The plasmid generated by the program is based on the [http://partsregistry.org/Part:pSB1A3 pSB1A3 backbone] which is a frequently-used plasmid carrying an ampicillin resistance. The design used for the logic gates is based on the His-Terminator design (see project for details). If required for output proteins the ribosome binding site [http://partsregistry.org/Part:BBa_B0034 B0034] was used. For the constitutive promoter, positioned upstream of every logic gate, the software uses the [http://partsregistry.org/Part:BBa_J23100 J23100] promoter. Details about input and output Biobricks are supplied within the program. For all input BioBricks, the program only incorporates the target DNA sequence of the corresponding BioBrick. If a separate protein is required to bind the DNA, please note that this protein will not be included on the plasmid.

A logic network can be designed by adding gates (via double clicking) and interconnecting them (via selecting two gates and pressing the 'C' key).

There are five different types of gates: inputs, outputs, AND-gates, OR-gates and NOT-gates. The type of a gate can be changed by clicking on the combo box on the gate and selecting a type. Gates can be interconnected by selecting (via clicking inside the area of a gate) two gates and then pressing the C key (for connect). A complete logic network has to have at least one input and at least one output. Different gates may require different numbers of ingoing and outgoing connections (e.g. a NOT-gate requires one ingoing connection and allows for an arbitrary number of outgoing connections, whereas the AND-gate requires two ingoing connections and allows for a arbitrary number of outgoing connections; an input may not have an incoming connection, an output no outgoing connection). In addition the logic network may not include loops.

The user has to assign DNA sequences (promoter sequences or either custom RNA sequences or sequences coding for proteins) to all input and output gates by clicking on the "Set input" button of the gates.

Invalid inputs (e.g. a letter different from G, C, T, A or N in a nucleotide sequence; loop(s) in the logic network; no sequences assigned to input(s)/output(s); input or output sequences that are too similar) are reported back to the users as error messages providing a description of the errors and advices how to correct the errors. The Check and Turn-to-DNA modules can only be entered when the network contains no errors.

The logic network designed in step 1 can now be verified.

Logical values are represented by colors (green = true, red = false). Thus a green box represents a gates (e.g. an AND-gate) with the logical value true, a red box a gates with the logical value false. The flow of logical value can be followed by following the colored edges between the gates.

The logical value(s) of the input(s) can be manipulated by clicking on their checkbox(es).

A set of genetic gates (categorized as input, logic gates and output) representing the logical network designed in step 1 is calculated and displayed.

All elements consist of a promoter, a ribosome binding site, up to two toggle switches, one output transmitter sequences and at least one terminator.

This information may at a later point, when the functionality of our toggle switches has been demonstrated in the lab and not only in silicio, be used for synthesizing the genetic networks.

The following "Read more" section will provide step-by-step instructions for creating a simple network, connecting two Biobricks with a NOT gate.

Step 01: After starting the program this screen is displayed. It has of three views: Construct, Verify and Synthesize. The later two can only be entered if a valid logic network has been constructed.

Step 02: Add a new gate via double clicking.

Step 03: Add two more gates in the same way.

Step 04: You can change the type of the logic gates via the combo box

Step 05: Change the type to: Input, Not, Output.

Step 06: Clicking inside the area of a gate selects it (indicated by the blue color). You can select as many logical gates as you like. To deselect, click on the empty space between the gates. Once a gate is selected you can delete it by pressing the DEL or BACKSPACE key.

Step 07: To connect two gates select both. Note that the connections has a direction (which will be indicated by an arrow), thus you have to select the gate in the correct order: first, select the box from which the connection starts and then select the box where the connection ends (The arrow points from the box that generates an output transmitter molecule, to the target box that will be activated by this output transmitter). You can only connect gates pairwise.

Step 08: Two gates have been connected.

Step 09: Connected the whole network.

Step 10: Press the "Set input ..." button on the input to select a promoter that controls the input.

Step 11: Choose one of the exemplary chosen BioBricks and press set.

Step 12: Press the "Set output ..." button on the output to select an output.

Step 13: You can chose a BioBrick or enter a custom made sequence (DNA with or without RBS, RNA).

Step 14: The logic network has been constructed. Press on the Button "2. Verify your network" to leave the construction view. If you have made mistakes during the construction process, an error message will be displayed.

Step 15: Check your network.

Step 16: By selecting or deselecting the checkbox on the inputs one can study the flow of logical value through the network.

Step 17: Press "Synthesize" and the logic network gets turned into DNA. The resulting DNA can get represented in four different views depending on the level of detail you wish to see.