This post shares a basic C# implementation of a FASTA reader and writer. FASTA is one of the simplest file formats used in bioinformatics. It can store nucleic and protein sequences. Each file can contain any non-negative integer number of sequences. Each sequence entry consists of a header line and
NCBI provides a web interface to run BLAST searches. However, it is also possible to download the databases to search locally. This post shares the process of downloading the BLAST+ suite of command-line tools, setting up the Swiss-Prot database, and performing a simple blastp search. The source code is available
Sequences, in particular protein and nucleic acid sequences, are at the core of bioinformatics. This post shares development of a simple project to start working with sequences. The project implements absolute basics: sequence representation and equality comparisons. Access the project’s source code on GitHub 📁, check the initial state 0️
This post presents an example of using workflow sets in the tidymodels framework with cross-validation and varying recipes and models. The dataset in use is Pima Indians Diabetes. The previous post established the baseline accuracy of 73%. The goal for this time is to improve upon this number. Preliminary This
This post walks through a starter analysis of the Pima Indians Diabetes dataset using R. The dataset has been sourced from Kaggle - one of the data sources mentioned in the previous post. The dataset is in tabular format. Each row represents a patient of Pima Indian heritage. The columns
R is a tool for working with data. As a beginner to R, where to get data to practice on? This post outlines two types of data sources: ready-to-go datasets and synthetic data. Ready-to-go Datasets Ready-to-go datasets are datasets which are immediately usable for analysis, visualisation, and machine learning. They
The last three toy projects showcased on this blog are Arithmetic Trainer, Achievement Quantifier, and Noter. Besides being written in C#, the commonality between all three is involvement of randomness. Arithmetic Trainer generates random practice questions. Achievement Quantifier uses AutoFixture to generate random data for unit testing. Noter uses Bogus
The other two posts - First Look into ASP.NET Core MVC - Notes Management App and Before and After - Transforming Noter with Bootstrap - introduce the Noter project and implement basic functionality and styling. This post extends Noter to support users. Users can register, log in, and log
Another post introduces Noter - an ASP.NET Core MVC app for managing notes. The app provides basic functionality: viewing, editing, and creating notes, as well as navigating between pages. The problem is its UI elements are unstyled, making the interface visually unappealing. This post applies Bootstrap 5.3 styling
This post showcases Noter - an ASP.NET Core MVC app for managing notes. A note consists of a title and content. This post comes from the perspective of a complete beginner in MVC. As such, certain details may be overlooked, while others explained excessively. Styling (i.e. applying CSS)
This post improves the usability the Achievement Quantifier project by adding a small feature - reporting - and showcases a complex LINQ query behind it. The reporting command counts the number of completed achievements today, yesterday, and past week: > aq stats ┌────────────────────────────────────┬───────┐ │ Statistic │ Value │ ├────────────────────────────────────┼───────┤ │ Achievements Completed Today │ 6 │ │ Achievements Completed
This post marks the milestone of 31 posts published over the span of 10 months. This is a good opportunity to review and classify all these posts. A possible tool to help with the classification of posts is tagging. Tagging refers to the process of creating tags. Tags are labels