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− | <div id="Figure_1"><img src="https://static.igem.org/mediawiki/2017/ | + | <div id="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" /></div> |
The next step is to check whether NFsim is also installed correctly. This is done by first changing the directory of the command prompt to the directory were NFsim is installed / unzipped. We already mentioned that we installed it on our D-drive, so the first step is to change the drive. The easiest way to do this is by typing: "D:", which lets you go the D-drive after you use the "enter" key on your keyboard. Next, change the directory to the NFsim directory. This can be done with: "cd D:\NFsim\NFsim_v1.11" where cd stands for Change Directory and after a space you type the folders where NFsim is installed. This path can be found easily by using the windows explorer, going to the correct folder and then clicking on it. The path then changes from the one in Figure 2 to a selectable name, like "D:\NFsim\NFsim_v1.11", which can be copied and then placed in the command prompt. The shortcut "ctrl + v" does not work in the command prompt, so you will need the right mouse button and paste the text. | The next step is to check whether NFsim is also installed correctly. This is done by first changing the directory of the command prompt to the directory were NFsim is installed / unzipped. We already mentioned that we installed it on our D-drive, so the first step is to change the drive. The easiest way to do this is by typing: "D:", which lets you go the D-drive after you use the "enter" key on your keyboard. Next, change the directory to the NFsim directory. This can be done with: "cd D:\NFsim\NFsim_v1.11" where cd stands for Change Directory and after a space you type the folders where NFsim is installed. This path can be found easily by using the windows explorer, going to the correct folder and then clicking on it. The path then changes from the one in Figure 2 to a selectable name, like "D:\NFsim\NFsim_v1.11", which can be copied and then placed in the command prompt. The shortcut "ctrl + v" does not work in the command prompt, so you will need the right mouse button and paste the text. | ||
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− | <div id="Figure_2"><img src="https://static.igem.org/mediawiki/2017/ | + | <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> |
The next step is to verify that the installation of NFsim was successful, which can be done by typing: "perl BNG2.pl -v". If the installation is correct, the command prompt will look like the command prompt in Figure 3, after pressing the "enter" key. | The next step is to verify that the installation of NFsim was successful, which can be done by typing: "perl BNG2.pl -v". If the installation is correct, the command prompt will look like the command prompt in Figure 3, after pressing the "enter" key. | ||
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− | <div id="Figure_3"><img src="https://static.igem.org/mediawiki/2017/ | + | <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> |
Together with the installation of NFsim, you installed also some example models, which can be found in the folder "models". The simple_system.bngl file is very nice as a start to see how output can be generated. We recommend that you open the bngl files with Notepad ++, as this is a very easy way to not only look at the files, but also to edit them if desired. | Together with the installation of NFsim, you installed also some example models, which can be found in the folder "models". The simple_system.bngl file is very nice as a start to see how output can be generated. We recommend that you open the bngl files with Notepad ++, as this is a very easy way to not only look at the files, but also to edit them if desired. | ||
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The xml-file is created by typing the following line in the command prompt, as shown in Figure 4: | The xml-file is created by typing the following line in the command prompt, as shown in Figure 4: | ||
"perl BNG2.pl -xml models/system_example.bngl" | "perl BNG2.pl -xml models/system_example.bngl" | ||
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− | <div id="Figure_4"><img src="https://static.igem.org/mediawiki/2017/ | + | <div id="Figure_4"><img src="https://static.igem.org/mediawiki/2017/5/50/T--TU-Eindhoven--Software_running_dump_via_windows.png" width="804" height="647" alt="Figure_2_of_model_part" /></div> |
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. |
Revision as of 13:04, 30 October 2017