C# For Bioinformatics and Biological Data Processing: BioSyS.Net

Bioinformatics is an interdisciplinary field that analyzes biological data using computer science. I have created a new package for bioinformatics and computational analysis built in C#. This package can analyze biological data such as DNA, RNA, and protein sequences, as well as perform tasks such as Biological Database Scraping. Additionally, 'GEO Analysis' offers a variety of analyses for RNA-seq preprocessing, parsing various biological file formats (FASTA, PDB, SOFT, FASTQ, etc.). BioSySNet also utilizes the Python interpreter to run certain plotting functions (i.e., it uses IronPython to execute Python functions, "so first, you need to make sure that Python is installed on your machine").

Features

• Scrape useful information from various databases like, DrugBank, UnipProt, PDB etcand PDB.
• Download and parse some of the important biological file formats such as .pdb, .fasta, .fastq, .soft, and CSV.
• Built-in statistical functions for differential expression analysis and pre-processing.
• Built-in CSV reader and manipulation.
• Graphs for fastq quality analysis, GC plots, and enrichment analysis using Python.
• Different array computation programs and matrix calculations.
• Built-in data structures for data science and statistics.

Requirements

BioSyS requires Python on your machine for plotting and for providing some functionalities. First of all, download the Python 3.x version. Then, download the supported version of BioSyS and configure it to your Python interpreter.

Softwares Requirement:

• .Net >= 5.0.x
• Python >= 3.0.x

Packages Requirement:

• HtmlAgilityPack >= 1.11.x
• IronPython >= 3.4.1
• MathNet.Numerics >= 4.9.0
• Matplotlib >= 3.6.0
• beautifulsoup4 == 4.11.0
• seaborn >= 0.12.1

Download

You can easily download the package with nuget package manager:

PM> NuGet\Install-Package BioSySNet -Version x.y.z

OR, Can also be installed by CLI using dotnet:

> dotnet add package BioSySNet --version x.y.z

Where, x.y.z will be desired version i.e. -version 0.0.4 OR --version 0.0.4 (LATEST)

Releases

v0.0.3 [3n2h3i28] (Latest Release)

• Class csvReader has been changed to new name CSVArray.
• The readCSV function of the CSVArray class (formerly known as csvReader) has been renamed to readNumericCSV in this version. This change allows the CSV file to be read as numeric points only.
• A new class feature called ImportData has been added, which allows for importing or reading datasets from CSV, tab, or other delimiter symbols. Additionally, a class called DataFrame has been introduced for dataset handling and manipulations.
• TrainTest_Split function now takes an array of double type as arguments and returns a floating point value.
• ReadSoftFile has been changed to ReadMetaDataBySOFT in the BioFormats class, which is responsible for reading metadata in the SOFT file format.
• Lastly, the ArrayExpression function in the BioFormats class enables access to microarray data from the Gene Expression Omnibus database.

Uses

Go through the Medium Link:

• Chapter 1 (Configure Python, Class BioTools and BioFormats)

In the next Part, we will discuss about classes for statistical analysis on biological data (GEOAnalysis, GEOCSVTable, Statistics and descriptiveAnalysis classes of BioSySNet) and scraping information from Drug Bank (drugScraping class of BioSySNet).

Sometimes the features of Python functions can be defective and cause errors!