Parts customization
This page explains how to customize the genetic parts in your database.
The following five buttons let you manage the parts in your database:
- : Add a new, unregistered part
- : Delete a part from your collection
- : Edit the parameters of a registered part
- : Import a complete collection of parts
- : Export your current collection of parts
Add parts¶
Click the button to open a form for entering details about a new part. After filling out the form, click "Save" to add the part to your database.
Tip
By clicking "Fill form with existing part", you can select an existing part and automatically load its information into the form. This is useful when creating a new part that closely resembles an existing one.
Common parameters¶
The following parameters apply to all part types:
| Parameter | Description |
|---|---|
| Name | The part’s name. It must be unique within the database. |
| Description | A brief explanation of the part. |
| Category | The part's category (Promoter, Protein, Terminator). |
| DNA sequence | The DNA sequence for the part, containing only the letters A, T, G, and C. |
Promoter-specific parameters¶
Promoters have additional parameters:
| Parameter | Description |
|---|---|
| Ydef | The expression strength of the gate in the absence of transcriptional regulators (in [RPU]). For repressive promoters, this value is the same as Ymax. For activating promoters, it is the same as Ymin. |
Interaction parameters¶
If a promoter interacts with a specific protein, configure the interaction in the "Controlled By" section:
| Parameter | Description |
|---|---|
| name | The name of the protein (must already exist in the database). |
| type | The type of interaction (Repression or Activation). |
| Ymax | The maximum expression rate of the gate (in [RPU]). |
| Ymin | The minimum expression rate of the gate (in [RPU]), indicating leakage expression. |
| K | The Michaelis–Menten constant, i.e., the protein expression level at which the gate’s expression is half of its maximum (in [RPU]). |
| n | The Hill coefficient of the gate. |
Protein-specific parameters¶
Proteins have additional parameters:
| Parameter | Description |
|---|---|
| Dp | The protein degradation rate (in [RPU]). The default values are theoretical, calculated from the steady-state condition when the gate’s expression is at its maximum. Whenever possible, use experimentally measured values. |
| TIRb | The Translation Initiation Rate measured in baseline experiments to determine parameter values. This represents RBS strength. For more details on the translation initiation rate, see H. M. Salis, C. A. Voigt, Nat. Biotech. 2009 |
Note
If any parameters are invalid, an error message will appear. Check the message and correct your input accordingly.
Delete parts¶
Click the button to see a list of registered parts. Select the part you want to remove, then confirm the deletion.
Edit parts¶
Click the button to see a list of registered parts. Select the part you want to edit, then modify its settings in the same type of form used for adding parts.
Import parts collection¶
Click the button to import a collection of parts in bulk. The file you import must follow the same format as the export file described below.
Warning
This action overwrites your existing parts database.
Export parts collection¶
Click the button to export your current parts database as a JSON file.
Note
The parts database is reset each time the application is restarted. To avoid losing your data, export it beforehand. You can then restore it later by importing the saved JSON file.