Toy example
We provide a simple example that we use to test the basic functions of the FALCON pipeline. It only contains six nodes: four inputs (A, B, C and N) and two outputs (M and T). The relationships between the nodes are shown in the following diagram:
Despite its simplicity, this small network presents the main characteristics of the types of interaction network FALCON is able to contextualize: two activating interactions with additive effect with an inhibitive interaction and a logical (AND) operator/gate.
The synthetic data is presented in the following table. It has been generated by a model in which the values for k1 and k2 are 0.6 and 0.4, respectively, and the value for ki is 0.5. In other words, a full activation of A can only produce a 60% activation of M, and a full activation of B can only produce a 40% activation of M. The effects of A and B are additive, giving a full activation once both A and B are fully activated. C has an inhibitory action on M, and a full activation of C decreases the activation of M by 50%. In contrast, the effects of M and N on T are not additive but subjected to the AND logical gate where both species have to be present to activate T and the relationship from each of M and N to T is non-linear.
| Condition | A | B | C | N | M | T |
|---|---|---|---|---|---|---|
| 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| 2 | 1 | 0 | 0 | 0 | 0.6 | 0 |
| 3 | 1 | 1 | 0 | 0 | 1 | 0 |
| 4 | 1 | 1 | 1 | 0 | 0.5 | 0 |
| 5 | 1 | 1 | 1 | 1 | 0.5 | 0.5 |
Users are encouraged to open the text file corresponding to this example (Falcon/Examples/example.txt and Falcon/Examples/example_meas.txt) and familiarise with the setting-up of the input files for analysis.
| Model Summary (Number of …) | Toy example |
|---|---|
| Nodes | 6 |
| (optimized) Parameters / Interactions | 3 |
| Logical gates | 1 |
| Inputs | 4 |
| Outputs | 2 |
| Experimental conditions | 5 |
| Optimisation time | 0.12 second |
The input files for this study are provided as Text (.txt) files. Fitting this network should be very fast on most computers (<1 second). The theoretical optimal fitting cost is 0.