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− | < | + | <h1>NFsim manual for dummies</h1> |
<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> | ||
+ | <br/> | ||
+ | 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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− | <div | + | <div class="Figure_1"><img src="https://static.igem.org/mediawiki/2017/3/34/T--TU-Eindhoven--Software_command_prompt.png" width="832" height="503" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 1: Command Prompt</figcaption></div> | ||
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− | <div | + | <div class="Figure_2"><img src="https://static.igem.org/mediawiki/2017/8/8a/T--TU-Eindhoven--Software_select_path.png" width="593" height="87" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 2: Select Path with Windows Explorer</figcaption></div> | ||
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− | <div | + | <div class="Figure_3"><img src="https://static.igem.org/mediawiki/2017/2/2d/T--TU-Eindhoven--Software_change_directory.png" width="382" height="187" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 3: Change directory of the command prompt</figcaption></div> | ||
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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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− | <div | + | <div class="Figure_4"><img src="https://static.igem.org/mediawiki/2017/a/a6/T--TU-Eindhoven--Software_running_example_via_perl.png" width="804" height="647" alt="Figure_2_of_model_part" /> |
− | + | <figcaption>Figure 4: Command Prompt when running example via perl</figcaption></div> | |
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After generating an xml-file, you can run the model in another way, namely via a windows executable. The advantage is that you then can give additional commands, like the command "dump". NFsim calls this a flag and they made a whole table that describes the command line arguments and their function. The table can be found on pages 38-40 of the manual. | After generating an xml-file, you can run the model in another way, namely via a windows executable. The advantage is that you then can give additional commands, like the command "dump". NFsim calls this a flag and they made a whole table that describes the command line arguments and their function. The table can be found on pages 38-40 of the manual. | ||
For the dump flag, we first need to make an empty folder. This can be done easily with the command "mkdir" followed by the name of the folder you want to create, for example "dumpDir_example_dump". Furthermore, with -Steps you can redefine the number of steps, with -sim you can define the end time of the simulation and with -o, you can specify the output file of your simulation. The command line can for example look like below and in Figure 5: | For the dump flag, we first need to make an empty folder. This can be done easily with the command "mkdir" followed by the name of the folder you want to create, for example "dumpDir_example_dump". Furthermore, with -Steps you can redefine the number of steps, with -sim you can define the end time of the simulation and with -o, you can specify the output file of your simulation. The command line can for example look like below and in Figure 5: | ||
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− | <div | + | <div class="Figure_5"><img src="https://static.igem.org/mediawiki/2017/5/50/T--TU-Eindhoven--Software_running_dump_via_windows.png" width="802" height="615" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 5: Command Prompt when running example via windows executor</figcaption></div> | ||
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</h6> | </h6> | ||
<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. |
− | <br/> | + | <br/><br/> |
− | + | <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. | ||
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− | <div | + | |
+ | <div class="Figure_6"><img src="https://static.igem.org/mediawiki/2017/b/bd/T--TU-Eindhoven--Software_matlab_set_path.png" width="1000" alt="Figure_2_of_model_part" /> | ||
+ | <figcaption>Figure 6: Home Tab of Matlab </figcaption></div> | ||
+ | <br/> | ||
+ | <div class="Figure_7"><img src="https://static.igem.org/mediawiki/2017/e/e9/T--TU-Eindhoven--Software_matlab_set_path_icon.png" width="95" height="34" alt="Figure_2_of_model_part" /> | ||
+ | <figcaption>Figure 7: Matlab Set Path icon</figcaption></div> | ||
+ | <br/> | ||
The window "Set Path" then opens and by clicking on "Add with Subfolders…" you can select the NFtools folder. This is done by first going to the driver (D-drive), followed by the NFsim folder, then NFsim_v1.11 and there you will see the folder NFtools, as in Figure 8. Select the NFtools folder, press Save and then Matlab will add the folders and their subfolders. | The window "Set Path" then opens and by clicking on "Add with Subfolders…" you can select the NFtools folder. This is done by first going to the driver (D-drive), followed by the NFsim folder, then NFsim_v1.11 and there you will see the folder NFtools, as in Figure 8. Select the NFtools folder, press Save and then Matlab will add the folders and their subfolders. | ||
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− | <div | + | <div class="Figure_8"><img src="https://static.igem.org/mediawiki/2017/b/bb/T--TU-Eindhoven--Software_select_folder_matlab.png" width="740" height="222" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 8: Select the folder NFtools in Matlab</figcaption></div> | ||
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− | <div | + | <div class="Figure_9"><img src="https://static.igem.org/mediawiki/2017/f/fe/T--TU-Eindhoven--Software_matlab_directory.png" width="1000" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 9: Editor Tab Matlab</figcaption></div> | ||
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− | <div | + | |
+ | <div class="Figure_10"><img src="https://static.igem.org/mediawiki/2017/0/02/T--TU-Eindhoven--Software_change_directory_icon.png" width="48" height="29" alt="Figure_2_of_model_part" /> | ||
+ | <figcaption>Figure 10: Matlab Change Directory icon</figcaption></div> | ||
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− | <div | + | <div class="Figure_11"><img src="https://static.igem.org/mediawiki/2017/2/2b/T--TU-Eindhoven--Software_command_window_matlab.png" width="1000" height="270" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 11: Matlab Command Window</figcaption></div> | ||
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− | <div | + | <div class="Figure_12"><img src="https://static.igem.org/mediawiki/2017/c/c3/T--TU-Eindhoven--Software_tool_graph_a_300.png" width="500" height="375" alt="Figure_2_of_model_part" /> |
− | <div | + | <figcaption>Figure 12: Figure a, showing the amount of molecules over time</figcaption></div> |
− | <div | + | <div class="Figure_13"><img src="https://static.igem.org/mediawiki/2017/1/16/T--TU-Eindhoven--Software_figureb_w500.png" width="500" height="375" alt="Figure_2_of_model_part" /> |
+ | <figcaption>Figure 13: Figure b, showing the total amount of complexes over time</figcaption></div> | ||
+ | <div class="Figure_14"><img src="https://static.igem.org/mediawiki/2017/2/21/T--TU-Eindhoven--Software_figurec_w500.png" width="500" height="375" alt="Figure_2_of_model_part" /> | ||
+ | <figcaption>Figure 14: Figure c, showing the average complex size time</figcaption></div> | ||
+ | <br/> | ||
If you look at the legends, you see that we used different methods to generate the graphs in the figures. Which method is most useful depends on the system that is implemented in the model. Therefore, it is useful to look at the data in the workspace (Figure 15) of Matlab to see which method works the best for generating your output. In our example, the results of method 1 and method 2 are the same for the total amount of complexes and for the total amount of molecules, so therefore we choose to only depict the results of method 1 and 3 in our graphs. | If you look at the legends, you see that we used different methods to generate the graphs in the figures. Which method is most useful depends on the system that is implemented in the model. Therefore, it is useful to look at the data in the workspace (Figure 15) of Matlab to see which method works the best for generating your output. In our example, the results of method 1 and method 2 are the same for the total amount of complexes and for the total amount of molecules, so therefore we choose to only depict the results of method 1 and 3 in our graphs. | ||
− | <br/> | + | <br/><br/> |
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+ | <div class="Figure_15"><img src="https://static.igem.org/mediawiki/2017/2/2b/T--TU-Eindhoven--Software_workspace_matlab.png" width="393" height="534" alt="Figure_2_of_model_part" /> | ||
+ | <figcaption>Figure 15: Matlab Workspace Window</figcaption></div> | ||
Latest revision as of 09:31, 6 December 2017