Motivation

Link to project (and back).
Theoretical possibilities provided by our system - borders of lab work - future applications

Applet

applet

Tutorial

The applet consists of three parts: Design, Check and Turn-to-DNA. The first allows the user to enter inputs, whereas the second and third supply the user with information about his network. Below the different parts are described in detail.

1. Design a logic network

2. Check the logic network

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 devices (e.g. an AND-gate) with the logical value true, a red box a devices with the logical value false. The flow of logical value can be followed by following the colored edges between the boxes.

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

3. Turn the logic network into DNA

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

All elements (besides custom RNA input sequences) consist of a Escherichia coli promoter and up to two switches and two output sequences.

Disclaimer

Software

THIS SOFTWARE IS PROVIDED BY THE CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

(Inspired by: [http://en.wikipedia.org/wiki/BSD_licenses BSC license])

Biology

THIS SOFTWARE IS FOR DEMONSTRATION PURPOSES ONLY. THE WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE, INCLUDING THE DESIGN OF FUNCTIONAL GENE CIRCUITS, IS DISCLAIMED. ESPECIALLY DO NOT USE THE SOFTWARE IN THE PROCESS OF DESIGNING REAL EXPERIMENTS OR ORDERING GENETIC DEVICES / SEQUENCES.

Source Code

Download the source code.