The study presents a new way of implementing a new model for networks by creating networks through the application of the DNA translation model and a Java simulation configured to adapt the chosen model. A brief description of how the DNA translation works is discussed as well as how the process of translation is applied to the created nodes in order to create one or more networks. Different parameters will be used to obtain a wide variety of results and to further be able to study how these parameters affect the creation of nodes and networks.
Significant parameters include the property file, alphabet, initial nodes length, unit distance and max distance. As a result of the experiment, parameters with the most significant effects on network measures will be identified. It will also be presented that input parameters with different compositions lead to various behaviors of the network measures. ? Introduction Studies about linking nodes with each other to in order to form a network already exists but most of these studies did not concern itself with the organization of nodes such as giving it a name and analyzing its structure.
In this study, however, nodes are given names and the relationship between nodes through its name and structure is established. This is achieved by applying the model of the genetic code of a DNA to form a genetic network. To achieve the goals of the study, a model is used for the study specifically the translation of a DNA. The translation of a DNA is a perfect model in studying complex networks and how the nodes of these networks are connected. Similar to how nucleotides and codons pair up to produce proteins, the nodes in this study are paired to create a network. To apply the translation of DNA into a network, a simulation is used.
The codons in a DNA will be the nodes for the network. As for how these nodes will be linked, a genetic table will be applied. The resulting network will be like a protein molecule, a set of amino acids which resulted from the linking of codons or for this study, the nodes. Through the use of this model, nodes are created, structures developed and nodes connected to create an organized and intricate network. A simulation is used to perform the experiment although the simulation is not developed explicitly for this study. It is adapted as a tool to perform the study and create different networks based on a property file.
The simulation is written in java and has been developed with Netbeans. The simulation allows the user to create connected networks based on different models so that it can be studied according to various procedures. It also has the option of creating one or more networks. The input for this simulation is the property file property. txt which contains all the properties of the node. This file must be present in the same directory the program is invoked. This program may be run outside eclipse or Netbeans by double clicking the jar file created from the program. Aims of the Study There are two major aims of this study.
The first aim is to create networks with different properties so that the created networks may be studied further based on the genetic code, i. e. nodes as codons, the link between these nodes based on the genetic table and the output network as the protein molecule. The second aim is to understand how the input parameters for the simulation of a DNA translation model influence the generation of networks. The first aim will be achieved through the use of the simulation and the DNA translation model. The second aim will be achieved by first studying the input file for the simulation, specifically the property.
txt which contains all the significant parameters in order to create and connect nodes to form a network and how these parameters are used and what effects they cause in the creation and connection of nodes. Objectives of the Study The main objective of the study is to run various tests that would generate one or more networks whose nodes contain a fixed structure. In detail, the objectives are: • Apply DNA translation model to simulation • Configure simulation to adopt the chosen model • Create a stable property file which will contain the structure of the nodes • Run simulation to create nodes and connect nodes to form a network