdat) of the observables.<br/> |
Revision as of 17:51, 20 October 2017