Step 1

The first step is to create a XML file and an input file of your reaction network. You can do so on this website by heading over to the “XML Generator” section in our website. You can find an example of the Genetic Toggle Switch reaction network XML and init files below. I have attached them here below for your reference:

Click here to download the Genetic Toggle Switch Chemical Reaction XML File Click here to download the initial condition file

Step 2

Head over to our install our package on from our github:
https://github.com/alifarhat40/bioacme

You can install on your Linux system using: pip install bioacme

The github page also incudes instructions on how to write the commands.

Example: Genetic Toggle Switch

R1: GeneA →k1 GeneA + A, ksA = 40s-1,

R2: GeneB →k2 GeneB + B, ksB = 20s-1,

R3: A→k3Θ, kdA = 1s-1,

R4: B→k4Θ, kdB = 1s-1,

R5: 2A + GeneB →k5 bGeneB, kbA = 1 x 10-5nM-2s-1,

R6: 2B + GeneA →k6 bGeneA, kbB = 3.5 x 10-5nM-2s-1,

R7: bGeneB →k7 2A + GeneB, kuA = 0.1s-1

R8: bGeneA →k8 2B + GeneA, kuB = 0.1s-1

Note: if a reaction is neither a synthesis or degradation reaction, then you do not need to select the box in the XML Generator Page.
Click here to download the example of how to fill sections
Note: ACME is based on a multi-finite buffer. Our model here assumes 2 buffers. One for protein A and another for protein B. Therefore, in the init file we set buffA = 120 and buffB = 80. We also set GeneA and GeneB equal to 1 because their values will only switch between 0 or 1 depending on whether they are bound or not bound. The first line in the init file says we have 8 species and start at one state only. That start state is written in the second line with a probability of 1. Theoretically, you could start with any distribution of states and probabilities, and our ACME model is capable of handling it.
For any issues or concerns please send correspondence to both: Ali (student maintaining the package) and Dr. Jie Liang (corresponding PI):

afarha5 [at] uic [dot] edu
jliang [at] uic [dot] edu