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<h6>NFsim is useful if you want to simulate a system with many interacting molecules in different states and/or molecules with many interacting sites where a bond can be formed. For an in depth explanation about how NFsim works, we refer to the first chapter of the NFsim manual provided by Yale University, which can be found here: | <h6>NFsim is useful if you want to simulate a system with many interacting molecules in different states and/or molecules with many interacting sites where a bond can be formed. For an in depth explanation about how NFsim works, we refer to the first chapter of the NFsim manual provided by Yale University, which can be found here: | ||
<a href="http://emonet.biology.yale.edu/sites/default/files/files/NFsim_manual_v1_11.pdf" target="_blank">NFsim_manual_v1_11.pdf</a> | <a href="http://emonet.biology.yale.edu/sites/default/files/files/NFsim_manual_v1_11.pdf" target="_blank">NFsim_manual_v1_11.pdf</a> | ||
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+ | If you prefer to read a pdf booklet, you can donwload it <a href="https://static.igem.org/mediawiki/2017/b/ba/T--TU-Eindhoven--Software_pdf_book.pdf" target="_blank">here.</a> | ||
</h6> | </h6> | ||
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− | Link to download the bngl file | + | <a href="https://static.igem.org/mediawiki/2017/4/4f/T--TU-Eindhoven--Software_system_example.txt" target="_blank">Link to download the bngl file.</a><br/> |
− | (You need to save this file in the "models" folder of "NFsim_v1.11") | + | (You need to save this file in the "models" folder of "NFsim_v1.11" and change .txt to .bngl) |
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<h2>Codes for visualization</h2> | <h2>Codes for visualization</h2> | ||
− | <h6>It is easy to visualize the results generated with Matlab. NFsim also provides some tools that you can use in the folder NFtools, but we will explain how you need to prepare Matlab and how you can use them. We ourselves already had Matlab 2016b installed, so the visualization may differ a bit, depending on your matlab version. There are also some functions that have changed over the time that Matlab exists, so it is possible that you will get a warning if you use another version. In most cases it | + | <h6>It is easy to visualize the results generated with Matlab. NFsim also provides some tools that you can use in the folder NFtools, but we will explain how you need to prepare Matlab and how you can use them. We ourselves already had Matlab 2016b installed, so the visualization may differ a bit, depending on your matlab version. There are also some functions that have changed over the time that Matlab exists, so it is possible that you will get a warning if you use another version. In most cases it is not a problem. |
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+ | <a href="https://static.igem.org/mediawiki/2017/f/f3/T--TU-Eindhoven--Software_system_example_matlab.txt" target="_blank">Here you can find the matlab code we used for the visualization.</a> (Don't forget to change .txt to .m) | ||
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After opening Matlab you will end up in the home tab, shown in Figure 6. In this tab you can find an icon with the description: "Set Path", like in Figure 7. | After opening Matlab you will end up in the home tab, shown in Figure 6. In this tab you can find an icon with the description: "Set Path", like in Figure 7. |
Latest revision as of 09:31, 6 December 2017