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<div id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 2: Select Path with Windows Explorer</figcaption> | ||
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<div id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 3: Change directory of the command prompt</figcaption> | ||
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<div id="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" /></div> | <div id="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" /></div> | ||
− | + | <figcaption>Figure 4: Command Prompt when running example via perl</figcaption> | |
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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 id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 6: Command Prompt when running example via windows executor</figcaption> | ||
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</h6> | </h6> | ||
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<div id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 6: Home Tab of Matlab </figcaption> | ||
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<div id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 7: Matlab Set Path icon</figcaption> | ||
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 id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 8: Select the folder NFtools in Matlab</figcaption> | ||
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<div id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 9: Editor Tab Matlab</figcaption> | ||
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<div id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 10: Matlab Change Directory icon</figcaption> | ||
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<div id="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" /></div> | <div id="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" /></div> | ||
+ | <figcaption>Figure 11: Matlab Command Window</figcaption> | ||
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− | <div id="Figure_12"><img src="https://static.igem.org/mediawiki/2017/c/c3/T--TU-Eindhoven--Software_tool_graph_a_300.png" width=" | + | <div id="Figure_12"><img src="https://static.igem.org/mediawiki/2017/c/c3/T--TU-Eindhoven--Software_tool_graph_a_300.png" width="490" alt="Figure_2_of_model_part" /></div> |
− | <div id="Figure_13"><img src="https://static.igem.org/mediawiki/2017/1/16/T--TU-Eindhoven--Software_figureb_w500.png" width=" | + | <figcaption>Figure 12: Figure a, showing the amount of molecules over time</figcaption> |
+ | <div id="Figure_13"><img src="https://static.igem.org/mediawiki/2017/1/16/T--TU-Eindhoven--Software_figureb_w500.png" width="490" height="375" alt="Figure_2_of_model_part" /></div> | ||
+ | <figcaption>Figure 13: Figure b, showing the total amount of complexes over time</figcaption> | ||
<div id="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" /></div> | <div id="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" /></div> | ||
Revision as of 17:28, 30 October 2017