Develop a Networked Application Using TCP Sockets - IT Assignment Help

Assignment Task

Aims
• Develop a networked application using TCP sockets
• Implement a protocol according to a given specification from both the client and server side
• Implement client-side checking to ensure only valid messages are sent to the server

Introduction
In this assignment, you will be converting input virus RNA to an optimised form that is likely to create a better vaccine. Your task is to use TCP sockets to create a client process that sends unoptimised RNA to a server, which replies with optimised RNA. The protocol that your solution must implement is described below.

Background Information
It is strongly recommended you read Bert Hubert's post Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine for relevant background information.
The basic idea is that vaccines can be developed by slightly modifying some RNA from a virus. Nature groups three nucleotides into a codon which can be represented as a group of three G, C, A, or T characters. Thus, there are 64=43 possible codons. Each codon is converted into an amino acid when processed by a cell to fold into a protein. But there are only 20 different amino acids. This means a given amino acid may be able to be encoded by multiple different codons. For this assignment, you must implement a set of optimisation rules that take a string of RNA as input and return an optimised version.

Optimisation Rules

To determine your optimisation rules, you can use details of how RNA from the COVID-19 virus S protein has been modified to create the extremely efficient BioNTech/Pfizer SARS-CoV-2 Vaccine S protein.
It is not acceptable to simply return the input RNA as the output. Your rules must make some attempt to optimise the input while ensuring that the associated amino acids for each codon are identical in the output. For this purpose, you are provided with codon-aminoacid.csv which specifies the amino acid associated with each codon.

As a starting point, it is generally the case that a higher number of G and/or C characters improves the efficiency of an mRNA vaccine. So one approach would be to consider the amino acid generated by a given codon and replace it with the codon with the most G and/or C characters that produces the same amino acid. Please do not feel that you must limit your approach to this guideline.

Protocol
Each message in the protocol consists of a string of ASCII characters followed by the line feed character (ASCII code 10). All messages from the client should be case insensitive. All messages from the server should be uppercase. An interaction begins with the client sending a START RNA message to the server. The client then sends a message consisting of G, C, A, and/or T characters to represent codons.
The server then responds with a message consisting of G, C, A, and/or T characters to represent optimised codons.
The client can then either send a new START RNA message (in which case the process repeats) or send a DISCONNECT message.
Once the client has sent a DISCONNECT message, it should exit. Once the server has recieved a DISCONNECT message, it should close the socket and wait for a new connection.

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