DSDPy is a processor for DNA strand displacement systems. DSDPy generates the whole reaction network given the initial species and supports the simulation of such reaction network.
The full documentation of DSDPy can be found at https://dsdpy.readthedocs.io/en/latest/.
DSDPy (scripts in src package) is written in
Python3. The
recommended way to install all the packages needed in src is through
Anaconda. For those who are
familiar with pip installation, note that the required packages can
also be installed through standard way, but the details are not included
in this documentation.
-
PySB
PySB is a framework for building mathematical rule-based models of biochemical systems as Python programs. The installation command with Anaconda is:
conda install -c alubbock pysb -
Numpy
Numpy is a fundamental package for scientific computing with Python. The installation command with Anaconda is:
conda install -c anaconda numpy -
Networkx
Networkx is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. This package is used in src for output incidence matrix. The installation command with Anaconda is:
conda install -c conda-forge networkx -
Matplotlib
Matplotlib is a Python 2D plotting library, used in src for visualization of the simulation results. The installation command with Anaconda is:
conda install -c conda-forge matplotlib -
PyQt
PyQt is a set of Python v2 and v3 bindings for The Qt Company's Qt application framework and runs on all platforms supported by Qt including Windows, macOS, Linux, iOS and Android. The installation command with Anaconda is:
conda install -c anaconda pyqt -
Bidict
Bidict is the bidirectional mapping library for Python. One can use one of the following commands to install:
conda install -c conda-forge bidict conda install -c conda-forge/label/gcc7 bidict conda install -c conda-forge/label/cf201901 bidict conda install -c conda-forge/label/cf202003 bidict
The core is a Python package (src) that includes scripts to run a DSD system analysis. One should be able to run the scripts if the required packages above have been downloaded.
DSDPy has a graphical user interface implemented as interface.py in the project root directory. To run this interface from command line interface, simply do:
python interface.py
Please make sure you have the Python package (src) in the same directory before you run the interface.
The entry point to the analysis of a DSD system is through [start_processor] function. To get test inputs for DSDPy, you need to download the res package (In the case you would like to make your own input, simply pass the file directory accordingly to function [start_processor] as suggested). After that, you can test if the DSDPy works by running the following command from a Python interpreter:
>>> from src import start_processor as sp
>>> sp.start_processor(filedir='./res/input')
RB: {(2, 0), (0, 3)}
R4: {(0, 2), (2, 1)}
R3: {(1, 0), (3, 1)}
RU: {(2, 0), (0, 3)}
R4: {(0, 2), (2, 1)}
R4: {(1, 1), (0, 2)}
R3: {(1, 0), (3, 1)}
RU: {(0, 1), (1, 2)}
R4: {(1, 1), (0, 2)}
RU: {(0, 1), (1, 2)}
R3: {(0, 0), (1, 1)}
RB: {(0, 1), (2, 2)}
RB: {(0, 1), (2, 2)}
Note: This test input is res/input.
The ideal way to generate the input to DSDPy is through a GUI interface which enables a quickstart for people with DSD systems to test. However, such interface is now under development and one needs to manually type the input for DSDPy.
An input for DSDPy needs at least three sections:
-
Species
Initial species of the DSD system in their canonical forms.
<> denotes a strand
// denotes seperation of species
^ denotes toehold
* denotes complementary
! denotes bonded, what follows is the bond name
The strands are parsed always from 5'-end to 3'-end.
An example format:
<L T2^!i2 X*!i1 T1^> <A X!i1 T2^*!i2> // <T1^* X!j1 R> <X*!j1 A*!j2> <A!j2> -
Information on Species
Names of the initial species (order corresponds to the order of species above) and their initial copies. An example format:
SomeName 1000 -
Kinetics
Rates of the reactions, includes 3-way migration, 4-way migration, binding and unbinding (R3, R4, RB and RU). An example format:
RB 1e6 RU 1.2 R3 78.12 R4 5.6e-3
Note that the sections are all seperated by --.
<L T2^!i2 X*!i1 T1^>
<A X!i1 T2^*!i2>
//
<T1^* X!j1 R>
<X*!j1 A*!j2>
<A!j2>
--
ss1 1000
ss2 1000
--
RB 1e6
RU 1.2
R3 78.12
R4 5.6e-3
The output files includes a text file containing the information of the reaction network and a png file visualizing the BNG simulation results. These files can be found under the output directory or an user defined output directory.
The file contains three parts of information:
- A species list that includes all the possible species in the network.
- A reaction list that includes all the possible reactions in the network.
- An incidence matrix based on the reaction network. (Its row denotes species and its column denotes the edge from one species to another)
Based on the example input :
-----Species-----
1
<L T2^!1 X*!2 T1^>
<A X!2 T2^*!1>
2
<T1^* X!1 R>
<X*!1 A*!2>
<A!2>
3
<L T2^!1 X*!2 T1^!3>
<A X!2 T2^*!1>
<T1^*!3 X!4 R>
<X*!4 A*!5>
<A!5>
4
<L T2^!1 X*!2 T1^!3>
<A!4 X!2 T2^*!1>
<T1^*!3 X!5 R>
<X*!5 A*!4>
5
<A>
6
<L T2^!1 X*!2 T1^!3>
<A X!4 T2^*!1>
<T1^*!3 X!2 R>
<X*!4 A*!5>
<A!5>
7
<L T2^!1 X*!2 T1^!3>
<A!4 X!5 T2^*!1>
<T1^*!3 X!2 R>
<X*!5 A*!4>
8
<L T2^ X*!1 T1^!2>
<T1^*!2 X!1 R>
9
<A X!1 T2^*>
<X*!1 A*!2>
<A!2>
10
<A!1 X!2 T2^*>
<X*!2 A*!1>
-----Reactions-----
RB 1 + 2 --> 3 rate=0.0003
R3 3 --> 4 + 5 rate=20.0
R4 3 --> 6 rate=20.0
RU 3 --> 1 + 2 rate=0.1126
R4 4 --> 7 rate=20.0
R3 6 --> 7 + 5 rate=20.0
R4 6 --> 3 rate=20.0
RU 6 --> 8 + 9 rate=0.1126
R4 7 --> 4 rate=20.0
RU 7 --> 8 + 10 rate=0.1126
R3 9 --> 10 + 5 rate=20.0
RB 8 + 9 --> 6 rate=0.0003
RB 8 + 10 --> 7 rate=0.0003
-----Incidence Matrix-----
[1, 3] [2, 3] [3, 4] [3, 5] [3, 6] [3, 1] [3, 2] [4, 7] [6, 7] [6, 5] [6, 3] [6, 8] [6, 9] [7, 4] [7, 8] [7, 10] [9, 10] [9, 5] [8, 6] [9, 6] [8, 7] [10, 7]
1 [[ 1. 0. 0. 0. 0. -1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0.]]
2 [[ 0. 1. 0. 0. 0. 0. -1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0.]]
3 [[-1. -1. 1. 1. 1. 1. 1. 0. 0. 0. -1. 0. 0. 0. 0. 0. 0. 0.
0. 0. 0. 0.]]
4 [[ 0. 0. -1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 0. -1. 0. 0. 0. 0.
0. 0. 0. 0.]]
5 [[ 0. 0. 0. -1. 0. 0. 0. 0. 0. -1. 0. 0. 0. 0. 0. 0. 0. 0.
0. -1. 0. 0.]]
6 [[ 0. 0. 0. 0. -1. 0. 0. 0. 1. 1. 1. 1. 1. 0. 0. 0. -1. 0.
0. 0. -1. 0.]]
7 [[ 0. 0. 0. 0. 0. 0. 0. -1. -1. 0. 0. 0. 0. 1. 1. 1. 0. -1.
0. 0. 0. -1.]]
8 [[ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. -1. 0. 0. -1. 0. 1. 1.
0. 0. 0. 0.]]
9 [[ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. -1. 0. 0. 0. 0. 0.
1. 1. 1. 0.]]
10 [[ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. -1. 0. 0.
-1. 0. 0. 1.]]
Based on the example input
