Output

Writing simulation output to a file

It is possible to write the output of a NetBuilder simulation to a tab terminated text file, which can then be imported other programs, such as Excel.

To write any data at all, firstly you need to choose the symbols whose value you want to record. This is done by selecting them, and then pressing the Monitor button on the Simulation toolbar. The output port (the main one, if there are more then one) of a monitored symbol is red and permanently visible, as in the picture below. You can switch the monitor status off again by selecting the monitored symbol, and pressing the Monitor button again.

To record a simulation press the Record button, and enter a file name for the output in the file dialog box that pops up. The record button will stay pressed, to indicate that NetBuilder is in recording mode. When you press Go, NetBuilder will store the values of the monitored symbols for each evaluation round. You may stop the simulation, set or reset values, and continue. If you reset the evaluation round counter, new data with the same evaluation round number will replace the old, if you don't all data will be stored. When you press Record again, the data will be written to the file whose name you specified in the previous step.

The data in the file can be organised in one of three different ways. Choose the menu option Settings : Output file organisation to specify the format.

In the examples below, TF3, the gene, and the receptor were monitored, and 9 evaluation rounds were recorded (in simulation shown here, all delays were 0). The three different output formats are shown.

Menu option Settings : Output file organisation : By cell, Rows: simulation round, Columns: component (default):

Cell	Round	TF3	Receptor1	Gene3

A	0	0	0	0
A	1	0	0	0
A	2	0	0	0.5
A	3	0	0	0.5
A	4	0	0	0.5
A	5	0	0	0.5
A	6	0	0	0.5
A	7	0.01	0.18	0.5
A	8	0.17	0.36	0.5
A	9	0.17	0.36	0.51

B1	0	0	0	0
B1	1	0	0	0
B1	2	0.63	0.5	0
B1	3	0.63	0.5	0
B1	4	0.63	0.5	0.38
B1	5	0.63	0.5	0.38
B1	6	0.63	0.5	0.38
B1	7	0.63	0.5	0.38
B1	8	0.63	0.5	0.38
B1	9	0.65	0.51	0.38

B2	0	0	0	0
B2	1	0	0	0
B2	2	0	0	0
B2	3	0	0	0
B2	4	0	0	0
B2	5	0.22	0.38	0
B2	6	0.22	0.38	0
B2	7	0.22	0.38	0.18
B2	8	0.22	0.38	0.18
B2	9	0.22	0.38	0.18

B3	0	0	0	0
B3	1	0	0	0
B3	2	0	0	0
B3	3	0	0	0
B3	4	0	0	0
B3	5	0.22	0.38	0
B3	6	0.22	0.38	0
B3	7	0.22	0.38	0.18
B3	8	1.01	0.56	0.18
B3	9	1.01	0.56	0.18

Cell	Component	0	1	2	3	4	5	6	7	8	9

A	TF3	0	0	0	0	0	0	0	0.01	0.17	0.17
A	Receptor1	0	0	0	0	0	0	0	0.18	0.36	0.36
A	Gene3	0	0	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.51

B1	TF3	0	0	0.63	0.63	0.63	0.63	0.63	0.63	0.63	0.65
B1	Receptor1	0	0	0.5	0.5	0.5	0.5	0.5	0.5	0.5	0.51
B1	Gene3	0	0	0	0	0.38	0.38	0.38	0.38	0.38	0.38

B2	TF3	0	0	0	0	0	0.22	0.22	0.22	0.22	0.22
B2	Receptor1	0	0	0	0	0	0.38	0.38	0.38	0.38	0.38
B2	Gene3	0	0	0	0	0	0	0	0.18	0.18	0.18

B3	TF3	0	0	0	0	0	0.22	0.22	0.22	1.01	1.01
B3	Receptor1	0	0	0	0	0	0.38	0.38	0.38	0.56	0.56
B3	Gene3	0	0	0	0	0	0	0	0.18	0.18	0.18

Round	Component	A	B1	B2	B3

0	TF3	0	0	0	0
0	Receptor1	0	0	0	0
0	Gene3	0	0	0	0

1	TF3	0	0	0	0
1	Receptor1	0	0	0	0
1	Gene3	0	0	0	0

2	TF3	0	0.63	0	0
2	Receptor1	0	0.5	0	0
2	Gene3	0.5	0	0	0

3	TF3	0	0.63	0	0
3	Receptor1	0	0.5	0	0
3	Gene3	0.5	0	0	0

4	TF3	0	0.63	0	0
4	Receptor1	0	0.5	0	0
4	Gene3	0.5	0.38	0	0

5	TF3	0	0.63	0.22	0.22
5	Receptor1	0	0.5	0.38	0.38
5	Gene3	0.5	0.38	0	0

6	TF3	0	0.63	0.22	0.22
6	Receptor1	0	0.5	0.38	0.38
6	Gene3	0.5	0.38	0	0

7	TF3	0.01	0.63	0.22	0.22
7	Receptor1	0.18	0.5	0.38	0.38
7	Gene3	0.5	0.38	0.18	0.18

8	TF3	0.17	0.63	0.22	1.01
8	Receptor1	0.36	0.5	0.38	0.56
8	Gene3	0.5	0.38	0.18	0.18

9	TF3	0.17	0.65	0.22	1.01
9	Receptor1	0.36	0.51	0.38	0.56
9	Gene3	0.51	0.38	0.18	0.18